From zonexo at gmail.com Fri Jun 1 07:13:56 2007 From: zonexo at gmail.com (Ben Tay) Date: Fri, 1 Jun 2007 20:13:56 +0800 Subject: libc.lib error when linking test examples Message-ID: <804ab5d40706010513u5fb11523rf3170d393756f041@mail.gmail.com> Hi, I'm using ms vc++ and vf in windows xp. I tried to compile PETSc 2.3.3p0. Running configure has no problem. Compiling seems ok but in the last part when it tried to test examples, the error is --------------Error detected during compile or link!----------------------- See http://www.mcs.anl.gov/petsc/petsc-2/documentation/troubleshooting.html /codes/petsc-2.3.3-p0/bin/win32fe/win32fe cl -o ex19.o -c -MT -Z7 -I/codes/petsc-2.3.3-p0 -I/codes/petsc-2.3.3-p0/bmake/ win32_mpi -I/codes/petsc-2.3.3-p0/include -I/cygdrive/d/cygwin/codes/MPICH/SDK/include -D__SDIR__="src/snes/examples/tut orials/" ex19.c ex19.c /codes/petsc-2.3.3-p0/bin/win32fe/win32fe cl -MT -Z7 -o ex19 ex19.o-L/codes/petsc- 2.3.3-p0/lib/win32_mpi -L/codes/pet sc-2.3.3-p0/lib/win32_mpi -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc /cygdrive/d/cygwin/codes/MPIC H/SDK/lib/mpich.lib -L/codes/petsc-2.3.3-p0/externalpackages/fblaslapack/win32_mpi -L/codes/petsc-2.3.3-p0/externalpacka ges/fblaslapack/win32_mpi -lflapack -L/codes/petsc-2.3.3-p0/externalpackages/fblaslapack/win32_mpi -L/codes/petsc-2.3.3- p0/externalpackages/fblaslapack/win32_mpi -lfblas Gdi32.lib User32.lib Advapi32.lib Kernel32.lib Ws2_32.lib -L'/cygdriv e/c/Program Files/Microsoft Visual Studio/DF98/LIB' dformt.lib(matherr.obj) : error LNK2005: __matherr already defined in LIBCMT.lib(matherr.obj) libc.lib(crt0dat.obj) : error LNK2005: __cinit already defined in LIBCMT.lib (crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: _exit already defined in LIBCMT.lib( crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __exit already defined in LIBCMT.lib( crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __cexit already defined in LIBCMT.lib (crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __c_exit already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __C_Exit_Done already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __C_Termination_Done already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __exitflag already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __wpgmptr already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __pgmptr already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: ___winitenv already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __wenviron already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: ___initenv already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __environ already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: ___wargv already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: ___argv already defined in LIBCMT.lib (crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: ___argc already defined in LIBCMT.lib (crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __winminor already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __winmajor already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __winver already defined in LIBCMT.lib(crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __osver already defined in LIBCMT.lib (crt0dat.obj) libc.lib(crt0dat.obj) : error LNK2005: __umaskval already defined in LIBCMT.lib(crt0dat.obj) LINK : warning LNK4098: defaultlib "libc.lib" conflicts with use of other libs; use /NODEFAULTLIB:library d:\cygwin\codes\PETSC-~1.3-P\src\snes\examples\TUTORI~1\ex19.exe : fatal error LNK1169: one or more multiply defined sym bols found make[3]: [ex19] Error 2 (ignored) /usr/bin/rm -f ex19.o My configure command is : ./config/configure.py --with-cc='win32fe cl' --with-fc='win32fe f90' --download-f-blas-lapack=1 LIBS="-L'/cygdrive/c/Program Files/Microsoft Visual Studio/DF98/LIB'" --with-x=0 --with-mpi-dir=/cygdrive/d/cygwin/codes/MPICH/SDK Hope someone can help. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Fri Jun 1 08:57:54 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 1 Jun 2007 08:57:54 -0500 (CDT) Subject: libc.lib error when linking test examples In-Reply-To: <804ab5d40706010513u5fb11523rf3170d393756f041@mail.gmail.com> References: <804ab5d40706010513u5fb11523rf3170d393756f041@mail.gmail.com> Message-ID: Is this compaq visual fortran? You'll have to use FLINKER for c examples as well. [because of fortran blas - and only compaq f90 know how to do the linking correctly - when fortran objects are involved]. Configure can't handle this case automatically. One way to do this is to manualy edit bmake/$PETSC_ARCH/petscconf and change PCC_LINKER to use 'win32fe f90' Satish On Fri, 1 Jun 2007, Ben Tay wrote: > Hi, > > I'm using ms vc++ and vf in windows xp. I tried to compile PETSc 2.3.3p0. > Running configure has no problem. Compiling seems ok but in the last part > when it tried to test examples, the error is > > --------------Error detected during compile or link!----------------------- > See http://www.mcs.anl.gov/petsc/petsc-2/documentation/troubleshooting.html > /codes/petsc-2.3.3-p0/bin/win32fe/win32fe cl -o ex19.o -c -MT -Z7 > -I/codes/petsc-2.3.3-p0 -I/codes/petsc-2.3.3-p0/bmake/ > win32_mpi -I/codes/petsc-2.3.3-p0/include > -I/cygdrive/d/cygwin/codes/MPICH/SDK/include > -D__SDIR__="src/snes/examples/tut > orials/" ex19.c > ex19.c > /codes/petsc-2.3.3-p0/bin/win32fe/win32fe cl -MT -Z7 -o ex19 > ex19.o-L/codes/petsc- > 2.3.3-p0/lib/win32_mpi -L/codes/pet > sc-2.3.3-p0/lib/win32_mpi -lpetscsnes -lpetscksp -lpetscdm -lpetscmat > -lpetscvec -lpetsc /cygdrive/d/cygwin/codes/MPIC > H/SDK/lib/mpich.lib > -L/codes/petsc-2.3.3-p0/externalpackages/fblaslapack/win32_mpi > -L/codes/petsc-2.3.3-p0/externalpacka > ges/fblaslapack/win32_mpi -lflapack > -L/codes/petsc-2.3.3-p0/externalpackages/fblaslapack/win32_mpi > -L/codes/petsc-2.3.3- > p0/externalpackages/fblaslapack/win32_mpi -lfblas Gdi32.lib User32.lib > Advapi32.lib Kernel32.lib Ws2_32.lib -L'/cygdriv > e/c/Program Files/Microsoft Visual Studio/DF98/LIB' > dformt.lib(matherr.obj) : error LNK2005: __matherr already defined in > LIBCMT.lib(matherr.obj) > libc.lib(crt0dat.obj) : error LNK2005: __cinit already defined in LIBCMT.lib > (crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: _exit already defined in LIBCMT.lib( > crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __exit already defined in LIBCMT.lib( > crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __cexit already defined in LIBCMT.lib > (crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __c_exit already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __C_Exit_Done already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __C_Termination_Done already defined > in LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __exitflag already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __wpgmptr already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __pgmptr already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: ___winitenv already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __wenviron already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: ___initenv already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __environ already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: ___wargv already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: ___argv already defined in LIBCMT.lib > (crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: ___argc already defined in LIBCMT.lib > (crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __winminor already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __winmajor already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __winver already defined in > LIBCMT.lib(crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __osver already defined in LIBCMT.lib > (crt0dat.obj) > libc.lib(crt0dat.obj) : error LNK2005: __umaskval already defined in > LIBCMT.lib(crt0dat.obj) > LINK : warning LNK4098: defaultlib "libc.lib" conflicts with use of other > libs; use /NODEFAULTLIB:library > d:\cygwin\codes\PETSC-~1.3-P\src\snes\examples\TUTORI~1\ex19.exe : fatal > error LNK1169: one or more multiply defined sym > bols found > make[3]: [ex19] Error 2 (ignored) > /usr/bin/rm -f ex19.o > > My configure command is : > > ./config/configure.py --with-cc='win32fe cl' --with-fc='win32fe f90' > --download-f-blas-lapack=1 LIBS="-L'/cygdrive/c/Program Files/Microsoft > Visual Studio/DF98/LIB'" --with-x=0 > --with-mpi-dir=/cygdrive/d/cygwin/codes/MPICH/SDK > > Hope someone can help. > > Thank you. > From zonexo at gmail.com Fri Jun 1 11:13:23 2007 From: zonexo at gmail.com (Ben Tay) Date: Sat, 2 Jun 2007 00:13:23 +0800 Subject: libc.lib error when linking test examples In-Reply-To: References: <804ab5d40706010513u5fb11523rf3170d393756f041@mail.gmail.com> Message-ID: <804ab5d40706010913m4647d192t66ab31d9f4949afa@mail.gmail.com> yes it's compaq vf. so how do i change the pcc_linker to use 'win32fe f90`? can u elaborate? but anyway, maybe it's not so impt now. i just compiled 2.3.2p8 and it worked. moreover, i tried to run my own code in vf, replacing the 2.3.2p8files with the 2.3.3p0 and it worked. On 6/1/07, Satish Balay wrote: > > Is this compaq visual fortran? > > You'll have to use FLINKER for c examples as well. [because of fortran > blas - and only compaq f90 know how to do the linking correctly - when > fortran objects are involved]. Configure can't handle this case > automatically. > > One way to do this is to manualy edit bmake/$PETSC_ARCH/petscconf and > change PCC_LINKER to use 'win32fe f90' > > Satish > > On Fri, 1 Jun 2007, Ben Tay wrote: > > > Hi, > > > > I'm using ms vc++ and vf in windows xp. I tried to compile PETSc 2.3.3p0 > . > > Running configure has no problem. Compiling seems ok but in the last > part > > when it tried to test examples, the error is > > > > --------------Error detected during compile or > link!----------------------- > > See > http://www.mcs.anl.gov/petsc/petsc-2/documentation/troubleshooting.html > > /codes/petsc-2.3.3-p0/bin/win32fe/win32fe cl -o ex19.o -c -MT -Z7 > > -I/codes/petsc-2.3.3-p0 -I/codes/petsc-2.3.3-p0/bmake/ > > win32_mpi -I/codes/petsc-2.3.3-p0/include > > -I/cygdrive/d/cygwin/codes/MPICH/SDK/include > > -D__SDIR__="src/snes/examples/tut > > orials/" ex19.c > > ex19.c > > /codes/petsc-2.3.3-p0/bin/win32fe/win32fe cl -MT -Z7 -o ex19 > > ex19.o-L/codes/petsc- > > 2.3.3-p0/lib/win32_mpi -L/codes/pet > > sc-2.3.3-p0/lib/win32_mpi -lpetscsnes -lpetscksp -lpetscdm -lpetscmat > > -lpetscvec -lpetsc /cygdrive/d/cygwin/codes/MPIC > > H/SDK/lib/mpich.lib > > -L/codes/petsc-2.3.3-p0/externalpackages/fblaslapack/win32_mpi > > -L/codes/petsc-2.3.3-p0/externalpacka > > ges/fblaslapack/win32_mpi -lflapack > > -L/codes/petsc-2.3.3-p0/externalpackages/fblaslapack/win32_mpi > > -L/codes/petsc-2.3.3- > > p0/externalpackages/fblaslapack/win32_mpi -lfblas Gdi32.lib User32.lib > > Advapi32.lib Kernel32.lib Ws2_32.lib -L'/cygdriv > > e/c/Program Files/Microsoft Visual Studio/DF98/LIB' > > dformt.lib(matherr.obj) : error LNK2005: __matherr already defined in > > LIBCMT.lib(matherr.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __cinit already defined in > LIBCMT.lib > > (crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: _exit already defined in > LIBCMT.lib( > > crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __exit already defined in > LIBCMT.lib( > > crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __cexit already defined in > LIBCMT.lib > > (crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __c_exit already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __C_Exit_Done already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __C_Termination_Done already > defined > > in LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __exitflag already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __wpgmptr already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __pgmptr already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: ___winitenv already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __wenviron already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: ___initenv already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __environ already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: ___wargv already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: ___argv already defined in > LIBCMT.lib > > (crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: ___argc already defined in > LIBCMT.lib > > (crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __winminor already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __winmajor already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __winver already defined in > > LIBCMT.lib(crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __osver already defined in > LIBCMT.lib > > (crt0dat.obj) > > libc.lib(crt0dat.obj) : error LNK2005: __umaskval already defined in > > LIBCMT.lib(crt0dat.obj) > > LINK : warning LNK4098: defaultlib "libc.lib" conflicts with use of > other > > libs; use /NODEFAULTLIB:library > > d:\cygwin\codes\PETSC-~1.3-P\src\snes\examples\TUTORI~1\ex19.exe : fatal > > error LNK1169: one or more multiply defined sym > > bols found > > make[3]: [ex19] Error 2 (ignored) > > /usr/bin/rm -f ex19.o > > > > My configure command is : > > > > ./config/configure.py --with-cc='win32fe cl' --with-fc='win32fe f90' > > --download-f-blas-lapack=1 LIBS="-L'/cygdrive/c/Program Files/Microsoft > > Visual Studio/DF98/LIB'" --with-x=0 > > --with-mpi-dir=/cygdrive/d/cygwin/codes/MPICH/SDK > > > > Hope someone can help. > > > > Thank you. > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Fri Jun 1 11:18:43 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 1 Jun 2007 11:18:43 -0500 (CDT) Subject: libc.lib error when linking test examples In-Reply-To: <804ab5d40706010913m4647d192t66ab31d9f4949afa@mail.gmail.com> References: <804ab5d40706010513u5fb11523rf3170d393756f041@mail.gmail.com> <804ab5d40706010913m4647d192t66ab31d9f4949afa@mail.gmail.com> Message-ID: On Sat, 2 Jun 2007, Ben Tay wrote: > yes it's compaq vf. so how do i change the pcc_linker to use 'win32fe f90`? > can u elaborate? - edit bmake/$PETSC_ARCH/petscconf - look for 'PCC_LINKER = win32fe cl ............' - change 'cl' to 'f90' > but anyway, maybe it's not so impt now. i just compiled 2.3.2p8 and > it worked. moreover, i tried to run my own code in vf, replacing the > 2.3.2p8files with the 2.3.3p0 and it worked. Ok - If you are using project files - then you don't need to fix the makefiles. satish > On 6/1/07, Satish Balay wrote: > > One way to do this is to manualy edit bmake/$PETSC_ARCH/petscconf and > > change PCC_LINKER to use 'win32fe f90' From zonexo at gmail.com Mon Jun 4 09:19:43 2007 From: zonexo at gmail.com (Ben Tay) Date: Mon, 4 Jun 2007 22:19:43 +0800 Subject: 30mins lecture tutorial on using PETSc on laplace eqns Message-ID: <804ab5d40706040719m61e2151cg27639dac3021bfb@mail.gmail.com> Hi, I found this link when doing a PETSc search.It is 30mins online lecture which introduces and explains the use of PETSc on solving the laplace eqn. Hope it's useful to new users http://infostream.rus.uni-stuttgart.de/lec/307/537/real/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From zonexo at gmail.com Wed Jun 6 22:56:46 2007 From: zonexo at gmail.com (Ben Tay) Date: Thu, 7 Jun 2007 11:56:46 +0800 Subject: Fortran could not successfully link C++ objects problem Message-ID: <804ab5d40706062056m60b9746cl853a05a984779656@mail.gmail.com> Hi, I got this error during configure: Fortran could not successfully link C++ objects My command is : ./config/configure.py --with-vendor-compilers=intel --with-blas-lapack-dir=/usr/local/intel/mkl721cluster/ --with-debugging=0 --download-hypre=1 --with-x=0 --with-mpi-dir=/usr/local/topspin/mpi/mpich/ --with-batch=1 --with-shared May I know what's wrong? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Wed Jun 6 23:49:07 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Wed, 6 Jun 2007 23:49:07 -0500 (CDT) Subject: Fortran could not successfully link C++ objects problem In-Reply-To: <804ab5d40706062056m60b9746cl853a05a984779656@mail.gmail.com> References: <804ab5d40706062056m60b9746cl853a05a984779656@mail.gmail.com> Message-ID: Please send such issues [with the corresponding configure.log file] to petsc-maint at mcs.anl.gov Satish On Thu, 7 Jun 2007, Ben Tay wrote: > Hi, > > I got this error during configure: Fortran could not successfully link C++ > objects > > My command is : > > ./config/configure.py --with-vendor-compilers=intel > --with-blas-lapack-dir=/usr/local/intel/mkl721cluster/ --with-debugging=0 > --download-hypre=1 --with-x=0 --with-mpi-dir=/usr/local/topspin/mpi/mpich/ > --with-batch=1 --with-shared > > May I know what's wrong? > > Thank you. > From stephan.kramer at imperial.ac.uk Thu Jun 7 11:44:24 2007 From: stephan.kramer at imperial.ac.uk (Stephan Kramer) Date: Thu, 7 Jun 2007 17:44:24 +0100 Subject: PCShellSetContext fortran interface Message-ID: <200706071744.24549.stephan.kramer@imperial.ac.uk> Hi, I don't know if this is the expected behaviour but calling PCShellSetContext from fortran, the thing that is stored is not the integer value of context, but the pointer to this integer. Thus problems arise when supplying an integer variable that goes out of scope (e.g. on the stack) inbetween PCShellSetContext and the call to the 'apply shell preconditioner' routine. I know this makes sense from the C point of view, where you are merely supplying a void pointer, but this is not what you expect in Fortran were the only use of context could be as a reference/index itself to another object, and you thus expect the value of context to be stored. Cheers Stephan Kramer From bsmith at mcs.anl.gov Thu Jun 7 16:22:49 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Thu, 7 Jun 2007 16:22:49 -0500 (CDT) Subject: PCShellSetContext fortran interface In-Reply-To: <200706071744.24549.stephan.kramer@imperial.ac.uk> References: <200706071744.24549.stephan.kramer@imperial.ac.uk> Message-ID: Stephan, Even from Fortran the context is treated as a memory address, not an integer value. You could use a common block (yuck) or some array that is alloacated higher in the stack as the context, but as you note you cannot use a local variable. Barry You could argue that we should have implemented the way you suggest as only allow an integer value, but I would respond that in Fortran 90 one can pass in address of derived types, allocated arrays etc so I prefer our current design. On Thu, 7 Jun 2007, Stephan Kramer wrote: > Hi, > > I don't know if this is the expected behaviour but calling PCShellSetContext > from fortran, the thing that is stored is not the integer value of context, > but the pointer to this integer. Thus problems arise when supplying an > integer variable that goes out of scope (e.g. on the stack) inbetween > PCShellSetContext and the call to the 'apply shell preconditioner' routine. I > know this makes sense from the C point of view, where you are merely > supplying a void pointer, but this is not what you expect in Fortran were the > only use of context could be as a reference/index itself to another object, > and you thus expect the value of context to be stored. > > Cheers > Stephan Kramer > > From stephan.kramer at imperial.ac.uk Thu Jun 7 17:03:37 2007 From: stephan.kramer at imperial.ac.uk (Stephan Kramer) Date: Thu, 7 Jun 2007 23:03:37 +0100 Subject: PCShellSetContext fortran interface In-Reply-To: References: <200706071744.24549.stephan.kramer@imperial.ac.uk> Message-ID: <200706072303.37236.stephan.kramer@imperial.ac.uk> Hi Barry, Thanks, just wanted some clarification. Might I suggest in the documentation as well? I don't understand what you mean by: in Fortran 90 one can pass in address of derived types, allocated arrays etc Do you mean to rely on the fact that, without an explicit interface, fortran will (in practice) pass in the derived type by reference, which granted you do for the integer as well? This is quite in contradiction what it says in the documentation, and has nothing to do with any Fortran 90 standard. Also you would have to rely on the fact that this is gonna work for the supplied apply routine as well. As I said, I am merely being curious here. Thanks for any clarification. BTW is there a fortran interface for PCShellSetDestroy coming any soon? Thanks Stephan On Thursday 07 June 2007 22:22:49 Barry Smith wrote: > Stephan, > > Even from Fortran the context is treated as a memory address, not > an integer value. You could use a common block (yuck) or some array that > is alloacated higher in the stack as the context, but as you note you > cannot use a local variable. > > Barry > > You could argue that we should have implemented the way you suggest as > only allow an integer value, but I would respond that in Fortran 90 one > can pass in address of derived types, allocated arrays etc so I prefer our > current design. > > On Thu, 7 Jun 2007, Stephan Kramer wrote: > > Hi, > > > > I don't know if this is the expected behaviour but calling > > PCShellSetContext from fortran, the thing that is stored is not the > > integer value of context, but the pointer to this integer. Thus problems > > arise when supplying an integer variable that goes out of scope (e.g. on > > the stack) inbetween PCShellSetContext and the call to the 'apply shell > > preconditioner' routine. I know this makes sense from the C point of > > view, where you are merely supplying a void pointer, but this is not what > > you expect in Fortran were the only use of context could be as a > > reference/index itself to another object, and you thus expect the value > > of context to be stored. > > > > Cheers > > Stephan Kramer From bsmith at mcs.anl.gov Fri Jun 8 12:58:08 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 8 Jun 2007 12:58:08 -0500 (CDT) Subject: PCShellSetContext fortran interface In-Reply-To: <200706072303.37236.stephan.kramer@imperial.ac.uk> References: <200706071744.24549.stephan.kramer@imperial.ac.uk> <200706072303.37236.stephan.kramer@imperial.ac.uk> Message-ID: On Thu, 7 Jun 2007, Stephan Kramer wrote: > Hi Barry, > > Thanks, just wanted some clarification. Might I suggest in the documentation > as well? I don't understand what you mean by: > > in Fortran 90 one can pass in address of derived types, allocated arrays etc > > Do you mean to rely on the fact that, without an explicit interface, fortran > will (in practice) pass in the derived type by reference, which granted you > do for the integer as well? Yes > This is quite in contradiction what it says in > the documentation, and has nothing to do with any Fortran 90 standard. This could be true; but logically what else could it do in this situation? It seems to me the only other logical approach would be to generate an error at compile time. Also you can provide a "fake" interface for the function in your code, for example module somename Interface PCShelSetContext Subroutine PCShellSetContext(pc,ctx,ierr) PC pc type(myderivedtype), pointer :: ctx PetscErrorCode ierr End Subroutine End Interface DAVecGetArrayF90 We have not tested all Fortran compilers so yes you are potentially taking a chance that the code is not portable. Barry >Also > you would have to rely on the fact that this is gonna work for the supplied > apply routine as well. > > As I said, I am merely being curious here. Thanks for any clarification. BTW > is there a fortran interface for PCShellSetDestroy coming any soon? > > Thanks > Stephan > > On Thursday 07 June 2007 22:22:49 Barry Smith wrote: > > Stephan, > > > > Even from Fortran the context is treated as a memory address, not > > an integer value. You could use a common block (yuck) or some array that > > is alloacated higher in the stack as the context, but as you note you > > cannot use a local variable. > > > > Barry > > > > You could argue that we should have implemented the way you suggest as > > only allow an integer value, but I would respond that in Fortran 90 one > > can pass in address of derived types, allocated arrays etc so I prefer our > > current design. > > > > On Thu, 7 Jun 2007, Stephan Kramer wrote: > > > Hi, > > > > > > I don't know if this is the expected behaviour but calling > > > PCShellSetContext from fortran, the thing that is stored is not the > > > integer value of context, but the pointer to this integer. Thus problems > > > arise when supplying an integer variable that goes out of scope (e.g. on > > > the stack) inbetween PCShellSetContext and the call to the 'apply shell > > > preconditioner' routine. I know this makes sense from the C point of > > > view, where you are merely supplying a void pointer, but this is not what > > > you expect in Fortran were the only use of context could be as a > > > reference/index itself to another object, and you thus expect the value > > > of context to be stored. > > > > > > Cheers > > > Stephan Kramer > > > From jinzishuai at yahoo.com Fri Jun 8 13:39:03 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Fri, 8 Jun 2007 11:39:03 -0700 (PDT) Subject: Do not ignore errors in Makefile Message-ID: <429510.48340.qm@web36209.mail.mud.yahoo.com> Hi,there, I found that the default behavior of compiling a PETSc program composed of many source files is that errors are ignored and compilations continue to the next source file when an error is encountered during "make". I think it is caused by the "-" sign in the Makefile. There may be a good reason to have this feature but for my code, I really don't want it. I want to he process to stop so that I can immediately deal with the error. Is there a way to accomplish this feature? I guess something must be changed inside ${PETSC_DIR}/bmake/common/base etc but it seems quite complicated to figure it out. Could you please help me here? Thank you very much. Shi ____________________________________________________________________________________ Food fight? Enjoy some healthy debate in the Yahoo! Answers Food & Drink Q&A. http://answers.yahoo.com/dir/?link=list&sid=396545367 From bsmith at mcs.anl.gov Fri Jun 8 20:17:00 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 8 Jun 2007 20:17:00 -0500 (CDT) Subject: Do not ignore errors in Makefile In-Reply-To: <429510.48340.qm@web36209.mail.mud.yahoo.com> References: <429510.48340.qm@web36209.mail.mud.yahoo.com> Message-ID: You can edit bmake/common/rules and look for the rule .c.o For fortran files look in bmake/$PETSC_ARCH/petscrules Barry I'll see about making this an option in petsc-dev On Fri, 8 Jun 2007, Shi Jin wrote: > Hi,there, > > I found that the default behavior of compiling a PETSc > program composed of many source files is that errors > are ignored and compilations continue to the next > source file when an error is encountered during > "make". > I think it is caused by the "-" sign in the Makefile. > There may be a good reason to have this feature but > for my code, I really don't want it. I want to he > process to stop so that I can immediately deal with > the error. Is there a way to accomplish this feature? > I guess something must be changed inside > ${PETSC_DIR}/bmake/common/base etc but it seems quite > complicated to figure it out. Could you please help me > here? Thank you very much. > > Shi > > > > ____________________________________________________________________________________ > Food fight? Enjoy some healthy debate > in the Yahoo! Answers Food & Drink Q&A. > http://answers.yahoo.com/dir/?link=list&sid=396545367 > > From jinzishuai at yahoo.com Sat Jun 9 19:48:25 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Sat, 9 Jun 2007 17:48:25 -0700 (PDT) Subject: Need a simple unstructured grid example Message-ID: <994087.91971.qm@web36202.mail.mud.yahoo.com> Hi there, I am desperately looking for an example of code using PETSc to deal with unstructured grid, either in finite element or finite difference or any other method. Thanks. Shi ____________________________________________________________________________________ It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/ From knepley at gmail.com Sat Jun 9 19:58:27 2007 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 9 Jun 2007 19:58:27 -0500 Subject: Need a simple unstructured grid example In-Reply-To: <994087.91971.qm@web36202.mail.mud.yahoo.com> References: <994087.91971.qm@web36202.mail.mud.yahoo.com> Message-ID: Are you using the dev version or 2.3.3? Thanks, Matt On 6/9/07, Shi Jin wrote: > Hi there, > > I am desperately looking for an example of code using > PETSc to deal with unstructured grid, either in finite > element or finite difference or any other method. > Thanks. > > Shi > > > > ____________________________________________________________________________________ > It's here! Your new message! > Get new email alerts with the free Yahoo! Toolbar. > http://tools.search.yahoo.com/toolbar/features/mail/ > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From jinzishuai at yahoo.com Sat Jun 9 23:00:02 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Sat, 9 Jun 2007 21:00:02 -0700 (PDT) Subject: Need a simple unstructured grid example In-Reply-To: Message-ID: <997939.52623.qm@web36202.mail.mud.yahoo.com> I am using petsc-2.3.3-p1. I've taken a look at src/snes/examples/tutorials/ex10d/ and src/dm/ao/examples/tutorials/ However they are not really complete. I am hoping to have something that shows how to deal with the geometry and the parallel issues. The problem itself can be very simple. Thanks. Shi --- Matthew Knepley wrote: > Are you using the dev version or 2.3.3? > > Thanks, > > Matt > > On 6/9/07, Shi Jin wrote: > > Hi there, > > > > I am desperately looking for an example of code > using > > PETSc to deal with unstructured grid, either in > finite > > element or finite difference or any other method. > > Thanks. > > > > Shi > > > > > > > > > ____________________________________________________________________________________ > > It's here! Your new message! > > Get new email alerts with the free Yahoo! Toolbar. > > > http://tools.search.yahoo.com/toolbar/features/mail/ > > > > > > > -- > What most experimenters take for granted before they > begin their > experiments is infinitely more interesting than any > results to which > their experiments lead. > -- Norbert Wiener > > ____________________________________________________________________________________ Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC From knepley at gmail.com Sun Jun 10 03:45:06 2007 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 10 Jun 2007 03:45:06 -0500 Subject: Need a simple unstructured grid example In-Reply-To: <997939.52623.qm@web36202.mail.mud.yahoo.com> References: <997939.52623.qm@web36202.mail.mud.yahoo.com> Message-ID: Can you take a look at the latest tutorial under the Tutorials link? It works with 2.3.3 and discusses the Bratu problem with both structured and unstructured meshes and has running code for it. Matt On 6/9/07, Shi Jin wrote: > I am using petsc-2.3.3-p1. > I've taken a look at > src/snes/examples/tutorials/ex10d/ and > src/dm/ao/examples/tutorials/ > However they are not really complete. > I am hoping to have something that shows how to deal > with the geometry and the parallel issues. The problem > itself can be very simple. > > Thanks. > > Shi > > --- Matthew Knepley wrote: > > > Are you using the dev version or 2.3.3? > > > > Thanks, > > > > Matt > > > > On 6/9/07, Shi Jin wrote: > > > Hi there, > > > > > > I am desperately looking for an example of code > > using > > > PETSc to deal with unstructured grid, either in > > finite > > > element or finite difference or any other method. > > > Thanks. > > > > > > Shi > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > It's here! Your new message! > > > Get new email alerts with the free Yahoo! Toolbar. > > > > > http://tools.search.yahoo.com/toolbar/features/mail/ > > > > > > > > > > > > -- > > What most experimenters take for granted before they > > begin their > > experiments is infinitely more interesting than any > > results to which > > their experiments lead. > > -- Norbert Wiener > > > > > > > > > ____________________________________________________________________________________ > Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. > http://mobile.yahoo.com/go?refer=1GNXIC > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From zonexo at gmail.com Sun Jun 10 09:13:04 2007 From: zonexo at gmail.com (Ben Tay) Date: Sun, 10 Jun 2007 22:13:04 +0800 Subject: How to zero all values on a particular row? Message-ID: <804ab5d40706100713jec08cd8q3a4df577866f414@mail.gmail.com> Hi, I need to insert values into a matrix and then solve this poisson eqn as part of my cfd code. For efficiency sake, I simply use "do j=1,size_y do i=1,size_x matsetvalue .... end do end do" to insert values into all the cells Then for specific cells, I need to enter some other values. In other words, for specific rows of the matrix, I need to zero the whole row and insert new values. How can I do that? I tried to use MatZeroRows but it says it's not for unassembled matrix. But I need to zero the particular row, insert values, and then finally assembly it. Is there a command to do this? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From jinzishuai at yahoo.com Sun Jun 10 18:16:04 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Sun, 10 Jun 2007 16:16:04 -0700 (PDT) Subject: Error installing PETSc with --download-triangle Message-ID: <20070610231604.1392.qmail@web36206.mail.mud.yahoo.com> Hi there, I am studying the tutorial given at http://www-unix.mcs.anl.gov/petsc/petsc-2/documentation/tutorials/PCFD2007.pdf At revision 4, I need to use triangle to generate or refine the mesh. So I reinstalled my PETSc-2.3.3-p1 with ./config/configure.py --with-cc=gcc --with-fc=g77 --with-cxx=g++ --download-f-blas-lapack=1 --download-mpich=1 --with-clanguage=cxx --with-sieve=1 --download-boost=1 --download-chaco --with-triangle I got an error saying that included in externalpackages/Triangle/src/triangle.h is missing. So I modified it to be "config.h" and then it seemed to generate the libtriangle.o file. However, I still get the error saying: /usr/bin/ld: src/libtriangle.o: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC src/libtriangle.o: could not read symbols: Bad value collect2: ld returned 1 exit status I am attaching the build.log file. I would appreciate any help. Thanks. Shi ____________________________________________________________________________________ Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545433 -------------- next part -------------- A non-text attachment was scrubbed... Name: build.log Type: application/octet-stream Size: 26669 bytes Desc: 988914365-build.log URL: From bsmith at mcs.anl.gov Sun Jun 10 18:54:12 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sun, 10 Jun 2007 18:54:12 -0500 (CDT) Subject: How to zero all values on a particular row? In-Reply-To: <804ab5d40706100713jec08cd8q3a4df577866f414@mail.gmail.com> References: <804ab5d40706100713jec08cd8q3a4df577866f414@mail.gmail.com> Message-ID: On Sun, 10 Jun 2007, Ben Tay wrote: > Hi, > > I need to insert values into a matrix and then solve this poisson eqn as > part of my cfd code. For efficiency sake, I simply use > > "do j=1,size_y > > do i=1,size_x > > matsetvalue .... > > end do > > end do" > > to insert values into all the cells > > Then for specific cells, I need to enter some other values. In other words, > for specific rows of the matrix, I need to zero the whole row and insert new > values. How can I do that? > > I tried to use MatZeroRows but it says it's not for unassembled matrix. But > I need to zero the particular row, insert values, and then finally assembly > it. Is there a command to do this? matassemblybegin/end matzerorows matsetvalues, matsetvalues, matsetvalue matssemblybegin/end For improved efficiency you will want to call MatSetOption(mat,MAT_KEEP_ZEROED_ROWS); before the matzerorows() > > Thanks > From zonexo at gmail.com Sun Jun 10 19:47:17 2007 From: zonexo at gmail.com (Ben Tay) Date: Mon, 11 Jun 2007 08:47:17 +0800 Subject: How to zero all values on a particular row? In-Reply-To: References: <804ab5d40706100713jec08cd8q3a4df577866f414@mail.gmail.com> Message-ID: <804ab5d40706101747l7059b624i88cfe0bdb3893d14@mail.gmail.com> Thanks Barry, I managed to get it working. I realise that I had to call matssemblybegin/end each time after I zero a particular row. I also tried MatSetOption(mat,MAT_KEEP_ZEROED_ROWS) as what you 've suggested. So do I have to callMatSetOption(mat,MAT_KEEP_ZEROED_ROWS) everytime just before I need to zero it or just once ie after the 1st matassemblybegin/end? Calling matassemblybegin/end each time before matzerorows gives me the impression that it is very inefficient. Is that so? In that case, I wonder if it is better for me to : 1 use matsetvalues to put zeros into those location where I earlier insert in the 1st full i,j sweep 2. insert correct value using matsetvalues 3. finally matassemblybegin/end - just once. Lastly, is MatZeroRowsIS exactly the same as matzerorows, except that it is meant for just 1 row instead of consecutive no. of rows? Thanks again On 6/11/07, Barry Smith wrote: > > > > On Sun, 10 Jun 2007, Ben Tay wrote: > > > Hi, > > > > I need to insert values into a matrix and then solve this poisson eqn as > > part of my cfd code. For efficiency sake, I simply use > > > > "do j=1,size_y > > > > do i=1,size_x > > > > matsetvalue .... > > > > end do > > > > end do" > > > > to insert values into all the cells > > > > Then for specific cells, I need to enter some other values. In other > words, > > for specific rows of the matrix, I need to zero the whole row and insert > new > > values. How can I do that? > > > > I tried to use MatZeroRows but it says it's not for unassembled matrix. > But > > I need to zero the particular row, insert values, and then finally > assembly > > it. Is there a command to do this? > > matassemblybegin/end > matzerorows > matsetvalues, matsetvalues, matsetvalue > matssemblybegin/end > > For improved efficiency you will want to call > MatSetOption(mat,MAT_KEEP_ZEROED_ROWS); before the matzerorows() > > > > > Thanks > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Sun Jun 10 19:52:49 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sun, 10 Jun 2007 19:52:49 -0500 (CDT) Subject: How to zero all values on a particular row? In-Reply-To: <804ab5d40706101747l7059b624i88cfe0bdb3893d14@mail.gmail.com> References: <804ab5d40706100713jec08cd8q3a4df577866f414@mail.gmail.com> <804ab5d40706101747l7059b624i88cfe0bdb3893d14@mail.gmail.com> Message-ID: On Mon, 11 Jun 2007, Ben Tay wrote: > Thanks Barry, > > I managed to get it working. I realise that I had to call > matssemblybegin/end each time after I zero a particular row. I also tried > MatSetOption(mat,MAT_KEEP_ZEROED_ROWS) as what you 've suggested. > > So do I have to callMatSetOption(mat,MAT_KEEP_ZEROED_ROWS) everytime just > before I need to zero it or just once ie after the 1st matassemblybegin/end? Call it once when the matrix is created is fine. > > Calling matassemblybegin/end each time before matzerorows gives me the > impression that it is very inefficient. Is that so? Yes, if you do this a bunch of imes > > In that case, I wonder if it is better for me to : > > 1 use matsetvalues to put zeros into those location where I earlier insert > in the 1st full i,j sweep > 2. insert correct value using matsetvalues > 3. finally matassemblybegin/end - just once. You can do this > > Lastly, is MatZeroRowsIS exactly the same as matzerorows, except that it is > meant for just 1 row instead of consecutive no. of rows? They are the same but one takes an array of integers while the other takes an IS. Neither require "consecutive no. of rows" you can zero whatever rows you want together. Barry > > Thanks again > > > On 6/11/07, Barry Smith wrote: > > > > > > > > On Sun, 10 Jun 2007, Ben Tay wrote: > > > > > Hi, > > > > > > I need to insert values into a matrix and then solve this poisson eqn as > > > part of my cfd code. For efficiency sake, I simply use > > > > > > "do j=1,size_y > > > > > > do i=1,size_x > > > > > > matsetvalue .... > > > > > > end do > > > > > > end do" > > > > > > to insert values into all the cells > > > > > > Then for specific cells, I need to enter some other values. In other > > words, > > > for specific rows of the matrix, I need to zero the whole row and insert > > new > > > values. How can I do that? > > > > > > I tried to use MatZeroRows but it says it's not for unassembled matrix. > > But > > > I need to zero the particular row, insert values, and then finally > > assembly > > > it. Is there a command to do this? > > > > matassemblybegin/end > > matzerorows > > matsetvalues, matsetvalues, matsetvalue > > matssemblybegin/end > > > > For improved efficiency you will want to call > > MatSetOption(mat,MAT_KEEP_ZEROED_ROWS); before the matzerorows() > > > > > > > > Thanks > > > > > > > > From bsmith at mcs.anl.gov Sun Jun 10 21:17:24 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sun, 10 Jun 2007 21:17:24 -0500 (CDT) Subject: Do not ignore errors in Makefile In-Reply-To: <429510.48340.qm@web36209.mail.mud.yahoo.com> References: <429510.48340.qm@web36209.mail.mud.yahoo.com> Message-ID: Shi, I have come up with a scheme that helps with this implemented in petsc-dev. The default behavior is the same, for example, [anlext2wls147:snes/examples/tutorials] bsmith% make ex37f90 gfortran -c -I/Users/bsmith/Src/petsc-dev/include/finclude -fPIC -Wall -Wno-unused-variable -g -I/Users/bsmith/Src/petsc-dev -I/Users/bsmith/Src/petsc-dev/c-gfortran/include -I/Users/bsmith/Src/petsc-dev/include -I/usr/X11R6/include -I/Users/bsmith/Src/petsc-dev/c-gfortran/include -o mex37f90.o mex37f90.F90 mex37f90.F90:4: ffv 1 Error: Unclassifiable statement at (1) mex37f90.F90:77.22: use mex37f90 1 Fatal Error: Can't open module file 'mex37f90.mod' for reading at (1): No such file or directory make: [mex37f90.o] Error 1 (ignored) gfortran -c -I/Users/bsmith/Src/petsc-dev/include/finclude -fPIC -Wall -Wno-unused-variable -g -I/Users/bsmith/Src/petsc-dev -I/Users/bsmith/Src/petsc-dev/c-gfortran/include -I/Users/bsmith/Src/petsc-dev/include -I/usr/X11R6/include -I/Users/bsmith/Src/petsc-dev/c-gfortran/include -o ex37f90.o ex37f90.F90 ex37f90.F90:14.18: use mex37f90 1 Fatal Error: Can't open module file 'mex37f90.mod' for reading at (1): No such file or directory make: [ex37f90.o] Error 1 (ignored) /Users/bsmith/Src/petsc-dev/c-gfortran/bin/mpif90 -fPIC -Wall -Wno-unused-variable -g -o ex37f90 ex37f90.o -L/Users/bsmith/Src/petsc-dev/c-gfortran/lib -L/Users/bsmith/Src/petsc-dev/c-gfortran/lib -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -L/usr/X11R6/lib -lX11 -llapack -lblas -L/usr/lib/gcc/i686-apple-darwin8/4.0.1 -L/usr/lib/gcc/i686-apple-darwin8/4.0.1/../../.. -ldl -lSystem -lgfortranbegin -lgfortran -L/usr/local/gfortran/lib/gcc/i386-apple-darwin8.8.1/4.3.0 -L/usr/local/gfortran/lib/gcc/i386-apple-darwin8.8.1/4.3.0/../../.. -lgcc_s.10.4 -ldl -L/usr/lib/gcc/i686-apple-darwin8/4.0.1 -L/usr/lib/gcc/i686-apple-darwin8/4.0.1/../../.. -ldl -lSystem -ldl gfortran: ex37f90.o: No such file or directory make: [ex37f90] Error 1 (ignored) /bin/rm -f ex37f90.o mex37f90.mod mex37f90.o mex37finterfaces.mod But [anlext2wls147:snes/examples/tutorials] bsmith% make ex37f90 PETSC_MAKE_STOP_ON_ERROR="" gfortran -c -I/Users/bsmith/Src/petsc-dev/include/finclude -fPIC -Wall -Wno-unused-variable -g -I/Users/bsmith/Src/petsc-dev -I/Users/bsmith/Src/petsc-dev/c-gfortran/include -I/Users/bsmith/Src/petsc-dev/include -I/usr/X11R6/include -I/Users/bsmith/Src/petsc-dev/c-gfortran/include -o mex37f90.o mex37f90.F90 mex37f90.F90:4: ffv 1 Error: Unclassifiable statement at (1) mex37f90.F90:77.22: use mex37f90 1 Fatal Error: Can't open module file 'mex37f90.mod' for reading at (1): No such file or directory make: *** [mex37f90.o] Error 1 Causes it to stop immediately. You can also put PETSC_MAKE_STOP_ON_ERROR = "" in the makefile UNDER all the includes in the makefile Hope this helps, Barry On Fri, 8 Jun 2007, Shi Jin wrote: > Hi,there, > > I found that the default behavior of compiling a PETSc > program composed of many source files is that errors > are ignored and compilations continue to the next > source file when an error is encountered during > "make". > I think it is caused by the "-" sign in the Makefile. > There may be a good reason to have this feature but > for my code, I really don't want it. I want to he > process to stop so that I can immediately deal with > the error. Is there a way to accomplish this feature? > I guess something must be changed inside > ${PETSC_DIR}/bmake/common/base etc but it seems quite > complicated to figure it out. Could you please help me > here? Thank you very much. > > Shi > > > > ____________________________________________________________________________________ > Food fight? Enjoy some healthy debate > in the Yahoo! Answers Food & Drink Q&A. > http://answers.yahoo.com/dir/?link=list&sid=396545367 > > From jinzishuai at yahoo.com Sun Jun 10 21:57:10 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Sun, 10 Jun 2007 19:57:10 -0700 (PDT) Subject: Error compile petsc-dev Message-ID: <20070611025710.79450.qmail@web36206.mail.mud.yahoo.com> Hi, Since I wanted to try Barry's implementation on the "Do not ignore errors in Makefile" issue, I checked out petsc-dev (both the Mercurial and the nightly tar ball). However, I had the same errors during make: home/seki/mywork/PETSc/petsc-dev/conf/variables:119: /home/seki/mywork/PETSc/petsc-dev//conf/petscconf: No such file or directory /home/seki/mywork/PETSc/petsc-dev/conf/rules:808: /home/seki/mywork/PETSc/petsc-dev//conf/petscrules: No such file or directory make: *** No rule to make target `/home/seki/mywork/PETSc/petsc-dev//conf/petscrules'. Stop. Please help. Thanks. Shi ____________________________________________________________________________________ Get the Yahoo! toolbar and be alerted to new email wherever you're surfing. http://new.toolbar.yahoo.com/toolbar/features/mail/index.php From bsmith at mcs.anl.gov Sun Jun 10 22:04:02 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sun, 10 Jun 2007 22:04:02 -0500 (CDT) Subject: Error compile petsc-dev In-Reply-To: <20070611025710.79450.qmail@web36206.mail.mud.yahoo.com> References: <20070611025710.79450.qmail@web36206.mail.mud.yahoo.com> Message-ID: Please send to petsc-maint at mcs.anl.gov instead of petsc-users The makefile system was changed slightly in petsc-dev see http://www-unix.mcs.anl.gov/web-mail-archive/lists/petsc-dev/2007/06/msg00003.html Most likely you have not set PETSC_ARCH Barry On Sun, 10 Jun 2007, Shi Jin wrote: > Hi, > Since I wanted to try Barry's implementation on the > "Do not ignore errors in Makefile" issue, I checked > out petsc-dev (both the Mercurial and the nightly tar > ball). > However, I had the same errors during make: > home/seki/mywork/PETSc/petsc-dev/conf/variables:119: > /home/seki/mywork/PETSc/petsc-dev//conf/petscconf: No > such file or directory > /home/seki/mywork/PETSc/petsc-dev/conf/rules:808: > /home/seki/mywork/PETSc/petsc-dev//conf/petscrules: No > such file or directory > make: *** No rule to make target > `/home/seki/mywork/PETSc/petsc-dev//conf/petscrules'. > Stop. > > Please help. > Thanks. > Shi > > > > ____________________________________________________________________________________ > Get the Yahoo! toolbar and be alerted to new email wherever you're surfing. > http://new.toolbar.yahoo.com/toolbar/features/mail/index.php > > From jinzishuai at yahoo.com Sun Jun 10 21:58:39 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Sun, 10 Jun 2007 19:58:39 -0700 (PDT) Subject: Do not ignore errors in Makefile In-Reply-To: Message-ID: <995057.95680.qm@web36213.mail.mud.yahoo.com> Great. This seems to be exactly what I want. I hope it will soon be available in the release. Shi --- Barry Smith wrote: > > Shi, > > I have come up with a scheme that helps with this > implemented > in petsc-dev. The default behavior is the same, for > example, > > [anlext2wls147:snes/examples/tutorials] bsmith% make > ex37f90 > gfortran -c > -I/Users/bsmith/Src/petsc-dev/include/finclude -fPIC > -Wall -Wno-unused-variable -g > -I/Users/bsmith/Src/petsc-dev > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -I/Users/bsmith/Src/petsc-dev/include > -I/usr/X11R6/include > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -o mex37f90.o mex37f90.F90 > mex37f90.F90:4: > > ffv > 1 > Error: Unclassifiable statement at (1) > mex37f90.F90:77.22: > > use mex37f90 > 1 > Fatal Error: Can't open module file 'mex37f90.mod' > for reading at (1): No such file or directory > make: [mex37f90.o] Error 1 (ignored) > gfortran -c > -I/Users/bsmith/Src/petsc-dev/include/finclude -fPIC > -Wall -Wno-unused-variable -g > -I/Users/bsmith/Src/petsc-dev > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -I/Users/bsmith/Src/petsc-dev/include > -I/usr/X11R6/include > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -o ex37f90.o ex37f90.F90 > ex37f90.F90:14.18: > > use mex37f90 > 1 > Fatal Error: Can't open module file 'mex37f90.mod' > for reading at (1): No such file or directory > make: [ex37f90.o] Error 1 (ignored) > /Users/bsmith/Src/petsc-dev/c-gfortran/bin/mpif90 > -fPIC -Wall -Wno-unused-variable -g -o ex37f90 > ex37f90.o > -L/Users/bsmith/Src/petsc-dev/c-gfortran/lib > -L/Users/bsmith/Src/petsc-dev/c-gfortran/lib > -lpetscsnes -lpetscksp -lpetscdm -lpetscmat > -lpetscvec -lpetsc -L/usr/X11R6/lib -lX11 > -llapack -lblas > -L/usr/lib/gcc/i686-apple-darwin8/4.0.1 > -L/usr/lib/gcc/i686-apple-darwin8/4.0.1/../../.. > -ldl -lSystem -lgfortranbegin -lgfortran > -L/usr/local/gfortran/lib/gcc/i386-apple-darwin8.8.1/4.3.0 > -L/usr/local/gfortran/lib/gcc/i386-apple-darwin8.8.1/4.3.0/../../.. > -lgcc_s.10.4 -ldl > -L/usr/lib/gcc/i686-apple-darwin8/4.0.1 > -L/usr/lib/gcc/i686-apple-darwin8/4.0.1/../../.. > -ldl -lSystem -ldl > gfortran: ex37f90.o: No such file or directory > make: [ex37f90] Error 1 (ignored) > /bin/rm -f ex37f90.o mex37f90.mod mex37f90.o > mex37finterfaces.mod > > But > [anlext2wls147:snes/examples/tutorials] bsmith% make > ex37f90 PETSC_MAKE_STOP_ON_ERROR="" > gfortran -c > -I/Users/bsmith/Src/petsc-dev/include/finclude -fPIC > -Wall -Wno-unused-variable -g > -I/Users/bsmith/Src/petsc-dev > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -I/Users/bsmith/Src/petsc-dev/include > -I/usr/X11R6/include > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -o mex37f90.o mex37f90.F90 > mex37f90.F90:4: > > ffv > 1 > Error: Unclassifiable statement at (1) > mex37f90.F90:77.22: > > use mex37f90 > 1 > Fatal Error: Can't open module file 'mex37f90.mod' > for reading at (1): No such file or directory > make: *** [mex37f90.o] Error 1 > > Causes it to stop immediately. You can also put > PETSC_MAKE_STOP_ON_ERROR = "" > in the makefile UNDER all the includes in the > makefile > > Hope this helps, > > Barry > > > On Fri, 8 Jun 2007, Shi Jin wrote: > > > Hi,there, > > > > I found that the default behavior of compiling a > PETSc > > program composed of many source files is that > errors > > are ignored and compilations continue to the next > > source file when an error is encountered during > > "make". > > I think it is caused by the "-" sign in the > Makefile. > > There may be a good reason to have this feature > but > > for my code, I really don't want it. I want to he > > process to stop so that I can immediately deal > with > > the error. Is there a way to accomplish this > feature? > > I guess something must be changed inside > > ${PETSC_DIR}/bmake/common/base etc but it seems > quite > > complicated to figure it out. Could you please > help me > > here? Thank you very much. > > > > Shi > > > > > > > > > ____________________________________________________________________________________ > > Food fight? Enjoy some healthy debate > > in the Yahoo! Answers Food & Drink Q&A. > > > http://answers.yahoo.com/dir/?link=list&sid=396545367 > > > > > > ____________________________________________________________________________________ Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/ From jinzishuai at yahoo.com Sun Jun 10 22:47:28 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Sun, 10 Jun 2007 20:47:28 -0700 (PDT) Subject: Do not ignore errors in Makefile In-Reply-To: Message-ID: <69457.1196.qm@web36214.mail.mud.yahoo.com> Hi Barry, The make PETSC_MAKE_STOP_ON_ERROR="" method works perfectly. However, when putting this line inside the Makefile after all the include statements, it showslots of script code and there is not detailed compiler errors. I changed it to PETSC_MAKE_STOP_ON_ERROR=, without the "" in the end and it works just like the command line case. Anyway, this is a very good feature and I can't wait for it to show up in the release. Thank you very much. Shi --- Barry Smith wrote: > > Shi, > > I have come up with a scheme that helps with this > implemented > in petsc-dev. The default behavior is the same, for > example, > > [anlext2wls147:snes/examples/tutorials] bsmith% make > ex37f90 > gfortran -c > -I/Users/bsmith/Src/petsc-dev/include/finclude -fPIC > -Wall -Wno-unused-variable -g > -I/Users/bsmith/Src/petsc-dev > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -I/Users/bsmith/Src/petsc-dev/include > -I/usr/X11R6/include > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -o mex37f90.o mex37f90.F90 > mex37f90.F90:4: > > ffv > 1 > Error: Unclassifiable statement at (1) > mex37f90.F90:77.22: > > use mex37f90 > 1 > Fatal Error: Can't open module file 'mex37f90.mod' > for reading at (1): No such file or directory > make: [mex37f90.o] Error 1 (ignored) > gfortran -c > -I/Users/bsmith/Src/petsc-dev/include/finclude -fPIC > -Wall -Wno-unused-variable -g > -I/Users/bsmith/Src/petsc-dev > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -I/Users/bsmith/Src/petsc-dev/include > -I/usr/X11R6/include > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -o ex37f90.o ex37f90.F90 > ex37f90.F90:14.18: > > use mex37f90 > 1 > Fatal Error: Can't open module file 'mex37f90.mod' > for reading at (1): No such file or directory > make: [ex37f90.o] Error 1 (ignored) > /Users/bsmith/Src/petsc-dev/c-gfortran/bin/mpif90 > -fPIC -Wall -Wno-unused-variable -g -o ex37f90 > ex37f90.o > -L/Users/bsmith/Src/petsc-dev/c-gfortran/lib > -L/Users/bsmith/Src/petsc-dev/c-gfortran/lib > -lpetscsnes -lpetscksp -lpetscdm -lpetscmat > -lpetscvec -lpetsc -L/usr/X11R6/lib -lX11 > -llapack -lblas > -L/usr/lib/gcc/i686-apple-darwin8/4.0.1 > -L/usr/lib/gcc/i686-apple-darwin8/4.0.1/../../.. > -ldl -lSystem -lgfortranbegin -lgfortran > -L/usr/local/gfortran/lib/gcc/i386-apple-darwin8.8.1/4.3.0 > -L/usr/local/gfortran/lib/gcc/i386-apple-darwin8.8.1/4.3.0/../../.. > -lgcc_s.10.4 -ldl > -L/usr/lib/gcc/i686-apple-darwin8/4.0.1 > -L/usr/lib/gcc/i686-apple-darwin8/4.0.1/../../.. > -ldl -lSystem -ldl > gfortran: ex37f90.o: No such file or directory > make: [ex37f90] Error 1 (ignored) > /bin/rm -f ex37f90.o mex37f90.mod mex37f90.o > mex37finterfaces.mod > > But > [anlext2wls147:snes/examples/tutorials] bsmith% make > ex37f90 PETSC_MAKE_STOP_ON_ERROR="" > gfortran -c > -I/Users/bsmith/Src/petsc-dev/include/finclude -fPIC > -Wall -Wno-unused-variable -g > -I/Users/bsmith/Src/petsc-dev > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -I/Users/bsmith/Src/petsc-dev/include > -I/usr/X11R6/include > -I/Users/bsmith/Src/petsc-dev/c-gfortran/include > -o mex37f90.o mex37f90.F90 > mex37f90.F90:4: > > ffv > 1 > Error: Unclassifiable statement at (1) > mex37f90.F90:77.22: > > use mex37f90 > 1 > Fatal Error: Can't open module file 'mex37f90.mod' > for reading at (1): No such file or directory > make: *** [mex37f90.o] Error 1 > > Causes it to stop immediately. You can also put > PETSC_MAKE_STOP_ON_ERROR = "" > in the makefile UNDER all the includes in the > makefile > > Hope this helps, > > Barry > > > On Fri, 8 Jun 2007, Shi Jin wrote: > > > Hi,there, > > > > I found that the default behavior of compiling a > PETSc > > program composed of many source files is that > errors > > are ignored and compilations continue to the next > > source file when an error is encountered during > > "make". > > I think it is caused by the "-" sign in the > Makefile. > > There may be a good reason to have this feature > but > > for my code, I really don't want it. I want to he > > process to stop so that I can immediately deal > with > > the error. Is there a way to accomplish this > feature? > > I guess something must be changed inside > > ${PETSC_DIR}/bmake/common/base etc but it seems > quite > > complicated to figure it out. Could you please > help me > > here? Thank you very much. > > > > Shi > > > > > > > > > ____________________________________________________________________________________ > > Food fight? Enjoy some healthy debate > > in the Yahoo! Answers Food & Drink Q&A. > > > http://answers.yahoo.com/dir/?link=list&sid=396545367 > > > > > > ____________________________________________________________________________________ Don't get soaked. Take a quick peak at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather From knepley at gmail.com Mon Jun 11 00:12:04 2007 From: knepley at gmail.com (Matthew Knepley) Date: Mon, 11 Jun 2007 00:12:04 -0500 Subject: Error installing PETSc with --download-triangle In-Reply-To: <20070610231604.1392.qmail@web36206.mail.mud.yahoo.com> References: <20070610231604.1392.qmail@web36206.mail.mud.yahoo.com> Message-ID: Yes, I fixed this error after release. If you a) Remove externalPackages/Triangle b) Reconfigure It should pull the new package and work. Thanks, Matt On 6/10/07, Shi Jin wrote: > Hi there, > > I am studying the tutorial given at > http://www-unix.mcs.anl.gov/petsc/petsc-2/documentation/tutorials/PCFD2007.pdf > > At revision 4, I need to use triangle to generate or > refine the mesh. So I reinstalled my PETSc-2.3.3-p1 > with > ./config/configure.py --with-cc=gcc --with-fc=g77 > --with-cxx=g++ --download-f-blas-lapack=1 > --download-mpich=1 --with-clanguage=cxx --with-sieve=1 > --download-boost=1 --download-chaco --with-triangle > > I got an error saying that included in > externalpackages/Triangle/src/triangle.h is missing. > So I modified it to be "config.h" and then it seemed > to generate the libtriangle.o file. However, I still > get the error saying: > /usr/bin/ld: src/libtriangle.o: relocation R_X86_64_32 > against `a local symbol' can not be used when making a > shared object; recompile with -fPIC > src/libtriangle.o: could not read symbols: Bad value > collect2: ld returned 1 exit status > > I am attaching the build.log file. > I would appreciate any help. Thanks. > > Shi > > > > > ____________________________________________________________________________________ > Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. > http://answers.yahoo.com/dir/?link=list&sid=396545433 > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From jinzishuai at yahoo.com Mon Jun 11 13:27:14 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Mon, 11 Jun 2007 11:27:14 -0700 (PDT) Subject: Error installing PETSc with --download-triangle In-Reply-To: Message-ID: <34768.39553.qm@web36208.mail.mud.yahoo.com> Thanks but I am not exactly sure how I can get your changes. I've tried the latest petsc-dev and 2.3.3-p2, they both give me ********************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------- Shi --- Matthew Knepley wrote: > Yes, I fixed this error after release. If you > > a) Remove externalPackages/Triangle > > b) Reconfigure > > It should pull the new package and work. > > Thanks, > > Matt > > On 6/10/07, Shi Jin wrote: > > Hi there, > > > > I am studying the tutorial given at > > > http://www-unix.mcs.anl.gov/petsc/petsc-2/documentation/tutorials/PCFD2007.pdf > > > > At revision 4, I need to use triangle to generate > or > > refine the mesh. So I reinstalled my > PETSc-2.3.3-p1 > > with > > ./config/configure.py --with-cc=gcc --with-fc=g77 > > --with-cxx=g++ --download-f-blas-lapack=1 > > --download-mpich=1 --with-clanguage=cxx > --with-sieve=1 > > --download-boost=1 --download-chaco > --with-triangle > > > > I got an error saying that included in > > externalpackages/Triangle/src/triangle.h is > missing. > > So I modified it to be "config.h" and then it > seemed > > to generate the libtriangle.o file. However, I > still > > get the error saying: > > /usr/bin/ld: src/libtriangle.o: relocation > R_X86_64_32 > > against `a local symbol' can not be used when > making a > > shared object; recompile with -fPIC > > src/libtriangle.o: could not read symbols: Bad > value > > collect2: ld returned 1 exit status > > > > I am attaching the build.log file. > > I would appreciate any help. Thanks. > > > > Shi > > > > > > > > > > > ____________________________________________________________________________________ > > Be a better Heartthrob. Get better relationship > answers from someone who knows. Yahoo! Answers - > Check it out. > > > http://answers.yahoo.com/dir/?link=list&sid=396545433 > > > > > -- > What most experimenters take for granted before they > begin their > experiments is infinitely more interesting than any > results to which > their experiments lead. > -- Norbert Wiener > > ____________________________________________________________________________________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097 From jinzishuai at yahoo.com Mon Jun 11 18:37:01 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Mon, 11 Jun 2007 16:37:01 -0700 (PDT) Subject: cannot find Python module Cxx and Cxxhelper Message-ID: <194017.75608.qm@web36209.mail.mud.yahoo.com> Hi, I am trying to use the FIAT external package and when it calls the FEM.py at $PETSC_DIR/python/PETSc, I always get the error: ImportError: No module named Cxx I figured out it is cause by the line import Cxx, CxxHelper I searched online and could only find a Python module called PyCXX. The module name is called CXX. ALso I there is no FEM.py in the 2.3.2 version. So I am wondering what Cxx and CxxHelper modules are and how I can obtain them. Please help. Thanks a lot. Shi ____________________________________________________________________________________ Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front From jinzishuai at yahoo.com Mon Jun 11 23:04:10 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Mon, 11 Jun 2007 21:04:10 -0700 (PDT) Subject: PETSc support for second-order elements? Message-ID: <420660.66528.qm@web36209.mail.mud.yahoo.com> Hi there, I am learning the PETSc tools provided in the latest version to deal with unstructured grid. I realize that with functions such as MeshCreatePCICE(MeshCreatePyLith), we can load the mesh directly from files, in the PCICE (PyLith) format. This is really a great news for us. However, we need to use second order elements, for example, 10-node tetrahedra. I tried to load it with MeshCreatePCICE but it seems to me that second order elements are not yet supported. I've learned this from the PyLith website also. I want to ask is there a plan to support second order elements? Roughly when would it be available? Also if someone can comment on how mature the current unstructured mesh library is, I would greatly appreciate it. Thank you for your help. Shi ____________________________________________________________________________________ No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started. http://mobile.yahoo.com/mail From knepley at gmail.com Tue Jun 12 02:16:54 2007 From: knepley at gmail.com (Matthew Knepley) Date: Tue, 12 Jun 2007 02:16:54 -0500 Subject: Error installing PETSc with --download-triangle In-Reply-To: <34768.39553.qm@web36208.mail.mud.yahoo.com> References: <34768.39553.qm@web36208.mail.mud.yahoo.com> Message-ID: I need the log to see what is wrong. Also, send these to petsc-maint at mcs.anl.gov. Thanks, Matt On 6/11/07, Shi Jin wrote: > Thanks but I am not exactly sure how I can get your > changes. > > I've tried the latest petsc-dev and 2.3.3-p2, they > both > give me > ********************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS > (see configure.log for details): > --------------------------------------------------------------------------------------- > > > Shi > --- Matthew Knepley wrote: > > > Yes, I fixed this error after release. If you > > > > a) Remove externalPackages/Triangle > > > > b) Reconfigure > > > > It should pull the new package and work. > > > > Thanks, > > > > Matt > > > > On 6/10/07, Shi Jin wrote: > > > Hi there, > > > > > > I am studying the tutorial given at > > > > > > http://www-unix.mcs.anl.gov/petsc/petsc-2/documentation/tutorials/PCFD2007.pdf > > > > > > At revision 4, I need to use triangle to generate > > or > > > refine the mesh. So I reinstalled my > > PETSc-2.3.3-p1 > > > with > > > ./config/configure.py --with-cc=gcc --with-fc=g77 > > > --with-cxx=g++ --download-f-blas-lapack=1 > > > --download-mpich=1 --with-clanguage=cxx > > --with-sieve=1 > > > --download-boost=1 --download-chaco > > --with-triangle > > > > > > I got an error saying that included in > > > externalpackages/Triangle/src/triangle.h is > > missing. > > > So I modified it to be "config.h" and then it > > seemed > > > to generate the libtriangle.o file. However, I > > still > > > get the error saying: > > > /usr/bin/ld: src/libtriangle.o: relocation > > R_X86_64_32 > > > against `a local symbol' can not be used when > > making a > > > shared object; recompile with -fPIC > > > src/libtriangle.o: could not read symbols: Bad > > value > > > collect2: ld returned 1 exit status > > > > > > I am attaching the build.log file. > > > I would appreciate any help. Thanks. > > > > > > Shi > > > > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > Be a better Heartthrob. Get better relationship > > answers from someone who knows. Yahoo! Answers - > > Check it out. > > > > > > http://answers.yahoo.com/dir/?link=list&sid=396545433 > > > > > > > > > -- > > What most experimenters take for granted before they > > begin their > > experiments is infinitely more interesting than any > > results to which > > their experiments lead. > > -- Norbert Wiener > > > > > > > > > ____________________________________________________________________________________ > Now that's room service! Choose from over 150,000 hotels > in 45,000 destinations on Yahoo! Travel to find your fit. > http://farechase.yahoo.com/promo-generic-14795097 > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From knepley at gmail.com Tue Jun 12 02:20:12 2007 From: knepley at gmail.com (Matthew Knepley) Date: Tue, 12 Jun 2007 02:20:12 -0500 Subject: cannot find Python module Cxx and Cxxhelper In-Reply-To: <194017.75608.qm@web36209.mail.mud.yahoo.com> References: <194017.75608.qm@web36209.mail.mud.yahoo.com> Message-ID: This comes from the 'Generator' module downloaded when you configure with --download-generator. I am guessing your confgure did not run. Thanks, Matt On 6/11/07, Shi Jin wrote: > Hi, > > I am trying to use the FIAT external package and when > it calls the FEM.py at $PETSC_DIR/python/PETSc, I > always get the error: > ImportError: No module named Cxx > > I figured out it is cause by the line > import Cxx, CxxHelper > > I searched online and could only find a Python module > called PyCXX. The module name is called CXX. > ALso I there is no FEM.py in the 2.3.2 version. > So I am wondering what Cxx and CxxHelper modules are > and how I can obtain them. > Please help. > Thanks a lot. > > Shi > > > > ____________________________________________________________________________________ > Bored stiff? Loosen up... > Download and play hundreds of games for free on Yahoo! Games. > http://games.yahoo.com/games/front > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From knepley at gmail.com Tue Jun 12 02:26:42 2007 From: knepley at gmail.com (Matthew Knepley) Date: Tue, 12 Jun 2007 02:26:42 -0500 Subject: PETSc support for second-order elements? In-Reply-To: <420660.66528.qm@web36209.mail.mud.yahoo.com> References: <420660.66528.qm@web36209.mail.mud.yahoo.com> Message-ID: 1) The library is not mature. It is alpha. However, it is being used for several projects. 2) The PCICE reader is just an example. Other formats could be easily implemented. 3) I am not sure I understand your question about quadratic elements. We do support higher order elements (see the Tutorial on the website). This has nothing to do with geometry, and thus you would just read in a tet mesh. Thanks, Matt On 6/11/07, Shi Jin wrote: > Hi there, > > I am learning the PETSc tools provided in the latest > version to deal with unstructured grid. I realize that > with functions such as > MeshCreatePCICE(MeshCreatePyLith), we can load the > mesh directly from files, in the PCICE (PyLith) > format. This is really a great news for us. > > However, we need to use second order elements, for > example, 10-node tetrahedra. I tried to load it with > MeshCreatePCICE but it seems to me that second order > elements are not yet supported. I've learned this from > the PyLith website also. > > I want to ask is there a plan to support second order > elements? Roughly when would it be available? > Also if someone can comment on how mature the current > unstructured mesh library is, I would greatly > appreciate it. > > Thank you for your help. > Shi > > > > ____________________________________________________________________________________ > No need to miss a message. Get email on-the-go > with Yahoo! Mail for Mobile. Get started. > http://mobile.yahoo.com/mail > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From jinzishuai at yahoo.com Tue Jun 12 10:35:55 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Tue, 12 Jun 2007 08:35:55 -0700 (PDT) Subject: cannot find Python module Cxx and Cxxhelper In-Reply-To: Message-ID: <789969.94629.qm@web36214.mail.mud.yahoo.com> No, I didn't use Generator. Thanks. However, after using generator, I got another error: ImportError: No module named ASE. Is there any other packages I need to install? Thanks. Shi However, the installation is --- Matthew Knepley wrote: > This comes from the 'Generator' module downloaded > when you configure > with --download-generator. I am guessing your > confgure did not run. > > Thanks, > > Matt > > On 6/11/07, Shi Jin wrote: > > Hi, > > > > I am trying to use the FIAT external package and > when > > it calls the FEM.py at $PETSC_DIR/python/PETSc, I > > always get the error: > > ImportError: No module named Cxx > > > > I figured out it is cause by the line > > import Cxx, CxxHelper > > > > I searched online and could only find a Python > module > > called PyCXX. The module name is called CXX. > > ALso I there is no FEM.py in the 2.3.2 version. > > So I am wondering what Cxx and CxxHelper modules > are > > and how I can obtain them. > > Please help. > > Thanks a lot. > > > > Shi > > > > > > > > > ____________________________________________________________________________________ > > Bored stiff? Loosen up... > > Download and play hundreds of games for free on > Yahoo! Games. > > http://games.yahoo.com/games/front > > > > > > > -- > What most experimenters take for granted before they > begin their > experiments is infinitely more interesting than any > results to which > their experiments lead. > -- Norbert Wiener > > ____________________________________________________________________________________ Got a little couch potato? Check out fun summer activities for kids. http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz From vijay.m at gmail.com Tue Jun 12 13:22:07 2007 From: vijay.m at gmail.com (Vijay M) Date: Tue, 12 Jun 2007 12:22:07 -0600 Subject: MatCreateMPIAIJWithArrays linker error Message-ID: Hi, I am trying to convert a serial code in fortran 90 to a parallel one using PETSc data structures. One of the ways i am trying to achieve the same is to use the serial code to create my matrices and then set PETSc mat values by passing in the arrays. When i used a single processor with MatCreateSeqAIJWithArrays, things worked just fine. But when i converted to MatCreateMPIAIJWithArrays, to create a parallel matrix that is distributed across different processors, i get a linker error saying that it could find the implementation for the function. Is there any specific library i should be including other than petsc, petscmat, petscksp, petscvec and petscfortran for this to work ? Thanks for any help in advance ! Vijay From bsmith at mcs.anl.gov Tue Jun 12 16:53:38 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Tue, 12 Jun 2007 16:53:38 -0500 (CDT) Subject: MatCreateMPIAIJWithArrays linker error In-Reply-To: References: Message-ID: What version of PETSc are you using? It it is not in 2.3.1 or earlier versions. You may need to upgrade to 2.3.3 Barry If you are using 2.3.2 or later please send the make_log* file from your petsc directory so we check for compiler errors On Tue, 12 Jun 2007, Vijay M wrote: > Hi, > > I am trying to convert a serial code in fortran 90 to a parallel one > using PETSc data structures. One of the ways i am trying to achieve > the same is to use the serial code to create my matrices and then set > PETSc mat values by passing in the arrays. When i used a single > processor with MatCreateSeqAIJWithArrays, things worked just fine. But > when i converted to MatCreateMPIAIJWithArrays, to create a parallel > matrix that is distributed across different processors, i get a linker > error saying that it could find the implementation for the function. > > Is there any specific library i should be including other than petsc, > petscmat, petscksp, petscvec and petscfortran for this to work ? > Thanks for any help in advance ! > > Vijay > > From vijay.m at gmail.com Tue Jun 12 17:14:34 2007 From: vijay.m at gmail.com (Vijay M) Date: Tue, 12 Jun 2007 16:14:34 -0600 Subject: MatCreateMPIAIJWithArrays linker error In-Reply-To: References: Message-ID: Barry, I am currently using 2.3.1. I will upgrade to 2.3.3 and let you know if i still have problems. Thanks for the help. Vijay On 6/12/07, Barry Smith wrote: > > What version of PETSc are you using? It it is not in 2.3.1 or earlier > versions. You may need to upgrade to 2.3.3 > > Barry > > If you are using 2.3.2 or later please send the make_log* file > from your petsc directory so we check for compiler errors > > > On Tue, 12 Jun 2007, Vijay M wrote: > > > Hi, > > > > I am trying to convert a serial code in fortran 90 to a parallel one > > using PETSc data structures. One of the ways i am trying to achieve > > the same is to use the serial code to create my matrices and then set > > PETSc mat values by passing in the arrays. When i used a single > > processor with MatCreateSeqAIJWithArrays, things worked just fine. But > > when i converted to MatCreateMPIAIJWithArrays, to create a parallel > > matrix that is distributed across different processors, i get a linker > > error saying that it could find the implementation for the function. > > > > Is there any specific library i should be including other than petsc, > > petscmat, petscksp, petscvec and petscfortran for this to work ? > > Thanks for any help in advance ! > > > > Vijay > > > > > > From knepley at gmail.com Wed Jun 13 02:01:31 2007 From: knepley at gmail.com (Matthew Knepley) Date: Wed, 13 Jun 2007 02:01:31 -0500 Subject: cannot find Python module Cxx and Cxxhelper In-Reply-To: <789969.94629.qm@web36214.mail.mud.yahoo.com> References: <789969.94629.qm@web36214.mail.mud.yahoo.com> Message-ID: Hmmm, it should not require ASE. That is an old package that we shuold not use anymore. Can you send the entire stack trace? I will debug it. Thanks, Matt On 6/12/07, Shi Jin wrote: > No, I didn't use Generator. Thanks. > However, after using generator, I got another error: > ImportError: No module named ASE. > Is there any other packages I need to install? > Thanks. > > Shi > However, the installation is > --- Matthew Knepley wrote: > > > This comes from the 'Generator' module downloaded > > when you configure > > with --download-generator. I am guessing your > > confgure did not run. > > > > Thanks, > > > > Matt > > > > On 6/11/07, Shi Jin wrote: > > > Hi, > > > > > > I am trying to use the FIAT external package and > > when > > > it calls the FEM.py at $PETSC_DIR/python/PETSc, I > > > always get the error: > > > ImportError: No module named Cxx > > > > > > I figured out it is cause by the line > > > import Cxx, CxxHelper > > > > > > I searched online and could only find a Python > > module > > > called PyCXX. The module name is called CXX. > > > ALso I there is no FEM.py in the 2.3.2 version. > > > So I am wondering what Cxx and CxxHelper modules > > are > > > and how I can obtain them. > > > Please help. > > > Thanks a lot. > > > > > > Shi > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > Bored stiff? Loosen up... > > > Download and play hundreds of games for free on > > Yahoo! Games. > > > http://games.yahoo.com/games/front > > > > > > > > > > > > -- > > What most experimenters take for granted before they > > begin their > > experiments is infinitely more interesting than any > > results to which > > their experiments lead. > > -- Norbert Wiener > > > > > > > > > ____________________________________________________________________________________ > Got a little couch potato? > Check out fun summer activities for kids. > http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From timothy.stitt at ichec.ie Thu Jun 14 07:01:37 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Thu, 14 Jun 2007 13:01:37 +0100 Subject: Problems with -eps_monitor_draw and mpiexec Message-ID: <200706141301.37757.timothy.stitt@ichec.ie> Hi all, I've finally got my parallel solver working in SLEPc. I want to monitor the eigenvalues and error tolerances graphically using -eps_monitor_draw. This works perfectly fine for the serial version of the code but when I test the parallel version I get the following errors from all nodes: [1]PETSC ERROR: --------------------- Error Message ------------------------------------ [1]PETSC ERROR: Error in external library! [1]PETSC ERROR: Unable to open display on localhost.localdomain:0.0 . Make sure your COMPUTE NODES are authorized to connect to this X server and either your DISPLAY variable is set or you use the -display name option FYI: I am testing these codes on a multi-core laptop so I am running mpiexec directly from the command-line. Without -eps_monitor_draw the code runs as aspected. Just wondering if someone can hint at a fix so that I can get the graphical monitoring working in parallel. Regards, Tim. -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From knepley at gmail.com Thu Jun 14 07:32:12 2007 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 14 Jun 2007 07:32:12 -0500 Subject: Problems with -eps_monitor_draw and mpiexec In-Reply-To: <200706141301.37757.timothy.stitt@ichec.ie> References: <200706141301.37757.timothy.stitt@ichec.ie> Message-ID: The X server does not like your hostname (localhost.localdomain). You can set your DISPLAY env variable, or just give the display argument -display :0.0 Matt On 6/14/07, Tim Stitt wrote: > Hi all, > > I've finally got my parallel solver working in SLEPc. I want to monitor the > eigenvalues and error tolerances graphically using -eps_monitor_draw. This > works perfectly fine for the serial version of the code but when I test the > parallel version I get the following errors from all nodes: > > [1]PETSC ERROR: --------------------- Error > Message ------------------------------------ > [1]PETSC ERROR: Error in external library! > [1]PETSC ERROR: Unable to open display on localhost.localdomain:0.0 > . Make sure your COMPUTE NODES are authorized to connect > to this X server and either your DISPLAY variable > is set or you use the -display name option > > FYI: I am testing these codes on a multi-core laptop so I am running mpiexec > directly from the command-line. Without -eps_monitor_draw the code runs as > aspected. > > Just wondering if someone can hint at a fix so that I can get the graphical > monitoring working in parallel. > > Regards, > > Tim. > > -- > Dr. Timothy Stitt > HPC Application Consultant - ICHEC (www.ichec.ie) > > Dublin Institute for Advanced Studies > 5 Merrion Square - Dublin 2 - Ireland > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From timothy.stitt at ichec.ie Thu Jun 14 08:09:08 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Thu, 14 Jun 2007 14:09:08 +0100 Subject: Problems with -eps_monitor_draw and mpiexec In-Reply-To: References: <200706141301.37757.timothy.stitt@ichec.ie> Message-ID: <200706141409.08369.timothy.stitt@ichec.ie> Matt, Perfect....thanks. Works now. Tim. On Thursday 14 June 2007 13:32, Matthew Knepley wrote: > The X server does not like your hostname (localhost.localdomain). You can > set your DISPLAY env variable, or just give the display argument -display > :0.0 -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From knutert at stud.ntnu.no Thu Jun 14 10:46:10 2007 From: knutert at stud.ntnu.no (Knut Erik Teigen) Date: Thu, 14 Jun 2007 17:46:10 +0200 Subject: Setting tolerances for multigrid In-Reply-To: <200706141409.08369.timothy.stitt@ichec.ie> References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> Message-ID: <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> Hello, How do I set the tolerances for the KSP solvers when using the DMMG routines without using command line arguments? It seems that I can use the argument -ksp_rtol on the command line, but in the code I can't use KSPSetTolerances since I don't have access to the KSP solver context? Also, I see there is a reference to the function DMMGSetUseGalerkin in the source code, but I can't find the documentation for it. Does this function not exist yet? Again I would like to use -dmmg_galerkin, but setting it in the code instead of on the command line. Regards, Knut Erik Teigen From knepley at gmail.com Thu Jun 14 11:32:10 2007 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 14 Jun 2007 11:32:10 -0500 Subject: Setting tolerances for multigrid In-Reply-To: <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> Message-ID: On 6/14/07, Knut Erik Teigen wrote: > Hello, > > How do I set the tolerances for the KSP solvers when using the > DMMG routines without using command line arguments? It seems that > I can use the argument -ksp_rtol on the command line, but in the code I > can't use KSPSetTolerances since I don't have access to the KSP solver > context? You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for any others. > Also, I see there is a reference to the function DMMGSetUseGalerkin > in the source code, but I can't find the documentation for it. > Does this function not exist yet? Again I would like to use > -dmmg_galerkin, but setting it in the code instead of on the command > line. I think you want this: http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html Matt > Regards, > Knut Erik Teigen > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From jinzishuai at yahoo.com Thu Jun 14 14:48:38 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Thu, 14 Jun 2007 12:48:38 -0700 (PDT) Subject: cannot find Python module Cxx and Cxxhelper In-Reply-To: Message-ID: <349473.56543.qm@web36205.mail.mud.yahoo.com> Hi Matthew, I have attached a tar ball containing the code directory. PETSc is configured with: seki at kalmar:~/mywork/PETSc/petsc-dev$ PETSC_DIR=`pwd` ./config/configure.py --with-cc=gcc --with-fc=g77 --with-cxx=g++ --download-f-blas-lapack=1 --download-mpich=1 --with-clanguage=cxx --with-sieve=1 --download-boost=1 --download-chaco --download-fiat --download-generator and it is built without problem. When I build this sample code by PCFD2007TutorialCode/revision8_fiat$ PETSC_DIR=/home/seki/mywork/PETSc/petsc-dev make I got the following out: ((-1.0,), (1.0,)) {0: {0: [0], 1: [1]}, 1: {0: []}} Perm: [0, 1] ((-1.0,), (1.0,)) {0: {0: [0], 1: [1]}, 1: {0: []}} Perm: [0, 1] Traceback (most recent call last): File "quadrature.fiat", line 56, in FEMQuadrature().run() File "quadrature.fiat", line 52, in run filename = sys.argv[1]) File "/home/seki/mywork/PETSc/petsc-dev/python/PETSc/FEM.py", line 583, in run self.outputElementSource(self.getElementSource(elements), filename) File "/home/seki/mywork/PETSc/petsc-dev/python/PETSc/FEM.py", line 545, in getElementSource defns.extend(self.getIntegratorSetup(n, element)) File "/home/seki/mywork/PETSc/petsc-dev/python/PETSc/FEM.py", line 208, in getIntegratorSetup decls.append(self.Cxx.getArray(refVar, self.Cxx.getType('double'), dim)) File "/home/seki/mywork/PETSc/petsc-dev/externalpackages/Generator/CxxHelper.py", line 306, in getArray import ASE.Compiler.Cxx.Array File "/home/seki/mywork/PETSc/petsc-dev/python/BuildSystem/importer.py", line 36, in import_module q, tail = self.find_head_package(parent, name) File "/home/seki/mywork/PETSc/petsc-dev/python/BuildSystem/importer.py", line 79, in find_head_package raise ImportError, "No module named " + qname ImportError: No module named ASE make: *** [quadrature.h] Error 1 Please let me know these information is sufficient. Thanks a lot. Shi --- Matthew Knepley wrote: > Hmmm, it should not require ASE. That is an old > package that we shuold not > use anymore. Can you send the entire stack trace? I > will debug it. > > Thanks, > > Matt > > On 6/12/07, Shi Jin wrote: > > No, I didn't use Generator. Thanks. > > However, after using generator, I got another > error: > > ImportError: No module named ASE. > > Is there any other packages I need to install? > > Thanks. > > > > Shi > > However, the installation is > > --- Matthew Knepley wrote: > > > > > This comes from the 'Generator' module > downloaded > > > when you configure > > > with --download-generator. I am guessing your > > > confgure did not run. > > > > > > Thanks, > > > > > > Matt > > > > > > On 6/11/07, Shi Jin > wrote: > > > > Hi, > > > > > > > > I am trying to use the FIAT external package > and > > > when > > > > it calls the FEM.py at > $PETSC_DIR/python/PETSc, I > > > > always get the error: > > > > ImportError: No module named Cxx > > > > > > > > I figured out it is cause by the line > > > > import Cxx, CxxHelper > > > > > > > > I searched online and could only find a Python > > > module > > > > called PyCXX. The module name is called CXX. > > > > ALso I there is no FEM.py in the 2.3.2 > version. > > > > So I am wondering what Cxx and CxxHelper > modules > > > are > > > > and how I can obtain them. > > > > Please help. > > > > Thanks a lot. > > > > > > > > Shi > > > > > > > > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > > Bored stiff? Loosen up... > > > > Download and play hundreds of games for free > on > > > Yahoo! Games. > > > > http://games.yahoo.com/games/front > > > > > > > > > > > > > > > > > -- > > > What most experimenters take for granted before > they > > > begin their > > > experiments is infinitely more interesting than > any > > > results to which > > > their experiments lead. > > > -- Norbert Wiener > > > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > Got a little couch potato? > > Check out fun summer activities for kids. > > > http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz > > > > > > > -- > What most experimenters take for granted before they > begin their > experiments is infinitely more interesting than any > results to which > their experiments lead. > -- Norbert Wiener > > ____________________________________________________________________________________ Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting -------------- next part -------------- A non-text attachment was scrubbed... Name: fiatProblem.tar.gz Type: application/x-gzip Size: 18891 bytes Desc: 1919390439-fiatProblem.tar.gz URL: From niriedith at gmail.com Thu Jun 14 15:57:04 2007 From: niriedith at gmail.com (Niriedith Karina ) Date: Thu, 14 Jun 2007 16:57:04 -0400 Subject: other software Message-ID: Hi !! Could anybody tell me about some software or library for unstructed mesh? if is a Hexahedron' s generator much better... and if is commercial doesn't matter Thanks anyway! :D -------------- next part -------------- An HTML attachment was scrubbed... URL: From xubinbin2004 at gmail.com Thu Jun 14 17:24:59 2007 From: xubinbin2004 at gmail.com (Bin) Date: Thu, 14 Jun 2007 16:24:59 -0600 Subject: other software In-Reply-To: References: Message-ID: <8f1c3d500706141524r124ee88sdb91cd9ecc4bdce8@mail.gmail.com> try *truegrid,* a commercial software On 6/14/07, Niriedith Karina wrote: > > Hi !! > > Could anybody tell me about some software or library for unstructed mesh? > if is a Hexahedron' s generator much better... > and if is commercial doesn't matter > > Thanks anyway! > :D > -- Best regards, Bin -------------- next part -------------- An HTML attachment was scrubbed... URL: From jinzishuai at yahoo.com Thu Jun 14 22:24:44 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Thu, 14 Jun 2007 20:24:44 -0700 (PDT) Subject: MeshDistribute() and Chaco Message-ID: <20070615032444.35778.qmail@web36206.mail.mud.yahoo.com> Hi, I am trying to study the new unstructured mesh part provided by the new Petsc. I have one particular question with regard to the function call MeshDistribute(serialMesh, PETSC_NULL, ¶llelMesh); This call obviously needs the chaco package to run in parallel since otherwise I will get a warning to configure with --download-chaco. So I ran it with chaco installed. The code works but the domain decomposition is valid but far from good. In the attached image, I am showing the domain decomposition for a 2-dimensional 1x1 box with two processes, using the following statements: MeshCreatePCICE(comm, 3, "bratu_2d.nodes","bratu_2d.lcon",PETSC_FALSE,PETSC_FALSE, &serialMesh); MeshDistribute(serialMesh, PETSC_NULL, ¶llelMesh); I am wondering if it is possible to improve the domain decomposition by passing some command arguments. I realized that there are Chaco options such as -mat_partitioning_chaco_global (found at http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/MatOrderings/MAT_PARTITIONING_Chaco.html) . However, when I pass these options to my code, it is not recognized. I wonder how chaco is used in Petsc and how I can change its behavior. In addition, is it possible to use other graph decomposition packages such as ParMetis to implement MeshDistribute()? I tried to enable ParMetis without chaco but the code didn't run and warned me to install chaco. Any advice is valuable. Thank you very much. Shi ____________________________________________________________________________________ Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 -------------- next part -------------- A non-text attachment was scrubbed... Name: NP2.png Type: image/png Size: 41739 bytes Desc: 88704069-NP2.png URL: From knepley at gmail.com Fri Jun 15 01:41:16 2007 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 15 Jun 2007 01:41:16 -0500 Subject: cannot find Python module Cxx and Cxxhelper In-Reply-To: <349473.56543.qm@web36205.mail.mud.yahoo.com> References: <349473.56543.qm@web36205.mail.mud.yahoo.com> Message-ID: Somehow you have an old copy of Generator. I replaced the tarball on our website to make sure. Please delete the directory externalpackages/Generator and reconfigure. Thanks, Matt On 6/14/07, Shi Jin wrote: > Hi Matthew, > > I have attached a tar ball containing the code > directory. > PETSc is configured with: > seki at kalmar:~/mywork/PETSc/petsc-dev$ PETSC_DIR=`pwd` > ./config/configure.py --with-cc=gcc --with-fc=g77 > --with-cxx=g++ --download-f-blas-lapack=1 > --download-mpich=1 --with-clanguage=cxx --with-sieve=1 > --download-boost=1 --download-chaco --download-fiat > --download-generator > and it is built without problem. > > When I build this sample code by > PCFD2007TutorialCode/revision8_fiat$ > PETSC_DIR=/home/seki/mywork/PETSc/petsc-dev make > I got the following out: > ((-1.0,), (1.0,)) > {0: {0: [0], 1: [1]}, 1: {0: []}} > Perm: [0, 1] > ((-1.0,), (1.0,)) > {0: {0: [0], 1: [1]}, 1: {0: []}} > Perm: [0, 1] > Traceback (most recent call last): > File "quadrature.fiat", line 56, in > FEMQuadrature().run() > File "quadrature.fiat", line 52, in run > filename = sys.argv[1]) > File > "/home/seki/mywork/PETSc/petsc-dev/python/PETSc/FEM.py", > line 583, in run > > self.outputElementSource(self.getElementSource(elements), > filename) > File > "/home/seki/mywork/PETSc/petsc-dev/python/PETSc/FEM.py", > line 545, in getElementSource > defns.extend(self.getIntegratorSetup(n, element)) > File > "/home/seki/mywork/PETSc/petsc-dev/python/PETSc/FEM.py", > line 208, in getIntegratorSetup > decls.append(self.Cxx.getArray(refVar, > self.Cxx.getType('double'), dim)) > File > "/home/seki/mywork/PETSc/petsc-dev/externalpackages/Generator/CxxHelper.py", > line 306, in getArray > import ASE.Compiler.Cxx.Array > File > "/home/seki/mywork/PETSc/petsc-dev/python/BuildSystem/importer.py", > line 36, in import_module > q, tail = self.find_head_package(parent, name) > File > "/home/seki/mywork/PETSc/petsc-dev/python/BuildSystem/importer.py", > line 79, in find_head_package > raise ImportError, "No module named " + qname > ImportError: No module named ASE > make: *** [quadrature.h] Error 1 > > Please let me know these information is sufficient. > Thanks a lot. > > Shi > --- Matthew Knepley wrote: > > > Hmmm, it should not require ASE. That is an old > > package that we shuold not > > use anymore. Can you send the entire stack trace? I > > will debug it. > > > > Thanks, > > > > Matt > > > > On 6/12/07, Shi Jin wrote: > > > No, I didn't use Generator. Thanks. > > > However, after using generator, I got another > > error: > > > ImportError: No module named ASE. > > > Is there any other packages I need to install? > > > Thanks. > > > > > > Shi > > > However, the installation is > > > --- Matthew Knepley wrote: > > > > > > > This comes from the 'Generator' module > > downloaded > > > > when you configure > > > > with --download-generator. I am guessing your > > > > confgure did not run. > > > > > > > > Thanks, > > > > > > > > Matt > > > > > > > > On 6/11/07, Shi Jin > > wrote: > > > > > Hi, > > > > > > > > > > I am trying to use the FIAT external package > > and > > > > when > > > > > it calls the FEM.py at > > $PETSC_DIR/python/PETSc, I > > > > > always get the error: > > > > > ImportError: No module named Cxx > > > > > > > > > > I figured out it is cause by the line > > > > > import Cxx, CxxHelper > > > > > > > > > > I searched online and could only find a Python > > > > module > > > > > called PyCXX. The module name is called CXX. > > > > > ALso I there is no FEM.py in the 2.3.2 > > version. > > > > > So I am wondering what Cxx and CxxHelper > > modules > > > > are > > > > > and how I can obtain them. > > > > > Please help. > > > > > Thanks a lot. > > > > > > > > > > Shi > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > > > Bored stiff? Loosen up... > > > > > Download and play hundreds of games for free > > on > > > > Yahoo! Games. > > > > > http://games.yahoo.com/games/front > > > > > > > > > > > > > > > > > > > > > > -- > > > > What most experimenters take for granted before > > they > > > > begin their > > > > experiments is infinitely more interesting than > > any > > > > results to which > > > > their experiments lead. > > > > -- Norbert Wiener > > > > > > > > > > > > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > Got a little couch potato? > > > Check out fun summer activities for kids. > > > > > > http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz > > > > > > > > > > > > -- > > What most experimenters take for granted before they > > begin their > > experiments is infinitely more interesting than any > > results to which > > their experiments lead. > > -- Norbert Wiener > > > > > > > > > ____________________________________________________________________________________ > Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. > http://smallbusiness.yahoo.com/webhosting > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From knepley at gmail.com Fri Jun 15 01:43:33 2007 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 15 Jun 2007 01:43:33 -0500 Subject: MeshDistribute() and Chaco In-Reply-To: <20070615032444.35778.qmail@web36206.mail.mud.yahoo.com> References: <20070615032444.35778.qmail@web36206.mail.mud.yahoo.com> Message-ID: 1) Please send these to petsc-maint at mcs.anl.gov On 6/14/07, Shi Jin wrote: > Hi, > > I am trying to study the new unstructured mesh part > provided by the new Petsc. I have one particular > question with regard to the function call > MeshDistribute(serialMesh, PETSC_NULL, ¶llelMesh); 2) The PETSC_NULL can be used to specify another partitioner like "parmetis" 3) Not sure about the argument. You would have to refer to the package. Matt > This call obviously needs the chaco package to run in > parallel since otherwise I will get a warning to > configure with --download-chaco. > So I ran it with chaco installed. The code works but > the domain decomposition is valid but far from good. > In the attached image, I am showing the domain > decomposition for a 2-dimensional 1x1 box with two > processes, using the following statements: > MeshCreatePCICE(comm, 3, > "bratu_2d.nodes","bratu_2d.lcon",PETSC_FALSE,PETSC_FALSE, > &serialMesh); > MeshDistribute(serialMesh, PETSC_NULL, ¶llelMesh); > > I am wondering if it is possible to improve the domain > decomposition by passing some command arguments. I > realized that there are Chaco options such as > -mat_partitioning_chaco_global (found at > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/MatOrderings/MAT_PARTITIONING_Chaco.html) > . However, when I pass these options to my code, it is > not recognized. I wonder how chaco is used in Petsc > and how I can change its behavior. > > In addition, is it possible to use other graph > decomposition packages such as ParMetis to implement > MeshDistribute()? I tried to enable ParMetis without > chaco but the code didn't run and warned me to install > chaco. > > Any advice is valuable. Thank you very much. > > Shi > > > > ____________________________________________________________________________________ > Finding fabulous fares is fun. > Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. > http://farechase.yahoo.com/promo-generic-14795097 > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From knutert at stud.ntnu.no Fri Jun 15 03:06:36 2007 From: knutert at stud.ntnu.no (Knut Erik Teigen) Date: Fri, 15 Jun 2007 10:06:36 +0200 Subject: Setting tolerances for multigrid In-Reply-To: References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> Message-ID: <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> Thanks, Matthew. It seems like the tolerances weren't my problem, though. Even with a tolerance of 1e-10, the computation diverges after only a few time steps when using multigrid. With ordinary linear solvers, I can use a tolerance of 1e-4 and still get a satisfactory solution. Could it be that the Galerkin approximation for the coarser levels is too inaccurate for my problem? -Knut Erik- On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > On 6/14/07, Knut Erik Teigen wrote: > > Hello, > > > > How do I set the tolerances for the KSP solvers when using the > > DMMG routines without using command line arguments? It seems that > > I can use the argument -ksp_rtol on the command line, but in the code I > > can't use KSPSetTolerances since I don't have access to the KSP solver > > context? > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > any others. > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > in the source code, but I can't find the documentation for it. > > Does this function not exist yet? Again I would like to use > > -dmmg_galerkin, but setting it in the code instead of on the command > > line. > > I think you want this: > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > Matt > > > Regards, > > Knut Erik Teigen > > > > > > From knepley at gmail.com Fri Jun 15 03:21:57 2007 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 15 Jun 2007 10:21:57 +0200 Subject: Setting tolerances for multigrid In-Reply-To: <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> Message-ID: This does not sound right to me. I think something must be configured incorrectly. All MG does is accelerate the solution of the fine grid problem. I think something must be wrong with the specification here. It is easy to check. Run with -dmmg_nlevels 1 which just solves on the fine grid. Matt On 6/15/07, Knut Erik Teigen wrote: > Thanks, Matthew. It seems like the tolerances weren't my problem, > though. Even with a tolerance of 1e-10, the computation diverges after > only a few time steps when using multigrid. With ordinary linear > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > solution. > Could it be that the Galerkin approximation for the coarser levels is > too inaccurate for my problem? > > -Knut Erik- > > On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > > On 6/14/07, Knut Erik Teigen wrote: > > > Hello, > > > > > > How do I set the tolerances for the KSP solvers when using the > > > DMMG routines without using command line arguments? It seems that > > > I can use the argument -ksp_rtol on the command line, but in the code I > > > can't use KSPSetTolerances since I don't have access to the KSP solver > > > context? > > > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > > any others. > > > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > > in the source code, but I can't find the documentation for it. > > > Does this function not exist yet? Again I would like to use > > > -dmmg_galerkin, but setting it in the code instead of on the command > > > line. > > > > I think you want this: > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > > > Matt > > > > > Regards, > > > Knut Erik Teigen > > > > > > > > > > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From heck at fnb.tu-darmstadt.de Fri Jun 15 03:23:35 2007 From: heck at fnb.tu-darmstadt.de (Marcus Heck) Date: Fri, 15 Jun 2007 10:23:35 +0200 Subject: Setting tolerances for multigrid In-Reply-To: <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> Message-ID: <20070615082335.GB6304@fnb.tu-darmstadt.de> Hi, On 2007-06-15 10:06, Knut Erik Teigen wrote: > Thanks, Matthew. It seems like the tolerances weren't my problem, > though. Even with a tolerance of 1e-10, the computation diverges after > only a few time steps when using multigrid. With ordinary linear > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > solution. How many grid levels do you have? How coarse is the coarsest grid? It can be possible, that a coarsgrid solution will "distroy" somehow the solution for the finer grids an leads to divergence. I observed this for geometric multigrid some time ago Marcus Heck > Could it be that the Galerkin approximation for the coarser levels is > too inaccurate for my problem? From knutert at stud.ntnu.no Fri Jun 15 05:02:51 2007 From: knutert at stud.ntnu.no (Knut Erik Teigen) Date: Fri, 15 Jun 2007 12:02:51 +0200 Subject: Setting tolerances for multigrid In-Reply-To: References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> Message-ID: <1181901771.3606.78.camel@iept0415.ivt.ntnu.no> The computation runs just fine with -dmmg_nlevels 1. I use a grid of 65x129, with three levels, so that the coarsest grid is 17x33. I've diffed the solutions, and they are equal for the first two time steps, but then they start to differ somewhat. Here is an excerpt: -dmmg_nlevels 1: 65.0427492820557 65.0216231814457 64.9793945321386 -dmmg_nlevels 3: 65.0920864319067 65.0711253401585 65.0292265582817 Using 2 or 4 levels produce the same result as 3 levels. -Knut Erik- On Fri, 2007-06-15 at 10:21 +0200, Matthew Knepley wrote: > This does not sound right to me. I think something must be > configured incorrectly. All MG does is accelerate the solution > of the fine grid problem. I think something must be wrong with > the specification here. It is easy to check. Run with -dmmg_nlevels 1 > which just solves on the fine grid. > > Matt > > On 6/15/07, Knut Erik Teigen wrote: > > Thanks, Matthew. It seems like the tolerances weren't my problem, > > though. Even with a tolerance of 1e-10, the computation diverges after > > only a few time steps when using multigrid. With ordinary linear > > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > > solution. > > Could it be that the Galerkin approximation for the coarser levels is > > too inaccurate for my problem? > > > > -Knut Erik- > > > > On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > > > On 6/14/07, Knut Erik Teigen wrote: > > > > Hello, > > > > > > > > How do I set the tolerances for the KSP solvers when using the > > > > DMMG routines without using command line arguments? It seems that > > > > I can use the argument -ksp_rtol on the command line, but in the code I > > > > can't use KSPSetTolerances since I don't have access to the KSP solver > > > > context? > > > > > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > > > any others. > > > > > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > > > in the source code, but I can't find the documentation for it. > > > > Does this function not exist yet? Again I would like to use > > > > -dmmg_galerkin, but setting it in the code instead of on the command > > > > line. > > > > > > I think you want this: > > > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > > > > > Matt > > > > > > > Regards, > > > > Knut Erik Teigen > > > > > > > > > > > > > > > > > > > > From heck at fnb.tu-darmstadt.de Fri Jun 15 06:53:55 2007 From: heck at fnb.tu-darmstadt.de (Marcus Heck) Date: Fri, 15 Jun 2007 13:53:55 +0200 Subject: PETSc, hangs, on, PetscInitialize Message-ID: <20070615115355.GC6304@fnb.tu-darmstadt.de> Hi, I am runing PETSc on the FE-solver FEAP. If I run a normal FE analysis everithing is fine! Then I want do run a coupled FSI computation. So I initialize PETSc and MpCCI (my coupling library) or the other way round (MpCCI, PETSc). But PETSc enters the PetscInitialize and never comes out. Does anyone has an idea. Thanks a lot Marcus Here some infos about PETSc and my code: ************** PETSc config: ./config/configure.py --prefix=/amd/software/linux/petsc-2.3.2-p10 --with-cc=gcc --with-fc=g77 --LD_SHARED= g++ --LDFLAGS="-O1" --with-mpi-dir=/usr/lib/mpich --with-mpi-shared=1 Compile and linking command in both cases are identical, except the MpCCI library includes. If there is any idea let me know please Thanks a lot in advance Marcus ************** CODE inside FEAP75.f write(*,*) 'FEAP starting MpCCI setup and interface definition.' call CCI_Init( iError ) write(*,*) 'FEAP starting MpCCI done' write(*,*)'pcontr(): initializing PETSC' call PetscInitialize(PETSC_NULL_CHARACTER,petsc_ierr) write(*,*)'pcontr(): initializing PETSC done' call pstart() ************** CODE OUTPUT: FEAP starting MpCCI setup and interface definition. =========================================================================== MpCCI 3.0.3 (for MPICH 1.2.5) - compilation date Dec 22 2004 20:08:09 FhG-SCAI, Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven, D-53754 Sankt Augustin, Germany Coupled computation started at 15-6-2007 11:16:16. Running on host 'ares'. =========================================================================== ************************************ * This MpCCI 3.0 Professional * * is licensed for * * TU Darmstadt, FB Maschinenbau, M * * until date 28-feb-2008. * ************************************ FEAP starting MpCCI done pcontr(): initializing PETSC ************** strace on the pid tells: 3p$ strace -p17164 Process 17164 attached - interrupt to quit select(5, [3 4], NULL, NULL, {6, 266000}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) select(5, [3 4], NULL, NULL, {9, 0} -- 8< --- snip -- 8< --- ************** Totalview telals following: main (f77) -> perscinitialize_ (C) -> PETScParseFortranArgs_Private (C) -> PMPI_Bcast -> inta_Bcast -> ... Please see screen shot. -------------- next part -------------- A non-text attachment was scrubbed... Name: 03.png Type: image/png Size: 48773 bytes Desc: not available URL: From bsmith at mcs.anl.gov Fri Jun 15 10:10:49 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 15 Jun 2007 10:10:49 -0500 (CDT) Subject: Setting tolerances for multigrid In-Reply-To: <1181901771.3606.78.camel@iept0415.ivt.ntnu.no> References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> <1181901771.3606.78.camel@iept0415.ivt.ntnu.no> Message-ID: You need to make sure the linear solvers are converging properly before even worrying about time-stepping. Run with -ksp_monitor_true_residual (-ksp_truemonitor on older versions of PETSc) and -ksp_converged_reason Barry On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > The computation runs just fine with -dmmg_nlevels 1. > I use a grid of 65x129, with three levels, so that the coarsest grid is > 17x33. > I've diffed the solutions, and they are equal for the first two time > steps, but then they start to differ somewhat. Here is an excerpt: > -dmmg_nlevels 1: > 65.0427492820557 65.0216231814457 64.9793945321386 > -dmmg_nlevels 3: > 65.0920864319067 65.0711253401585 65.0292265582817 > > Using 2 or 4 levels produce the same result as 3 levels. > > -Knut Erik- > > > > On Fri, 2007-06-15 at 10:21 +0200, Matthew Knepley wrote: > > This does not sound right to me. I think something must be > > configured incorrectly. All MG does is accelerate the solution > > of the fine grid problem. I think something must be wrong with > > the specification here. It is easy to check. Run with -dmmg_nlevels 1 > > which just solves on the fine grid. > > > > Matt > > > > On 6/15/07, Knut Erik Teigen wrote: > > > Thanks, Matthew. It seems like the tolerances weren't my problem, > > > though. Even with a tolerance of 1e-10, the computation diverges after > > > only a few time steps when using multigrid. With ordinary linear > > > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > > > solution. > > > Could it be that the Galerkin approximation for the coarser levels is > > > too inaccurate for my problem? > > > > > > -Knut Erik- > > > > > > On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > > > > On 6/14/07, Knut Erik Teigen wrote: > > > > > Hello, > > > > > > > > > > How do I set the tolerances for the KSP solvers when using the > > > > > DMMG routines without using command line arguments? It seems that > > > > > I can use the argument -ksp_rtol on the command line, but in the code I > > > > > can't use KSPSetTolerances since I don't have access to the KSP solver > > > > > context? > > > > > > > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > > > > any others. > > > > > > > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > > > > in the source code, but I can't find the documentation for it. > > > > > Does this function not exist yet? Again I would like to use > > > > > -dmmg_galerkin, but setting it in the code instead of on the command > > > > > line. > > > > > > > > I think you want this: > > > > > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > > > > > > > Matt > > > > > > > > > Regards, > > > > > Knut Erik Teigen > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From bsmith at mcs.anl.gov Fri Jun 15 10:13:18 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 15 Jun 2007 10:13:18 -0500 (CDT) Subject: PETSc, hangs, on, PetscInitialize In-Reply-To: <20070615115355.GC6304@fnb.tu-darmstadt.de> References: <20070615115355.GC6304@fnb.tu-darmstadt.de> Message-ID: I would run in the debugger and then stop it after it has hanged a long time (control c in gdb or dbx) then do where to determine what it is doing. Send the output from where to petsc-maint at mcs.anl.gov if you need to. Barry On Fri, 15 Jun 2007, Marcus Heck wrote: > Hi, > > I am runing PETSc on the FE-solver FEAP. If I run a normal FE analysis > everithing is fine! > > Then I want do run a coupled FSI computation. So I initialize PETSc and > MpCCI (my coupling library) or the other way round (MpCCI, PETSc). But > PETSc enters the PetscInitialize and never comes out. Does anyone has an > idea. > > Thanks a lot > Marcus > > Here some infos about PETSc and my code: > ************** > PETSc config: > ./config/configure.py --prefix=/amd/software/linux/petsc-2.3.2-p10 --with-cc=gcc --with-fc=g77 --LD_SHARED= g++ --LDFLAGS="-O1" --with-mpi-dir=/usr/lib/mpich --with-mpi-shared=1 > > > Compile and linking command in both cases are identical, except the > MpCCI library includes. > > If there is any idea let me know please > Thanks a lot in advance > Marcus > > ************** > CODE inside FEAP75.f > write(*,*) 'FEAP starting MpCCI setup and interface definition.' > call CCI_Init( iError ) > write(*,*) 'FEAP starting MpCCI done' > write(*,*)'pcontr(): initializing PETSC' > call PetscInitialize(PETSC_NULL_CHARACTER,petsc_ierr) > write(*,*)'pcontr(): initializing PETSC done' > call pstart() > > ************** > CODE OUTPUT: > FEAP starting MpCCI setup and interface definition. > =========================================================================== > MpCCI 3.0.3 (for MPICH 1.2.5) - compilation date Dec 22 2004 20:08:09 > FhG-SCAI, Fraunhofer Institute for Algorithms and Scientific Computing > Schloss Birlinghoven, D-53754 Sankt Augustin, Germany > Coupled computation started at 15-6-2007 11:16:16. > Running on host 'ares'. > =========================================================================== > > ************************************ > * This MpCCI 3.0 Professional * > * is licensed for * > * TU Darmstadt, FB Maschinenbau, M * > * until date 28-feb-2008. * > ************************************ > > FEAP starting MpCCI done > pcontr(): initializing PETSC > > ************** > strace on the pid tells: > 3p$ strace -p17164 > Process 17164 attached - interrupt to quit > select(5, [3 4], NULL, NULL, {6, 266000}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) > select(5, [3 4], NULL, NULL, {9, 0} > -- 8< --- snip -- 8< --- > > ************** > Totalview telals following: > > main (f77) -> perscinitialize_ (C) -> PETScParseFortranArgs_Private (C) > -> PMPI_Bcast -> inta_Bcast -> ... > > Please see screen shot. > > From knutert at stud.ntnu.no Fri Jun 15 12:09:00 2007 From: knutert at stud.ntnu.no (Knut Erik Teigen) Date: Fri, 15 Jun 2007 19:09:00 +0200 Subject: Setting tolerances for multigrid In-Reply-To: References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> <1181901771.3606.78.camel@iept0415.ivt.ntnu.no> Message-ID: <1181927340.3606.93.camel@iept0415.ivt.ntnu.no> When running with those options I get this after the first timestep for both one and two levels: 159 KSP preconditioned resid norm 1.397494864058e-07 true resid norm 4.996893774970e-02 ||Ae||/||Ax|| 1.577132216812e-10 Linear solve converged due to CONVERGED_RTOL However, after the second timestep they start to get different. With two levels the norm is actually lower, but still, the computation diverges after about 6 time steps. With one level the computation runs smoothly. Here are the numbers: -dmmg_nlevels 1 0 KSP preconditioned resid norm 1.674785901465e+02 true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 6.256839347623e+01 true resid norm 4.220478752135e+07 ||Ae||/||Ax|| 1.033434774147e-01 (...) 159 KSP preconditioned resid norm 1.318896741223e-07 true resid norm 5.104451971417e-02 ||Ae||/||Ax|| 1.249886204866e-10 Linear solve converged due to CONVERGED_RTOL -dmmg_nlevels 2 0 KSP preconditioned resid norm 1.674785901465e+02 true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 6.252455641723e+01 true resid norm 5.561545924132e+07 ||Ae||/||Ax|| 1.361811134129e-01 (...) 159 KSP preconditioned resid norm 1.305901659826e-07 true resid norm 4.297164043386e-02 ||Ae||/||Ax|| 1.052212086224e-10 Linear solve converged due to CONVERGED_RTOL -Knut Erik- On Fri, 2007-06-15 at 10:10 -0500, Barry Smith wrote: > You need to make sure the linear solvers are converging properly > before even worrying about time-stepping. Run with -ksp_monitor_true_residual > (-ksp_truemonitor on older versions of PETSc) and -ksp_converged_reason > > Barry > > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > The computation runs just fine with -dmmg_nlevels 1. > > I use a grid of 65x129, with three levels, so that the coarsest grid is > > 17x33. > > I've diffed the solutions, and they are equal for the first two time > > steps, but then they start to differ somewhat. Here is an excerpt: > > -dmmg_nlevels 1: > > 65.0427492820557 65.0216231814457 64.9793945321386 > > -dmmg_nlevels 3: > > 65.0920864319067 65.0711253401585 65.0292265582817 > > > > Using 2 or 4 levels produce the same result as 3 levels. > > > > -Knut Erik- > > > > > > > > On Fri, 2007-06-15 at 10:21 +0200, Matthew Knepley wrote: > > > This does not sound right to me. I think something must be > > > configured incorrectly. All MG does is accelerate the solution > > > of the fine grid problem. I think something must be wrong with > > > the specification here. It is easy to check. Run with -dmmg_nlevels 1 > > > which just solves on the fine grid. > > > > > > Matt > > > > > > On 6/15/07, Knut Erik Teigen wrote: > > > > Thanks, Matthew. It seems like the tolerances weren't my problem, > > > > though. Even with a tolerance of 1e-10, the computation diverges after > > > > only a few time steps when using multigrid. With ordinary linear > > > > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > > > > solution. > > > > Could it be that the Galerkin approximation for the coarser levels is > > > > too inaccurate for my problem? > > > > > > > > -Knut Erik- > > > > > > > > On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > > > > > On 6/14/07, Knut Erik Teigen wrote: > > > > > > Hello, > > > > > > > > > > > > How do I set the tolerances for the KSP solvers when using the > > > > > > DMMG routines without using command line arguments? It seems that > > > > > > I can use the argument -ksp_rtol on the command line, but in the code I > > > > > > can't use KSPSetTolerances since I don't have access to the KSP solver > > > > > > context? > > > > > > > > > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > > > > > any others. > > > > > > > > > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > > > > > in the source code, but I can't find the documentation for it. > > > > > > Does this function not exist yet? Again I would like to use > > > > > > -dmmg_galerkin, but setting it in the code instead of on the command > > > > > > line. > > > > > > > > > > I think you want this: > > > > > > > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > > > > > > > > > Matt > > > > > > > > > > > Regards, > > > > > > Knut Erik Teigen > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From tyoung at ippt.gov.pl Fri Jun 15 13:19:53 2007 From: tyoung at ippt.gov.pl (Toby Young) Date: Fri, 15 Jun 2007 20:19:53 +0200 (CEST) Subject: PETSc sparsity Message-ID: Hello petsc-users and petsc-dev. I am using PETSc to solve finite element problems. In particular I am working with the dealii package which has C++ wrappers designed to interface with PETSc. I am working on developing some of these wrappers. The difficulty I face is that, after applying boundary conditions to the matrices, these matrices return as nonsymmetric; I really need them to be symmetric! I can achieve this by performing the so-called Gauss elimination step; however this requires access to the sparsity pattern of the PETSc matrix. "The gauss elimination step "per se" is not a problem. The problem is that we don't have access to the sparsity of the matrix, so it is not so easy to find out which entries are not zero in the petsc matrices." -- dealii developer Is there *any* possible way to obtain the sparsity of the PETSc matrix? Maybe something like GetMatrixSparsity? I have done my research, but I cannot find any information on this so I am pretty clueless on how to proceed (sorry if I have missed something obvious). Any comments or suggests would be greatly appreciated. Best, Toby ----- Toby D. Young (Adiunkt) Department of Computational Science Institute of Fundamental Technological Research Polish Academy of Science Room 206, ul. Swietokrzyska 21 00-049 Warszawa, POLAND Luca. -- Luca Heltai http://www-dimat.unipv.it/heltai -- There are no answers, only cross references. On Jun 15, 2007, at 11:17 AM, Toby D. Young wrote: > On Thu, 14 Jun 2007 10:55:20 -0400 > Luca Heltai wrote: > >> Toby, if you do some serious development (like what you are >> doing... :) ...) I strongly suggest you switch to the subversion >> tree. > > Okay, fair suggestion, and not too tricky to do, I'm running of dealii > 5.3pre now. > >> In the subversion tree that is implemented. > > Yet it doesn't seem to be and the problem does not go away. I'll > have to > think of a way around this, either that or actually implement Guass > elimination for the Petsc SParseMatrix < scary thought :-) >. > > You can verify this yourself by running step-17, after first changing > the final flag false->true in apply_boundary_conditions. > > Here's what we find: > > Cycle 0: > Number of active cells : 1024 > Number of degrees of freedom : 1089 (by partition: 1089) > -------------------------------------------------------- > An error occurred in line <534> of file > > in function void dealii::PETScWrappers::apply_boundary_values(const > std::map, > std::allocator > >&, > PETScMatrix&, PETScVector&, PETScVector&, bool) [with PETScMatrix = > dealii::PETScWrappers::MPI::SparseMatrix, PETScVector = > dealii::PETScWrappers::MPI::Vector] > The violated condition was: > preserve_symmetry == false > The name and call sequence of the exception was: > ExcNotImplemented() > Additional Information: > (none) > > Stacktrace: > ----------- > #0 /home/tyoung/fem/deal.II/lib/libdeal_II_1d.g.so: void > dealii::PETScWrappers::apply_boundary_values I::SparseMatrix, > dealii::PETScWrappers::MPI::Vector>(std::map std::less, std::allocator double> > > const&, dealii::PETScWrappers::MPI::SparseMatrix&, > double> > > dealii::PETScWrappers::MPI::Vector&, > double> > > dealii::PETScWrappers::MPI::Vector&, bool) > double> > > #1 /home/tyoung/fem/deal.II/lib/libdeal_II_1d.g.so: > double> > > dealii::MatrixTools::apply_boundary_values > (std::map double> > > int, double, std::less, > double> > > std::allocator > > > double> > > const&, dealii::PETScWrappers::MPI::SparseMatrix&, > double> > > dealii::PETScWrappers::MPI::Vector&, > double> > > dealii::PETScWrappers::MPI::Vector&, bool) > #2 ./step-75: double> > > InfiniteWellProblem<2>::assemble_system() > #3 ./step-75: double> > > InfiniteWellProblem<2>::run() > #4 ./step-75: main > -------------------------------------------------------- > > > > -- > > Toby D. Young ( Adiunkt ) > Department of Computational Science > Institute of Fundamental Technical Research, Polish Academy of > Sciences > Room 206, Swietokrzyska 21, 00-049 Warsaw, POLAND From sanjay at ce.berkeley.edu Fri Jun 15 13:43:31 2007 From: sanjay at ce.berkeley.edu (Sanjay Govindjee) Date: Fri, 15 Jun 2007 20:43:31 +0200 Subject: PETSc, hangs, on, PetscInitialize In-Reply-To: References: <20070615115355.GC6304@fnb.tu-darmstadt.de> Message-ID: <4672DDD3.80805@ce.berkeley.edu> As the author of this bit of code, I can suggest the following issue. FEAP relies on an mpi implementation that send standard fortran writes, things like write(*,*), to the screen when issued, but this is in no way gaurenteed by the mpi standard. FEAP is probably sitting at a prompt waiting for your input but you simply can not see it. I have experienced this problem on several new installations. There are two solutions: (1) Run in a strictly batch mode, making sure that your feapname file is setup correctly, and that you have a means to read inputs from a file for the prompts that will appear (in this case a file with the letter y in it to accept the file names read from feapname). (2) re-write all the old non-parallel IO in the code (something I am thinking about but which is a lot of work to set it up so that it works\ in serial mode without petsc and in parallel mode with it). The fact that it looks like it is hanging in the initialize routine is probably a red-herring. -sg Barry Smith wrote: > I would run in the debugger and then stop it after it has > hanged a long time (control c in gdb or dbx) then do where to > determine what it is doing. Send the output from where to > petsc-maint at mcs.anl.gov if you need to. > > > Barry > > On Fri, 15 Jun 2007, Marcus Heck wrote: > > >> Hi, >> >> I am runing PETSc on the FE-solver FEAP. If I run a normal FE analysis >> everithing is fine! >> >> Then I want do run a coupled FSI computation. So I initialize PETSc and >> MpCCI (my coupling library) or the other way round (MpCCI, PETSc). But >> PETSc enters the PetscInitialize and never comes out. Does anyone has an >> idea. >> >> Thanks a lot >> Marcus >> >> Here some infos about PETSc and my code: >> ************** >> PETSc config: >> ./config/configure.py --prefix=/amd/software/linux/petsc-2.3.2-p10 --with-cc=gcc --with-fc=g77 --LD_SHARED= g++ --LDFLAGS="-O1" --with-mpi-dir=/usr/lib/mpich --with-mpi-shared=1 >> >> >> Compile and linking command in both cases are identical, except the >> MpCCI library includes. >> >> If there is any idea let me know please >> Thanks a lot in advance >> Marcus >> >> ************** >> CODE inside FEAP75.f >> write(*,*) 'FEAP starting MpCCI setup and interface definition.' >> call CCI_Init( iError ) >> write(*,*) 'FEAP starting MpCCI done' >> write(*,*)'pcontr(): initializing PETSC' >> call PetscInitialize(PETSC_NULL_CHARACTER,petsc_ierr) >> write(*,*)'pcontr(): initializing PETSC done' >> call pstart() >> >> ************** >> CODE OUTPUT: >> FEAP starting MpCCI setup and interface definition. >> =========================================================================== >> MpCCI 3.0.3 (for MPICH 1.2.5) - compilation date Dec 22 2004 20:08:09 >> FhG-SCAI, Fraunhofer Institute for Algorithms and Scientific Computing >> Schloss Birlinghoven, D-53754 Sankt Augustin, Germany >> Coupled computation started at 15-6-2007 11:16:16. >> Running on host 'ares'. >> =========================================================================== >> >> ************************************ >> * This MpCCI 3.0 Professional * >> * is licensed for * >> * TU Darmstadt, FB Maschinenbau, M * >> * until date 28-feb-2008. * >> ************************************ >> >> FEAP starting MpCCI done >> pcontr(): initializing PETSC >> >> ************** >> strace on the pid tells: >> 3p$ strace -p17164 >> Process 17164 attached - interrupt to quit >> select(5, [3 4], NULL, NULL, {6, 266000}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0}) = 0 (Timeout) >> select(5, [3 4], NULL, NULL, {9, 0} >> -- 8< --- snip -- 8< --- >> >> ************** >> Totalview telals following: >> >> main (f77) -> perscinitialize_ (C) -> PETScParseFortranArgs_Private (C) >> -> PMPI_Bcast -> inta_Bcast -> ... >> >> Please see screen shot. >> >> >> > > From bsmith at mcs.anl.gov Fri Jun 15 14:30:34 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 15 Jun 2007 14:30:34 -0500 (CDT) Subject: Setting tolerances for multigrid In-Reply-To: <1181927340.3606.93.camel@iept0415.ivt.ntnu.no> References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> <1181901771.3606.78.camel@iept0415.ivt.ntnu.no> <1181927340.3606.93.camel@iept0415.ivt.ntnu.no> Message-ID: What happens if you run the two level with -ksp_rtol 1.e-12 BTW: when you just change -dmmg_nlevels from 1 to 2 you are now solving a NEW problem that has twice as many points in each direction, this can also effect the time-stepping. You can use -dmmg_nlevels 2 -pc_type lu to compare with the -dmmg_nlevels 2 Always verify things with a direct solver before using multigrid or any other iterative linear solver. Multigrid is ONLY an optimization (faster, less memory), debug BEFORE turning on the optimizations. Barry On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > When running with those options I get this after the first timestep for > both one and two levels: > 159 KSP preconditioned resid norm 1.397494864058e-07 true resid norm > 4.996893774970e-02 ||Ae||/||Ax|| 1.577132216812e-10 > Linear solve converged due to CONVERGED_RTOL > > However, after the second timestep they start to get different. > With two levels the norm is actually lower, but still, the computation > diverges after about 6 time steps. With one level the computation runs > smoothly. Here are the numbers: > > -dmmg_nlevels 1 > 0 KSP preconditioned resid norm 1.674785901465e+02 > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 6.256839347623e+01 > true resid norm 4.220478752135e+07 ||Ae||/||Ax|| 1.033434774147e-01 > (...) > 159 KSP preconditioned resid norm 1.318896741223e-07 > true resid norm 5.104451971417e-02 ||Ae||/||Ax|| 1.249886204866e-10 > Linear solve converged due to CONVERGED_RTOL > > -dmmg_nlevels 2 > 0 KSP preconditioned resid norm 1.674785901465e+02 > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 6.252455641723e+01 > true resid norm 5.561545924132e+07 ||Ae||/||Ax|| 1.361811134129e-01 > (...) > 159 KSP preconditioned resid norm 1.305901659826e-07 > true resid norm 4.297164043386e-02 ||Ae||/||Ax|| 1.052212086224e-10 > Linear solve converged due to CONVERGED_RTOL > > -Knut Erik- > > On Fri, 2007-06-15 at 10:10 -0500, Barry Smith wrote: > > You need to make sure the linear solvers are converging properly > > before even worrying about time-stepping. Run with -ksp_monitor_true_residual > > (-ksp_truemonitor on older versions of PETSc) and -ksp_converged_reason > > > > Barry > > > > > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > > > The computation runs just fine with -dmmg_nlevels 1. > > > I use a grid of 65x129, with three levels, so that the coarsest grid is > > > 17x33. > > > I've diffed the solutions, and they are equal for the first two time > > > steps, but then they start to differ somewhat. Here is an excerpt: > > > -dmmg_nlevels 1: > > > 65.0427492820557 65.0216231814457 64.9793945321386 > > > -dmmg_nlevels 3: > > > 65.0920864319067 65.0711253401585 65.0292265582817 > > > > > > Using 2 or 4 levels produce the same result as 3 levels. > > > > > > -Knut Erik- > > > > > > > > > > > > On Fri, 2007-06-15 at 10:21 +0200, Matthew Knepley wrote: > > > > This does not sound right to me. I think something must be > > > > configured incorrectly. All MG does is accelerate the solution > > > > of the fine grid problem. I think something must be wrong with > > > > the specification here. It is easy to check. Run with -dmmg_nlevels 1 > > > > which just solves on the fine grid. > > > > > > > > Matt > > > > > > > > On 6/15/07, Knut Erik Teigen wrote: > > > > > Thanks, Matthew. It seems like the tolerances weren't my problem, > > > > > though. Even with a tolerance of 1e-10, the computation diverges after > > > > > only a few time steps when using multigrid. With ordinary linear > > > > > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > > > > > solution. > > > > > Could it be that the Galerkin approximation for the coarser levels is > > > > > too inaccurate for my problem? > > > > > > > > > > -Knut Erik- > > > > > > > > > > On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > > > > > > On 6/14/07, Knut Erik Teigen wrote: > > > > > > > Hello, > > > > > > > > > > > > > > How do I set the tolerances for the KSP solvers when using the > > > > > > > DMMG routines without using command line arguments? It seems that > > > > > > > I can use the argument -ksp_rtol on the command line, but in the code I > > > > > > > can't use KSPSetTolerances since I don't have access to the KSP solver > > > > > > > context? > > > > > > > > > > > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > > > > > > any others. > > > > > > > > > > > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > > > > > > in the source code, but I can't find the documentation for it. > > > > > > > Does this function not exist yet? Again I would like to use > > > > > > > -dmmg_galerkin, but setting it in the code instead of on the command > > > > > > > line. > > > > > > > > > > > > I think you want this: > > > > > > > > > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > > > > > > > > > > > Matt > > > > > > > > > > > > > Regards, > > > > > > > Knut Erik Teigen > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From bsmith at mcs.anl.gov Fri Jun 15 14:40:41 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 15 Jun 2007 14:40:41 -0500 (CDT) Subject: PETSc sparsity In-Reply-To: References: Message-ID: Toby, For Seq matrices you can call MatGetRowIJ() and it will give you exactly what you want. For MPI matrices the matrices are stored in two parts on each process (the "diagonal" part and the "off-diagonal" part) you can, of course, call the MatGetRowIJ() on each part but this is not exactly what you are looking for. For algorithms that require dealing with the sparsity structure of the matrix we generally just include the appropriate private include file for the matrix format and access the data directly in the underlying format. This allows the fastest performance. Other approaches to handling boundary conditions are to eliminated fixed boundary values at finite element assembly time. That is to NEVER form the matrix with all unknowns, instead form the matrix without the fixed values and adjust the right hand side load values at this time Or use MatGetSubMatrix() to pull out the interior unknowns, another MatGetSubMatrix() to get the part of the matrix coupling the interior and boundary unknowns and do a matrix vector product to undate the interior unknown right hand side values based on the fixed unknowns. MatGetSubMatrix() is actually fast and this is an efficient and easy way to handle the boundary conditions. Barry On Fri, 15 Jun 2007, Toby Young wrote: > > > Hello petsc-users and petsc-dev. > > I am using PETSc to solve finite element problems. In particular I am > working with the dealii package which has C++ wrappers designed to > interface with PETSc. I am working on developing some of these wrappers. > > The difficulty I face is that, after applying boundary conditions to the > matrices, these matrices return as nonsymmetric; I really need them to be > symmetric! I can achieve this by performing the so-called Gauss > elimination step; however this requires access to the sparsity pattern of > the PETSc matrix. > > "The gauss elimination step "per se" is not a problem. The problem is > that we don't have access to the sparsity of the matrix, so it is not > so easy to find out which entries are not zero in the petsc matrices." > -- dealii developer > > Is there *any* possible way to obtain the sparsity of the PETSc matrix? > Maybe something like GetMatrixSparsity? I have done my research, but I > cannot find any information on this so I am pretty clueless on how > to proceed (sorry if I have missed something obvious). > > Any comments or suggests would be greatly appreciated. > > Best, > Toby > > ----- > > Toby D. Young (Adiunkt) > Department of Computational Science > Institute of Fundamental Technological Research > Polish Academy of Science > Room 206, ul. Swietokrzyska 21 > 00-049 Warszawa, POLAND > > > > > Luca. > > -- > Luca Heltai > http://www-dimat.unipv.it/heltai > -- > There are no answers, only cross references. > > > > On Jun 15, 2007, at 11:17 AM, Toby D. Young wrote: > > > On Thu, 14 Jun 2007 10:55:20 -0400 > > Luca Heltai wrote: > > > >> Toby, if you do some serious development (like what you are > >> doing... :) ...) I strongly suggest you switch to the subversion > >> tree. > > > > Okay, fair suggestion, and not too tricky to do, I'm running of dealii > > 5.3pre now. > > > >> In the subversion tree that is implemented. > > > > Yet it doesn't seem to be and the problem does not go away. I'll > > have to > > think of a way around this, either that or actually implement Guass > > elimination for the Petsc SParseMatrix < scary thought :-) >. > > > > You can verify this yourself by running step-17, after first changing > > the final flag false->true in apply_boundary_conditions. > > > > Here's what we find: > > > > Cycle 0: > > Number of active cells : 1024 > > Number of degrees of freedom : 1089 (by partition: 1089) > > -------------------------------------------------------- > > An error occurred in line <534> of file > > > > in function void dealii::PETScWrappers::apply_boundary_values(const > > std::map, > > std::allocator > >&, > > PETScMatrix&, PETScVector&, PETScVector&, bool) [with PETScMatrix = > > dealii::PETScWrappers::MPI::SparseMatrix, PETScVector = > > dealii::PETScWrappers::MPI::Vector] > > The violated condition was: > > preserve_symmetry == false > > The name and call sequence of the exception was: > > ExcNotImplemented() > > Additional Information: > > (none) > > > > Stacktrace: > > ----------- > > #0 /home/tyoung/fem/deal.II/lib/libdeal_II_1d.g.so: void > > dealii::PETScWrappers::apply_boundary_values > I::SparseMatrix, > > dealii::PETScWrappers::MPI::Vector>(std::map > std::less, std::allocator > double> > > const&, dealii::PETScWrappers::MPI::SparseMatrix&, > > double> > > dealii::PETScWrappers::MPI::Vector&, > > double> > > dealii::PETScWrappers::MPI::Vector&, bool) > > double> > > #1 /home/tyoung/fem/deal.II/lib/libdeal_II_1d.g.so: > > double> > > dealii::MatrixTools::apply_boundary_values > > (std::map > double> > > int, double, std::less, > > double> > > std::allocator > > > > double> > > const&, dealii::PETScWrappers::MPI::SparseMatrix&, > > double> > > dealii::PETScWrappers::MPI::Vector&, > > double> > > dealii::PETScWrappers::MPI::Vector&, bool) > > #2 ./step-75: double> > > InfiniteWellProblem<2>::assemble_system() > > #3 ./step-75: double> > > InfiniteWellProblem<2>::run() > > #4 ./step-75: main > > -------------------------------------------------------- > > > > > > > > -- > > > > Toby D. Young ( Adiunkt ) > > Department of Computational Science > > Institute of Fundamental Technical Research, Polish Academy of > > Sciences > > Room 206, Swietokrzyska 21, 00-049 Warsaw, POLAND > > From tyoung at ippt.gov.pl Fri Jun 15 15:28:34 2007 From: tyoung at ippt.gov.pl (Toby Young) Date: Fri, 15 Jun 2007 22:28:34 +0200 (CEST) Subject: PETSc sparsity In-Reply-To: References: Message-ID: Barry, Thank you for an interesting response. > For algorithms that require dealing with the sparsity structure of > the matrix we generally just include the appropriate private include file > for the matrix format and access the data directly in the underlying format. Can you please elaborate. What do you mean by "the appropriate privat include file for the matrix"? Sorry, I got lost there. Best, Toby ----- Toby D. Young (Adiunkt) Department of Computational Science Institute of Fundamental Technological Research Polish Academy of Science Room 206, ul. Swietokrzyska 21 00-049 Warszawa, POLAND From bsmith at mcs.anl.gov Fri Jun 15 15:33:35 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 15 Jun 2007 15:33:35 -0500 (CDT) Subject: PETSc sparsity In-Reply-To: References: Message-ID: src/mat/impls/aij/seq/aij.h src/mat/impls/aij/mpi/mpiaij.h On Fri, 15 Jun 2007, Toby Young wrote: > > > Barry, > > Thank you for an interesting response. > > > For algorithms that require dealing with the sparsity structure of > > the matrix we generally just include the appropriate private include file > > for the matrix format and access the data directly in the underlying format. > > Can you please elaborate. What do you mean by "the appropriate privat > include file for the matrix"? Sorry, I got lost there. > > Best, > Toby > > ----- > > Toby D. Young (Adiunkt) > Department of Computational Science > Institute of Fundamental Technological Research > Polish Academy of Science > Room 206, ul. Swietokrzyska 21 > 00-049 Warszawa, POLAND > > From zonexo at gmail.com Sat Jun 16 00:17:45 2007 From: zonexo at gmail.com (Ben Tay) Date: Sat, 16 Jun 2007 13:17:45 +0800 Subject: KSPSetTolerances and processors size Message-ID: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> Hi, I am trying to use PETSc to solve my poisson eqn. In the past, when I'm not using MPI, I set KSPSetTolerances to 1.0e-5. This seems to be good enuff. Now, I'm trying to use PETSc with MPI to solve the eqn. I am using a very small no. of pts, only 16x4. On 1 processor, the ans is the same as the one without MPI. However, on 2 processors, I found that I've to increase the KSPSetTolerances to 1.0e-6, else those grid pts on the edge will be different. On 4 processors, KSPSetTolerances has to be decreased to 1.0e-7. On 8 processors, when KSPSetTolerances is 1.0e-8, the difference of the last pt between 1 and 8 processors is about 3%. May I know why this is so? Also, does this happens only on very small grids? Does it happen on large grids as well? I usually solve grids with approx 20000 to 55000 pts. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From knutert at stud.ntnu.no Sat Jun 16 03:47:09 2007 From: knutert at stud.ntnu.no (Knut Erik Teigen) Date: Sat, 16 Jun 2007 10:47:09 +0200 Subject: Setting tolerances for multigrid In-Reply-To: References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> <1181901771.3606.78.camel@iept0415.ivt.ntnu.no> <1181927340.3606.93.camel@iept0415.ivt.ntnu.no> Message-ID: <1181983629.3606.109.camel@iept0415.ivt.ntnu.no> On Fri, 2007-06-15 at 14:30 -0500, Barry Smith wrote: > What happens if you run the two level with -ksp_rtol 1.e-12 The exact same thing happens. At the third time step, the solution with two levels begin to deviate from the one with one level. > > BTW: when you just change -dmmg_nlevels from 1 to 2 you are now > solving a NEW problem that has twice as many points in each direction, > this can also effect the time-stepping. You can use -dmmg_nlevels 2 > -pc_type lu to compare with the -dmmg_nlevels 2 I forgot to mention that I adjust the coarsest level according to the number of levels, so that the finest level always contains the same amount of points. I.e. with one level it is 65x129, with two 33x65 and so on. > > Always verify things with a direct solver before using multigrid > or any other iterative linear solver. Multigrid is ONLY an optimization > (faster, less memory), debug BEFORE turning on the optimizations. Yes, I've already done this. With a direct solver, I get the same solution as with one level. Since multigrid is only an optimization as you mention, I don't understand why the solution should be different when running with two or more levels as opposed to only one. Here's the output when running with -pc_type lu. As you can see, with two levels, suddenly more iterations are needed for the third step. -dmmg_nlevels 1 Start of time loop: L-s reinit converged after 10 steps with norm 1.716E-09 0 KSP preconditioned resid norm 1.366287028032e+04 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 3.325862387561e+02 true resid norm 8.783238319618e-07 ||Ae||/||Ax|| 2.772187832207e-15 2 KSP preconditioned resid norm 4.237324220037e-10 true resid norm 9.365968491320e-07 ||Ae||/||Ax|| 2.956110598807e-15 Linear solve converged due to CONVERGED_RTOL 0 KSP preconditioned resid norm 1.366743784848e+04 true resid norm 3.168385551957e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 3.578541063222e+02 true resid norm 3.047639475331e-06 ||Ae||/||Ax|| 9.618903461571e-15 2 KSP preconditioned resid norm 2.490853654289e-10 true resid norm 2.047397542219e-06 ||Ae||/||Ax|| 6.461958333808e-15 Linear solve converged due to CONVERGED_RTOL 0 KSP preconditioned resid norm 1.373641039770e+04 true resid norm 4.083933364397e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 2.756300642422e+02 true resid norm 1.333942531534e-06 ||Ae||/||Ax|| 3.266318062786e-15 2 KSP preconditioned resid norm 1.967864218276e-09 true resid norm 4.708778143639e-06 ||Ae||/||Ax|| 1.153000728339e-14 Linear solve converged due to CONVERGED_RTOL -dmmg_nlevels 2 Start of time loop: L-s reinit converged after 10 steps with norm 1.716E-09 0 KSP preconditioned resid norm 1.366287028032e+04 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 3.325862387561e+02 true resid norm 8.783238319618e-07 ||Ae||/||Ax|| 2.772187832207e-15 2 KSP preconditioned resid norm 4.237324220037e-10 true resid norm 9.365968491320e-07 ||Ae||/||Ax|| 2.956110598807e-15 Linear solve converged due to CONVERGED_RTOL 0 KSP preconditioned resid norm 1.366743784848e+04 true resid norm 3.168385551957e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 3.578541063222e+02 true resid norm 3.047639475331e-06 ||Ae||/||Ax|| 9.618903461571e-15 2 KSP preconditioned resid norm 2.490853654289e-10 true resid norm 2.047397542219e-06 ||Ae||/||Ax|| 6.461958333808e-15 Linear solve converged due to CONVERGED_RTOL 0 KSP preconditioned resid norm 1.373641039770e+04 true resid norm 4.083933364397e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 2.826990181167e+02 true resid norm 3.621921471554e+07 ||Ae||/||Ax|| 8.868708542429e-02 2 KSP preconditioned resid norm 2.151728459050e+02 true resid norm 5.126312558070e+05 ||Ae||/||Ax|| 1.255239030774e-03 3 KSP preconditioned resid norm 9.420491033127e+01 true resid norm 7.221320422298e+02 ||Ae||/||Ax|| 1.768226799500e-06 (...) 118 KSP preconditioned resid norm 2.011348229632e-04 true resid norm 1.933530019765e-05 ||Ae||/||Ax|| 4.734479843920e-14 119 KSP preconditioned resid norm 1.002113384828e-04 true resid norm 1.933774400466e-05 ||Ae||/||Ax|| 4.735078239337e-14 120 KSP preconditioned resid norm 3.976002405523e-07 true resid norm 1.947236185243e-05 ||Ae||/||Ax|| 4.768041031762e-14 Linear solve converged due to CONVERGED_RTOL > > > Barry > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > When running with those options I get this after the first timestep for > > both one and two levels: > > 159 KSP preconditioned resid norm 1.397494864058e-07 true resid norm > > 4.996893774970e-02 ||Ae||/||Ax|| 1.577132216812e-10 > > Linear solve converged due to CONVERGED_RTOL > > > > However, after the second timestep they start to get different. > > With two levels the norm is actually lower, but still, the computation > > diverges after about 6 time steps. With one level the computation runs > > smoothly. Here are the numbers: > > > > -dmmg_nlevels 1 > > 0 KSP preconditioned resid norm 1.674785901465e+02 > > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 6.256839347623e+01 > > true resid norm 4.220478752135e+07 ||Ae||/||Ax|| 1.033434774147e-01 > > (...) > > 159 KSP preconditioned resid norm 1.318896741223e-07 > > true resid norm 5.104451971417e-02 ||Ae||/||Ax|| 1.249886204866e-10 > > Linear solve converged due to CONVERGED_RTOL > > > > -dmmg_nlevels 2 > > 0 KSP preconditioned resid norm 1.674785901465e+02 > > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 6.252455641723e+01 > > true resid norm 5.561545924132e+07 ||Ae||/||Ax|| 1.361811134129e-01 > > (...) > > 159 KSP preconditioned resid norm 1.305901659826e-07 > > true resid norm 4.297164043386e-02 ||Ae||/||Ax|| 1.052212086224e-10 > > Linear solve converged due to CONVERGED_RTOL > > > > -Knut Erik- > > > > On Fri, 2007-06-15 at 10:10 -0500, Barry Smith wrote: > > > You need to make sure the linear solvers are converging properly > > > before even worrying about time-stepping. Run with -ksp_monitor_true_residual > > > (-ksp_truemonitor on older versions of PETSc) and -ksp_converged_reason > > > > > > Barry > > > > > > > > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > > > > > The computation runs just fine with -dmmg_nlevels 1. > > > > I use a grid of 65x129, with three levels, so that the coarsest grid is > > > > 17x33. > > > > I've diffed the solutions, and they are equal for the first two time > > > > steps, but then they start to differ somewhat. Here is an excerpt: > > > > -dmmg_nlevels 1: > > > > 65.0427492820557 65.0216231814457 64.9793945321386 > > > > -dmmg_nlevels 3: > > > > 65.0920864319067 65.0711253401585 65.0292265582817 > > > > > > > > Using 2 or 4 levels produce the same result as 3 levels. > > > > > > > > -Knut Erik- > > > > > > > > > > > > > > > > On Fri, 2007-06-15 at 10:21 +0200, Matthew Knepley wrote: > > > > > This does not sound right to me. I think something must be > > > > > configured incorrectly. All MG does is accelerate the solution > > > > > of the fine grid problem. I think something must be wrong with > > > > > the specification here. It is easy to check. Run with -dmmg_nlevels 1 > > > > > which just solves on the fine grid. > > > > > > > > > > Matt > > > > > > > > > > On 6/15/07, Knut Erik Teigen wrote: > > > > > > Thanks, Matthew. It seems like the tolerances weren't my problem, > > > > > > though. Even with a tolerance of 1e-10, the computation diverges after > > > > > > only a few time steps when using multigrid. With ordinary linear > > > > > > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > > > > > > solution. > > > > > > Could it be that the Galerkin approximation for the coarser levels is > > > > > > too inaccurate for my problem? > > > > > > > > > > > > -Knut Erik- > > > > > > > > > > > > On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > > > > > > > On 6/14/07, Knut Erik Teigen wrote: > > > > > > > > Hello, > > > > > > > > > > > > > > > > How do I set the tolerances for the KSP solvers when using the > > > > > > > > DMMG routines without using command line arguments? It seems that > > > > > > > > I can use the argument -ksp_rtol on the command line, but in the code I > > > > > > > > can't use KSPSetTolerances since I don't have access to the KSP solver > > > > > > > > context? > > > > > > > > > > > > > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > > > > > > > any others. > > > > > > > > > > > > > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > > > > > > > in the source code, but I can't find the documentation for it. > > > > > > > > Does this function not exist yet? Again I would like to use > > > > > > > > -dmmg_galerkin, but setting it in the code instead of on the command > > > > > > > > line. > > > > > > > > > > > > > > I think you want this: > > > > > > > > > > > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > Regards, > > > > > > > > Knut Erik Teigen > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From knepley at gmail.com Sat Jun 16 10:18:52 2007 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 16 Jun 2007 10:18:52 -0500 Subject: KSPSetTolerances and processors size In-Reply-To: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> References: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> Message-ID: I assume you are setting a relative tolerance. This is just a vector norm so it will increase with dimension, and therefore the absolute difference will tend to increase. You can set an absolute tolerance as well if this is what you want. Matt On 6/16/07, Ben Tay wrote: > Hi, > > I am trying to use PETSc to solve my poisson eqn. In the past, when I'm not > using MPI, I set KSPSetTolerances to 1.0e-5. This seems to be good enuff. > > Now, I'm trying to use PETSc with MPI to solve the eqn. I am using a very > small no. of pts, only 16x4. On 1 processor, the ans is the same as the one > without MPI. However, on 2 processors, I found that I've to increase the > KSPSetTolerances to 1.0e-6, else those grid pts on the edge will be > different. On 4 processors, KSPSetTolerances has to be decreased to 1.0e-7. > On 8 processors, when KSPSetTolerances is 1.0e-8, the difference of the last > pt between 1 and 8 processors is about 3%. > > May I know why this is so? Also, does this happens only on very small grids? > Does it happen on large grids as well? I usually solve grids with approx > 20000 to 55000 pts. > > Thank you. > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From bsmith at mcs.anl.gov Sat Jun 16 11:42:50 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sat, 16 Jun 2007 11:42:50 -0500 (CDT) Subject: KSPSetTolerances and processors size In-Reply-To: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> References: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> Message-ID: Ben, On Sat, 16 Jun 2007, Ben Tay wrote: > Hi, > > I am trying to use PETSc to solve my poisson eqn. In the past, when I'm not > using MPI, I set KSPSetTolerances to 1.0e-5. This seems to be good enuff. > > Now, I'm trying to use PETSc with MPI to solve the eqn. I am using a very > small no. of pts, only 16x4. On 1 processor, the ans is the same as the one > without MPI. However, on 2 processors, I found that I've to increase the > KSPSetTolerances to 1.0e-6, else those grid pts on the edge will be > different. On 4 processors, KSPSetTolerances has to be decreased to 1.0e-7. > On 8 processors, when KSPSetTolerances is 1.0e-8, the difference of the last > pt between 1 and 8 processors is about 3%. > Are you using the same number of grid points when changing the number of processors? Run the cases with -ksp_monitor_true_residual and send us ALL the output. Barry > May I know why this is so? Also, does this happens only on very small grids? > Does it happen on large grids as well? I usually solve grids with approx > 20000 to 55000 pts. > > Thank you. > From timothy.stitt at ichec.ie Sat Jun 16 12:32:40 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Sat, 16 Jun 2007 18:32:40 +0100 Subject: MPI Initialisation Problem Message-ID: <200706161832.40634.timothy.stitt@ichec.ie> Hi all, I am having some difficulty getting my parallel eigensolver to run over multiple processes. When I execute my parallel code on my distributed-memory machine ( with > 1 processes) I keep getting the following runtime message: mpiexec: Warning: task 0 exited before completing MPI startup. mpiexec: Warning: task 1 exited oddly---report bug: status 0 done 0. MPI_Comm_Size returns 1 for #processes even though I mpiexec -n 2 or higher. The code still runs to completion but serially....... I have taken the same code and ran it on my shared-memory machine with no problems and all processes getting picked up so I know it is not a coding problem.....the sample ksp test codes that come with my petsc (2.3.3) distribution also exhibit this problem. So there seems to be a problem with the PETScInitialize routine with this particular architecture. I have tried both pathscale and pgi compilers with the same result. As far as I can see there are no noticeable warnings generated during the config and make phases. Others use MPI regularly on our cluster so I don't see how it could be a MPI library issue. Any thoughts on what could be happening gratefully received. Regards, Tim. -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From balay at mcs.anl.gov Sat Jun 16 13:22:40 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Sat, 16 Jun 2007 13:22:40 -0500 (CDT) Subject: MPI Initialisation Problem In-Reply-To: <200706161832.40634.timothy.stitt@ichec.ie> References: <200706161832.40634.timothy.stitt@ichec.ie> Message-ID: On Sat, 16 Jun 2007, Tim Stitt wrote: > Hi all, > > I am having some difficulty getting my parallel eigensolver to run over > multiple processes. > > When I execute my parallel code on my distributed-memory machine ( with > 1 > processes) I keep getting the following runtime message: > > mpiexec: Warning: task 0 exited before completing MPI startup. > mpiexec: Warning: task 1 exited oddly---report bug: status 0 done 0. > > MPI_Comm_Size returns 1 for #processes even though I mpiexec -n 2 or higher. > > The code still runs to completion but serially....... can you reproduce this problem with a PETSc example? If so, send us the complete log of your build [configure.log, make_log_PETSC_ARCH] and the log for test examples [test_log_PETSC_ARCH] to petsc-maint at mcs.anl.gov Satish > > I have taken the same code and ran it on my shared-memory machine with no > problems and all processes getting picked up so I know it is not a coding > problem.....the sample ksp test codes that come with my petsc (2.3.3) > distribution also exhibit this problem. > > So there seems to be a problem with the PETScInitialize routine with this > particular architecture. I have tried both pathscale and pgi compilers with > the same result. As far as I can see there are no noticeable warnings > generated during the config and make phases. Others use MPI regularly on our > cluster so I don't see how it could be a MPI library issue. > > Any thoughts on what could be happening gratefully received. > > Regards, > > Tim. > > From timothy.stitt at ichec.ie Sat Jun 16 14:53:03 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Sat, 16 Jun 2007 20:53:03 +0100 Subject: MPI Initialisation Problem In-Reply-To: References: <200706161832.40634.timothy.stitt@ichec.ie> Message-ID: <200706162053.04000.timothy.stitt@ichec.ie> Satish, I figured out the problem. It seems that our implementation of mpiexec has some issues: According to mpiexec documentation.... 12. Only one process is launched, and mpiexec says "task 0 exited before completing MPI startup". This happens when you are using MPICH2, but have told mpiexec that it should use the MPICH1/P4 communication method. Try with "-comm=pmi", and if that works, rebuild mpiexec using "--with-default-comm=pmi" for convenience. So I executed with -comm=pmi and everything was o.k. Sorry to bother you, Tim. On Saturday 16 June 2007 19:22, Satish Balay wrote: > On Sat, 16 Jun 2007, Tim Stitt wrote: > > Hi all, > > > > I am having some difficulty getting my parallel eigensolver to run over > > multiple processes. > > > > When I execute my parallel code on my distributed-memory machine ( with > > > 1 processes) I keep getting the following runtime message: > > > > mpiexec: Warning: task 0 exited before completing MPI startup. > > mpiexec: Warning: task 1 exited oddly---report bug: status 0 done 0. > > > > MPI_Comm_Size returns 1 for #processes even though I mpiexec -n 2 or > > higher. > > > > The code still runs to completion but serially....... > > can you reproduce this problem with a PETSc example? If so, send us > the complete log of your build [configure.log, make_log_PETSC_ARCH] > and the log for test examples [test_log_PETSC_ARCH] to > petsc-maint at mcs.anl.gov > > Satish > > > I have taken the same code and ran it on my shared-memory machine with no > > problems and all processes getting picked up so I know it is not a coding > > problem.....the sample ksp test codes that come with my petsc (2.3.3) > > distribution also exhibit this problem. > > > > So there seems to be a problem with the PETScInitialize routine with this > > particular architecture. I have tried both pathscale and pgi compilers > > with the same result. As far as I can see there are no noticeable > > warnings generated during the config and make phases. Others use MPI > > regularly on our cluster so I don't see how it could be a MPI library > > issue. > > > > Any thoughts on what could be happening gratefully received. > > > > Regards, > > > > Tim. -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From bsmith at mcs.anl.gov Sat Jun 16 16:56:59 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sat, 16 Jun 2007 16:56:59 -0500 (CDT) Subject: Setting tolerances for multigrid In-Reply-To: <1181983629.3606.109.camel@iept0415.ivt.ntnu.no> References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> <1181901771.3606.78.camel@iept0415.ivt.ntnu.no> <1181927340.3606.93.camel@iept0415.ivt.ntnu.no> <1181983629.3606.109.camel@iept0415.ivt.ntnu.no> Message-ID: On Sat, 16 Jun 2007, Knut Erik Teigen wrote: > On Fri, 2007-06-15 at 14:30 -0500, Barry Smith wrote: > > What happens if you run the two level with -ksp_rtol 1.e-12 > > The exact same thing happens. At the third time step, the solution with > two levels begin to deviate from the one with one level. > > > > > BTW: when you just change -dmmg_nlevels from 1 to 2 you are now > > solving a NEW problem that has twice as many points in each direction, > > this can also effect the time-stepping. You can use -dmmg_nlevels 2 > > -pc_type lu to compare with the -dmmg_nlevels 2 > > I forgot to mention that I adjust the coarsest level according to the > number of levels, so that the finest level always contains the same > amount of points. I.e. with one level it is 65x129, with two 33x65 and > so on. > > > > > Always verify things with a direct solver before using multigrid > > or any other iterative linear solver. Multigrid is ONLY an optimization > > (faster, less memory), debug BEFORE turning on the optimizations. > > Yes, I've already done this. With a direct solver, I get the same > solution as with one level. Since multigrid is only an optimization as > you mention, I don't understand why the solution should be different > when running with two or more levels as opposed to only one. > Here's the output when running with -pc_type lu. As you can see, with > two levels, suddenly more iterations are needed for the third step. > > -dmmg_nlevels 1 > Start of time loop: > L-s reinit converged after 10 steps with norm 1.716E-09 > 0 KSP preconditioned resid norm 1.366287028032e+04 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 3.325862387561e+02 true resid norm 8.783238319618e-07 ||Ae||/||Ax|| 2.772187832207e-15 > 2 KSP preconditioned resid norm 4.237324220037e-10 true resid norm 9.365968491320e-07 ||Ae||/||Ax|| 2.956110598807e-15 > Linear solve converged due to CONVERGED_RTOL 0 KSP preconditioned resid norm 1.366743784848e+04 true resid norm 3.168385551957e+08 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 3.578541063222e+02 true resid norm 3.047639475331e-06 ||Ae||/||Ax|| 9.618903461571e-15 > 2 KSP preconditioned resid norm 2.490853654289e-10 true resid norm 2.047397542219e-06 ||Ae||/||Ax|| 6.461958333808e-15 > Linear solve converged due to CONVERGED_RTOL > 0 KSP preconditioned resid norm 1.373641039770e+04 true resid norm 4.083933364397e+08 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 2.756300642422e+02 true resid norm 1.333942531534e-06 ||Ae||/||Ax|| 3.266318062786e-15 > 2 KSP preconditioned resid norm 1.967864218276e-09 true resid norm 4.708778143639e-06 ||Ae||/||Ax|| 1.153000728339e-14 > Linear solve converged due to CONVERGED_RTOL > > -dmmg_nlevels 2 > Start of time loop: > L-s reinit converged after 10 steps with norm 1.716E-09 > 0 KSP preconditioned resid norm 1.366287028032e+04 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 3.325862387561e+02 true resid norm 8.783238319618e-07 ||Ae||/||Ax|| 2.772187832207e-15 > 2 KSP preconditioned resid norm 4.237324220037e-10 true resid norm 9.365968491320e-07 ||Ae||/||Ax|| 2.956110598807e-15 > Linear solve converged due to CONVERGED_RTOL > 0 KSP preconditioned resid norm 1.366743784848e+04 true resid norm 3.168385551957e+08 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 3.578541063222e+02 true resid norm 3.047639475331e-06 ||Ae||/||Ax|| 9.618903461571e-15 > 2 KSP preconditioned resid norm 2.490853654289e-10 true resid norm 2.047397542219e-06 ||Ae||/||Ax|| 6.461958333808e-15 > Linear solve converged due to CONVERGED_RTOL > 0 KSP preconditioned resid norm 1.373641039770e+04 true resid norm 4.083933364397e+08 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 2.826990181167e+02 true resid norm 3.621921471554e+07 ||Ae||/||Ax|| 8.868708542429e-02 > 2 KSP preconditioned resid norm 2.151728459050e+02 true resid norm 5.126312558070e+05 ||Ae||/||Ax|| 1.255239030774e-03 > 3 KSP preconditioned resid norm 9.420491033127e+01 true resid norm 7.221320422298e+02 ||Ae||/||Ax|| 1.768226799500e-06 > (...) > 118 KSP preconditioned resid norm 2.011348229632e-04 true resid norm 1.933530019765e-05 ||Ae||/||Ax|| 4.734479843920e-14 > 119 KSP preconditioned resid norm 1.002113384828e-04 true resid norm 1.933774400466e-05 ||Ae||/||Ax|| 4.735078239337e-14 > 120 KSP preconditioned resid norm 3.976002405523e-07 true resid norm 1.947236185243e-05 ||Ae||/||Ax|| 4.768041031762e-14 > Linear solve converged due to CONVERGED_RTOL > > The true residuals both me, they are very big at "convergence" 1.e-5? Are you using KSPSetInitialGuessNonzero() and using the previous solution as initial guess? Run with -ksp_type gmres -pc_type lu -ksp_monitor_true_residual. I bet the converged true residual is much better. Send the output. Barry > > > > > > > Barry > > > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > > > When running with those options I get this after the first timestep for > > > both one and two levels: > > > 159 KSP preconditioned resid norm 1.397494864058e-07 true resid norm > > > 4.996893774970e-02 ||Ae||/||Ax|| 1.577132216812e-10 > > > Linear solve converged due to CONVERGED_RTOL > > > > > > However, after the second timestep they start to get different. > > > With two levels the norm is actually lower, but still, the computation > > > diverges after about 6 time steps. With one level the computation runs > > > smoothly. Here are the numbers: > > > > > > -dmmg_nlevels 1 > > > 0 KSP preconditioned resid norm 1.674785901465e+02 > > > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 6.256839347623e+01 > > > true resid norm 4.220478752135e+07 ||Ae||/||Ax|| 1.033434774147e-01 > > > (...) > > > 159 KSP preconditioned resid norm 1.318896741223e-07 > > > true resid norm 5.104451971417e-02 ||Ae||/||Ax|| 1.249886204866e-10 > > > Linear solve converged due to CONVERGED_RTOL > > > > > > -dmmg_nlevels 2 > > > 0 KSP preconditioned resid norm 1.674785901465e+02 > > > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 6.252455641723e+01 > > > true resid norm 5.561545924132e+07 ||Ae||/||Ax|| 1.361811134129e-01 > > > (...) > > > 159 KSP preconditioned resid norm 1.305901659826e-07 > > > true resid norm 4.297164043386e-02 ||Ae||/||Ax|| 1.052212086224e-10 > > > Linear solve converged due to CONVERGED_RTOL > > > > > > -Knut Erik- > > > > > > On Fri, 2007-06-15 at 10:10 -0500, Barry Smith wrote: > > > > You need to make sure the linear solvers are converging properly > > > > before even worrying about time-stepping. Run with -ksp_monitor_true_residual > > > > (-ksp_truemonitor on older versions of PETSc) and -ksp_converged_reason > > > > > > > > Barry > > > > > > > > > > > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > > > > > > > The computation runs just fine with -dmmg_nlevels 1. > > > > > I use a grid of 65x129, with three levels, so that the coarsest grid is > > > > > 17x33. > > > > > I've diffed the solutions, and they are equal for the first two time > > > > > steps, but then they start to differ somewhat. Here is an excerpt: > > > > > -dmmg_nlevels 1: > > > > > 65.0427492820557 65.0216231814457 64.9793945321386 > > > > > -dmmg_nlevels 3: > > > > > 65.0920864319067 65.0711253401585 65.0292265582817 > > > > > > > > > > Using 2 or 4 levels produce the same result as 3 levels. > > > > > > > > > > -Knut Erik- > > > > > > > > > > > > > > > > > > > > On Fri, 2007-06-15 at 10:21 +0200, Matthew Knepley wrote: > > > > > > This does not sound right to me. I think something must be > > > > > > configured incorrectly. All MG does is accelerate the solution > > > > > > of the fine grid problem. I think something must be wrong with > > > > > > the specification here. It is easy to check. Run with -dmmg_nlevels 1 > > > > > > which just solves on the fine grid. > > > > > > > > > > > > Matt > > > > > > > > > > > > On 6/15/07, Knut Erik Teigen wrote: > > > > > > > Thanks, Matthew. It seems like the tolerances weren't my problem, > > > > > > > though. Even with a tolerance of 1e-10, the computation diverges after > > > > > > > only a few time steps when using multigrid. With ordinary linear > > > > > > > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > > > > > > > solution. > > > > > > > Could it be that the Galerkin approximation for the coarser levels is > > > > > > > too inaccurate for my problem? > > > > > > > > > > > > > > -Knut Erik- > > > > > > > > > > > > > > On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > > > > > > > > On 6/14/07, Knut Erik Teigen wrote: > > > > > > > > > Hello, > > > > > > > > > > > > > > > > > > How do I set the tolerances for the KSP solvers when using the > > > > > > > > > DMMG routines without using command line arguments? It seems that > > > > > > > > > I can use the argument -ksp_rtol on the command line, but in the code I > > > > > > > > > can't use KSPSetTolerances since I don't have access to the KSP solver > > > > > > > > > context? > > > > > > > > > > > > > > > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > > > > > > > > any others. > > > > > > > > > > > > > > > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > > > > > > > > in the source code, but I can't find the documentation for it. > > > > > > > > > Does this function not exist yet? Again I would like to use > > > > > > > > > -dmmg_galerkin, but setting it in the code instead of on the command > > > > > > > > > line. > > > > > > > > > > > > > > > > I think you want this: > > > > > > > > > > > > > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > Knut Erik Teigen > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From jinzishuai at yahoo.com Sun Jun 17 00:11:55 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Sat, 16 Jun 2007 22:11:55 -0700 (PDT) Subject: Is it possible to build one Petsc that works for both C and C++? Message-ID: <686761.61517.qm@web36213.mail.mud.yahoo.com> Hi, I am learning the unstructured part of Petsc, which naturally uses C++(at least the sample I am studying is C++). On the other hand, my old Petsc codes are all written in C. I found that once I build the Petsc with C++, the old C codes cannot be compiled since it is trying to use mpicxx to compile the .c source files. However, I do see after the configuration stage that there is a list: C compiler: mpicc C++ compiler: mpicxx Fortran compiler: mpif77 Is it possible to instruct Petsc to use the corresponding compiler for different source codes? Thanks a lot. PS. This is how I configured my Petsc-2.3.3-p3: ./config/configure.py --with-cc=gcc --with-fc=g77 --with-cxx=g++ --download-f-blas-lapack=1 --download-mpich=1 --with-clanguage=cxx --with-sieve=1 --download-boost=1 --download-chaco --download-parmetis --download-fiat --download-generator ____________________________________________________________________________________ Get the Yahoo! toolbar and be alerted to new email wherever you're surfing. http://new.toolbar.yahoo.com/toolbar/features/mail/index.php From zonexo at gmail.com Sun Jun 17 02:21:32 2007 From: zonexo at gmail.com (Ben Tay) Date: Sun, 17 Jun 2007 15:21:32 +0800 Subject: Worthwhile to use PETSc to solve lots of small matrices? Message-ID: <804ab5d40706170021n11460fbbo9634d7b100ed8d82@mail.gmail.com> Hi, I am doing CFD and at each time step, I need to interpolate values at different points. I'm doing bi-quadratic interpolation and hence to get each interpolated value, I need to solve a 9x9 matrices. There's about 100+ pts and hence 100+ 9x9 matrices to solve per time step. I'm wondering if it is worthwhile to use PETSc to solve them or am I better off using those direct guassian elimination solvers? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Sun Jun 17 09:01:19 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sun, 17 Jun 2007 09:01:19 -0500 (CDT) Subject: Worthwhile to use PETSc to solve lots of small matrices? In-Reply-To: <804ab5d40706170021n11460fbbo9634d7b100ed8d82@mail.gmail.com> References: <804ab5d40706170021n11460fbbo9634d7b100ed8d82@mail.gmail.com> Message-ID: Don't use PETSc On Sun, 17 Jun 2007, Ben Tay wrote: > Hi, > > I am doing CFD and at each time step, I need to interpolate values at > different points. I'm doing bi-quadratic interpolation and hence to get each > interpolated value, I need to solve a 9x9 matrices. There's about 100+ pts > and hence 100+ 9x9 matrices to solve per time step. > > I'm wondering if it is worthwhile to use PETSc to solve them or am I better > off using those direct guassian elimination solvers? > > Thanks > From knutert at stud.ntnu.no Sun Jun 17 03:47:39 2007 From: knutert at stud.ntnu.no (Knut Erik Teigen) Date: Sun, 17 Jun 2007 10:47:39 +0200 Subject: Setting tolerances for multigrid In-Reply-To: References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> <1181901771.3606.78.camel@iept0415.ivt.ntnu.no> <1181927340.3606.93.camel@iept0415.ivt.ntnu.no> <1181983629.3606.109.camel@iept0415.ivt.ntnu.no> Message-ID: <1182070060.3606.116.camel@iept0415.ivt.ntnu.no> Ok, I've attached two files, one with ./run -dmmg_galerkin -dmmg_nlevels 1 -ksp_type gmres -pc_type lu -ksp_truemonitor -ksp_converged_reason > lev1 and one with ./run -dmmg_galerkin -dmmg_nlevels 2 -ksp_type gmres -pc_type lu -mg_levels_1_ksp_type gmres -mg_levels_1_pc_type lu -ksp_converged_reason -ksp_truemonitor > lev2 The relative residual is 1.e-12, and I am using KSPSetInitialGuessNonzero. I've also printed the solution, and if you diff the two files, you can see that there is a large difference in the third step, e.g. 71.7852 vs. 70.9845. This shouldn't happen, even with a true residual of 1.e-5? -Knut Erik- On Sat, 2007-06-16 at 16:56 -0500, Barry Smith wrote: > > On Sat, 16 Jun 2007, Knut Erik Teigen wrote: > > > On Fri, 2007-06-15 at 14:30 -0500, Barry Smith wrote: > > > What happens if you run the two level with -ksp_rtol 1.e-12 > > > > The exact same thing happens. At the third time step, the solution with > > two levels begin to deviate from the one with one level. > > > > > > > > BTW: when you just change -dmmg_nlevels from 1 to 2 you are now > > > solving a NEW problem that has twice as many points in each direction, > > > this can also effect the time-stepping. You can use -dmmg_nlevels 2 > > > -pc_type lu to compare with the -dmmg_nlevels 2 > > > > I forgot to mention that I adjust the coarsest level according to the > > number of levels, so that the finest level always contains the same > > amount of points. I.e. with one level it is 65x129, with two 33x65 and > > so on. > > > > > > > > Always verify things with a direct solver before using multigrid > > > or any other iterative linear solver. Multigrid is ONLY an optimization > > > (faster, less memory), debug BEFORE turning on the optimizations. > > > > Yes, I've already done this. With a direct solver, I get the same > > solution as with one level. Since multigrid is only an optimization as > > you mention, I don't understand why the solution should be different > > when running with two or more levels as opposed to only one. > > Here's the output when running with -pc_type lu. As you can see, with > > two levels, suddenly more iterations are needed for the third step. > > > > -dmmg_nlevels 1 > > Start of time loop: > > L-s reinit converged after 10 steps with norm 1.716E-09 > > 0 KSP preconditioned resid norm 1.366287028032e+04 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 3.325862387561e+02 true resid norm 8.783238319618e-07 ||Ae||/||Ax|| 2.772187832207e-15 > > 2 KSP preconditioned resid norm 4.237324220037e-10 true resid norm 9.365968491320e-07 ||Ae||/||Ax|| 2.956110598807e-15 > > Linear solve converged due to CONVERGED_RTOL > 0 KSP preconditioned resid norm 1.366743784848e+04 true resid norm 3.168385551957e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 3.578541063222e+02 true resid norm 3.047639475331e-06 ||Ae||/||Ax|| 9.618903461571e-15 > > 2 KSP preconditioned resid norm 2.490853654289e-10 true resid norm 2.047397542219e-06 ||Ae||/||Ax|| 6.461958333808e-15 > > Linear solve converged due to CONVERGED_RTOL > > 0 KSP preconditioned resid norm 1.373641039770e+04 true resid norm 4.083933364397e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 2.756300642422e+02 true resid norm 1.333942531534e-06 ||Ae||/||Ax|| 3.266318062786e-15 > > 2 KSP preconditioned resid norm 1.967864218276e-09 true resid norm 4.708778143639e-06 ||Ae||/||Ax|| 1.153000728339e-14 > > Linear solve converged due to CONVERGED_RTOL > > > > -dmmg_nlevels 2 > > Start of time loop: > > L-s reinit converged after 10 steps with norm 1.716E-09 > > 0 KSP preconditioned resid norm 1.366287028032e+04 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 3.325862387561e+02 true resid norm 8.783238319618e-07 ||Ae||/||Ax|| 2.772187832207e-15 > > 2 KSP preconditioned resid norm 4.237324220037e-10 true resid norm 9.365968491320e-07 ||Ae||/||Ax|| 2.956110598807e-15 > > Linear solve converged due to CONVERGED_RTOL > > 0 KSP preconditioned resid norm 1.366743784848e+04 true resid norm 3.168385551957e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 3.578541063222e+02 true resid norm 3.047639475331e-06 ||Ae||/||Ax|| 9.618903461571e-15 > > 2 KSP preconditioned resid norm 2.490853654289e-10 true resid norm 2.047397542219e-06 ||Ae||/||Ax|| 6.461958333808e-15 > > Linear solve converged due to CONVERGED_RTOL > > 0 KSP preconditioned resid norm 1.373641039770e+04 true resid norm 4.083933364397e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 2.826990181167e+02 true resid norm 3.621921471554e+07 ||Ae||/||Ax|| 8.868708542429e-02 > > 2 KSP preconditioned resid norm 2.151728459050e+02 true resid norm 5.126312558070e+05 ||Ae||/||Ax|| 1.255239030774e-03 > > 3 KSP preconditioned resid norm 9.420491033127e+01 true resid norm 7.221320422298e+02 ||Ae||/||Ax|| 1.768226799500e-06 > > (...) > > 118 KSP preconditioned resid norm 2.011348229632e-04 true resid norm 1.933530019765e-05 ||Ae||/||Ax|| 4.734479843920e-14 > > 119 KSP preconditioned resid norm 1.002113384828e-04 true resid norm 1.933774400466e-05 ||Ae||/||Ax|| 4.735078239337e-14 > > 120 KSP preconditioned resid norm 3.976002405523e-07 true resid norm 1.947236185243e-05 ||Ae||/||Ax|| 4.768041031762e-14 > > Linear solve converged due to CONVERGED_RTOL > > > > > > The true residuals both me, they are very big at "convergence" 1.e-5? Are you using KSPSetInitialGuessNonzero() and > using the previous solution as initial guess? > > Run with -ksp_type gmres -pc_type lu -ksp_monitor_true_residual. I bet the converged true residual is > much better. Send the output. > > Barry > > > > > > > > > > > > > Barry > > > > > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > > > > > When running with those options I get this after the first timestep for > > > > both one and two levels: > > > > 159 KSP preconditioned resid norm 1.397494864058e-07 true resid norm > > > > 4.996893774970e-02 ||Ae||/||Ax|| 1.577132216812e-10 > > > > Linear solve converged due to CONVERGED_RTOL > > > > > > > > However, after the second timestep they start to get different. > > > > With two levels the norm is actually lower, but still, the computation > > > > diverges after about 6 time steps. With one level the computation runs > > > > smoothly. Here are the numbers: > > > > > > > > -dmmg_nlevels 1 > > > > 0 KSP preconditioned resid norm 1.674785901465e+02 > > > > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > > 1 KSP preconditioned resid norm 6.256839347623e+01 > > > > true resid norm 4.220478752135e+07 ||Ae||/||Ax|| 1.033434774147e-01 > > > > (...) > > > > 159 KSP preconditioned resid norm 1.318896741223e-07 > > > > true resid norm 5.104451971417e-02 ||Ae||/||Ax|| 1.249886204866e-10 > > > > Linear solve converged due to CONVERGED_RTOL > > > > > > > > -dmmg_nlevels 2 > > > > 0 KSP preconditioned resid norm 1.674785901465e+02 > > > > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > > 1 KSP preconditioned resid norm 6.252455641723e+01 > > > > true resid norm 5.561545924132e+07 ||Ae||/||Ax|| 1.361811134129e-01 > > > > (...) > > > > 159 KSP preconditioned resid norm 1.305901659826e-07 > > > > true resid norm 4.297164043386e-02 ||Ae||/||Ax|| 1.052212086224e-10 > > > > Linear solve converged due to CONVERGED_RTOL > > > > > > > > -Knut Erik- > > > > > > > > On Fri, 2007-06-15 at 10:10 -0500, Barry Smith wrote: > > > > > You need to make sure the linear solvers are converging properly > > > > > before even worrying about time-stepping. Run with -ksp_monitor_true_residual > > > > > (-ksp_truemonitor on older versions of PETSc) and -ksp_converged_reason > > > > > > > > > > Barry > > > > > > > > > > > > > > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > > > > > > > > > The computation runs just fine with -dmmg_nlevels 1. > > > > > > I use a grid of 65x129, with three levels, so that the coarsest grid is > > > > > > 17x33. > > > > > > I've diffed the solutions, and they are equal for the first two time > > > > > > steps, but then they start to differ somewhat. Here is an excerpt: > > > > > > -dmmg_nlevels 1: > > > > > > 65.0427492820557 65.0216231814457 64.9793945321386 > > > > > > -dmmg_nlevels 3: > > > > > > 65.0920864319067 65.0711253401585 65.0292265582817 > > > > > > > > > > > > Using 2 or 4 levels produce the same result as 3 levels. > > > > > > > > > > > > -Knut Erik- > > > > > > > > > > > > > > > > > > > > > > > > On Fri, 2007-06-15 at 10:21 +0200, Matthew Knepley wrote: > > > > > > > This does not sound right to me. I think something must be > > > > > > > configured incorrectly. All MG does is accelerate the solution > > > > > > > of the fine grid problem. I think something must be wrong with > > > > > > > the specification here. It is easy to check. Run with -dmmg_nlevels 1 > > > > > > > which just solves on the fine grid. > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > On 6/15/07, Knut Erik Teigen wrote: > > > > > > > > Thanks, Matthew. It seems like the tolerances weren't my problem, > > > > > > > > though. Even with a tolerance of 1e-10, the computation diverges after > > > > > > > > only a few time steps when using multigrid. With ordinary linear > > > > > > > > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > > > > > > > > solution. > > > > > > > > Could it be that the Galerkin approximation for the coarser levels is > > > > > > > > too inaccurate for my problem? > > > > > > > > > > > > > > > > -Knut Erik- > > > > > > > > > > > > > > > > On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > > > > > > > > > On 6/14/07, Knut Erik Teigen wrote: > > > > > > > > > > Hello, > > > > > > > > > > > > > > > > > > > > How do I set the tolerances for the KSP solvers when using the > > > > > > > > > > DMMG routines without using command line arguments? It seems that > > > > > > > > > > I can use the argument -ksp_rtol on the command line, but in the code I > > > > > > > > > > can't use KSPSetTolerances since I don't have access to the KSP solver > > > > > > > > > > context? > > > > > > > > > > > > > > > > > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > > > > > > > > > any others. > > > > > > > > > > > > > > > > > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > > > > > > > > > in the source code, but I can't find the documentation for it. > > > > > > > > > > Does this function not exist yet? Again I would like to use > > > > > > > > > > -dmmg_galerkin, but setting it in the code instead of on the command > > > > > > > > > > line. > > > > > > > > > > > > > > > > > > I think you want this: > > > > > > > > > > > > > > > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > > > > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > > Knut Erik Teigen > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- nlevels 1 coarsest_x,coarsest_y: 65 129 Using SSP-RK3()4 (SSP) scheme for system 1 Using SSP-RK2()4 (SSP) scheme for system 2 Using SSP-RK3()4 (SSP) scheme for system 3 u : is f-variable number: 1 v : is f-variable number: 2 p : is f-variable number: 3 fi : is f-variable number: 4 Initial configuration: Rising bubble Using CFL-number= 0.3000 Exact area, phase 1: 3.491E-05 Numerical area, phase 1: 3.499E-05 Using WENO boundary trick! Writing inputfile to file: out.inp c_conv= 0.00E+00 c_visc= 6.07E+02 c_grav= 1.78E+02 c_st= 1.58E+03 ------------------------------------------- Start of time loop: L-s reinit converged after 10 steps with norm 1.716E-09 0 KSP preconditioned resid norm 3.168341703825e+08 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 0 KSP preconditioned resid norm 3.168341703825e+08 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 7.830661072700e-07 true resid norm 7.337644742621e-07 ||Ae||/||Ax|| 2.315925941246e-15 1 KSP preconditioned resid norm 7.830661072700e-07 true resid norm 7.337644742621e-07 ||Ae||/||Ax|| 2.315925941246e-15 Linear solve converged due to CONVERGED_RTOL Process [0] 66.5366 66.5153 66.473 66.4098 66.326 66.222 66.0984 65.9559 65.7952 65.6174 65.4234 65.2146 64.9923 64.7582 64.514 64.2616 64.0031 63.7408 63.4772 63.2148 62.9562 62.7043 62.4619 62.2317 62.0167 61.8195 61.6427 61.4887 61.3596 61.2572 61.1829 61.138 61.1229 61.138 61.1829 61.2572 61.3596 61.4887 61.6427 61.8195 62.0167 62.2317 62.4619 62.7043 62.9562 63.2148 63.4772 63.7408 64.0031 64.2616 64.514 64.7582 64.9923 65.2146 65.4234 65.6174 65.7952 65.9559 66.0984 66.222 66.326 66.4098 66.473 66.5153 66.5366 63.5162 63.4949 63.4524 63.3888 63.3046 63.2001 63.0758 62.9324 62.7708 62.5918 62.3966 62.1864 61.9625 61.7266 61.4804 61.2259 60.9651 60.7004 60.4341 60.169 59.9076 59.6528 59.4075 59.1745 58.9568 58.757 58.5778 58.4216 58.2906 58.1867 58.1114 58.0657 58.0504 58.0657 58.1114 58.1867 58.2906 58.4216 58.5778 58.757 58.9568 59.1745 59.4075 59.6528 59.9076 60.169 60.4341 60.7004 60.9651 61.2259 61.4804 61.7266 61.9625 62.1864 62.3966 62.5918 62.7708 62.9324 63.0758 63.2001 63.3046 63.3888 63.4524 63.4949 63.5162 60.5176 60.4961 60.4531 60.3889 60.3038 60.1982 60.0725 59.9276 59.764 59.5829 59.3851 59.172 58.9449 58.7054 58.4553 58.1965 57.9311 57.6614 57.39 57.1193 56.8523 56.5917 56.3406 56.1019 55.8785 55.6735 55.4894 55.3288 55.1941 55.0872 55.0097 54.9627 54.9469 54.9627 55.0097 55.0872 55.1941 55.3288 55.4894 55.6735 55.8785 56.1019 56.3406 56.5917 56.8523 57.1193 57.39 57.6614 57.9311 58.1965 58.4553 58.7054 58.9449 59.172 59.3851 59.5829 59.764 59.9276 60.0725 60.1982 60.3038 60.3889 60.4531 60.4961 60.5176 57.5408 57.5189 57.4754 57.4102 57.3238 57.2166 57.0889 56.9415 56.7752 56.5907 56.3892 56.1718 55.9399 55.6951 55.4391 55.1738 54.9015 54.6243 54.3449 54.066 53.7904 53.521 53.2611 53.0136 52.7818 52.5686 52.3771 52.2099 52.0694 51.9579 51.8769 51.8278 51.8114 51.8278 51.8769 51.9579 52.0694 52.2099 52.3771 52.5686 52.7818 53.0136 53.2611 53.521 53.7904 54.066 54.3449 54.6243 54.9015 55.1738 55.4391 55.6951 55.9399 56.1718 56.3892 56.5907 56.7752 56.9415 57.0889 57.2166 57.3238 57.4102 57.4754 57.5189 57.5408 54.5862 54.5639 54.5195 54.4531 54.3651 54.2556 54.1254 53.9748 53.8047 53.6159 53.4093 53.1863 52.948 52.6961 52.4323 52.1584 51.8767 51.5895 51.2995 51.0093 50.7221 50.4408 50.1689 49.9095 49.6661 49.4419 49.2401 49.0637 48.9154 48.7975 48.7118 48.6599 48.6425 48.6599 48.7118 48.7975 48.9154 49.0637 49.2401 49.4419 49.6661 49.9095 50.1689 50.4408 50.7221 51.0093 51.2995 51.5895 51.8767 52.1584 52.4323 52.6961 52.948 53.1863 53.4093 53.6159 53.8047 53.9748 54.1254 54.2556 54.3651 54.4531 54.5195 54.5639 54.5862 51.6541 51.6314 51.586 51.5181 51.428 51.3159 51.1824 51.0279 50.8532 50.659 50.4463 50.2162 49.97 49.7093 49.4356 49.1509 48.8575 48.5576 48.2541 47.9497 47.6477 47.3512 47.0638 46.7892 46.5308 46.2924 46.0774 45.8891 45.7305 45.6043 45.5125 45.4568 45.4382 45.4568 45.5125 45.6043 45.7305 45.8891 46.0774 46.2924 46.5308 46.7892 47.0638 47.3512 47.6477 47.9497 48.2541 48.5576 48.8575 49.1509 49.4356 49.7093 49.97 50.2162 50.4463 50.659 50.8532 51.0279 51.1824 51.3159 51.428 51.5181 51.586 51.6314 51.6541 48.7452 48.7219 48.6753 48.6057 48.5131 48.398 48.2607 48.1016 47.9215 47.721 47.501 47.2625 47.0069 46.7355 46.45 46.1524 45.8447 45.5295 45.2096 44.8878 44.5675 44.2524 43.946 43.6523 43.3753 43.1191 42.8875 42.6842 42.5128 42.3761 42.2766 42.2162 42.1959 42.2162 42.2766 42.3761 42.5128 42.6842 42.8875 43.1191 43.3753 43.6523 43.946 44.2524 44.5675 44.8878 45.2096 45.5295 45.8447 46.1524 46.45 46.7355 47.0069 47.2625 47.501 47.721 47.9215 48.1016 48.2607 48.398 48.5131 48.6057 48.6753 48.7219 48.7452 45.8599 45.836 45.7881 45.7165 45.6212 45.5026 45.361 45.1968 45.0104 44.8027 44.5743 44.3263 44.0597 43.776 43.4768 43.164 42.8396 42.5063 42.1668 41.8243 41.4823 41.1446 40.8152 40.4984 40.1988 39.9207 39.6688 39.4471 39.2597 39.1101 39.0011 38.9348 38.9125 38.9348 39.0011 39.1101 39.2597 39.4471 39.6688 39.9207 40.1988 40.4984 40.8152 41.1446 41.4823 41.8243 42.1668 42.5063 42.8396 43.164 43.4768 43.776 44.0597 44.3263 44.5743 44.8027 45.0104 45.1968 45.361 45.5026 45.6212 45.7165 45.7881 45.836 45.8599 42.999 42.9743 42.9251 42.8513 42.7531 42.6307 42.4843 42.3143 42.1212 41.9054 41.6677 41.4088 41.13 40.8323 40.5175 40.1872 39.8436 39.4893 39.1271 38.7604 38.3927 38.0283 37.6715 37.3272 37.0003 36.6959 36.4192 36.1752 35.9684 35.8029 35.6821 35.6086 35.5839 35.6086 35.6821 35.8029 35.9684 36.1752 36.4192 36.6959 37.0003 37.3272 37.6715 38.0283 38.3927 38.7604 39.1271 39.4893 39.8436 40.1872 40.5175 40.8323 41.13 41.4088 41.6677 41.9054 42.1212 42.3143 42.4843 42.6307 42.7531 42.8513 42.9251 42.9743 42.999 40.1631 40.1377 40.0869 40.0108 39.9095 39.783 39.6316 39.4554 39.2549 39.0304 38.7824 38.5117 38.2193 37.9062 37.5738 37.2239 36.8586 36.4804 36.0921 35.6973 35.2999 34.9042 34.5152 34.1382 33.7788 33.443 33.1366 32.8655 32.6351 32.4503 32.3152 32.2328 32.2051 32.2328 32.3152 32.4503 32.6351 32.8655 33.1366 33.443 33.7788 34.1382 34.5152 34.9042 35.2999 35.6973 36.0921 36.4804 36.8586 37.2239 37.5738 37.9062 38.2193 38.5117 38.7824 39.0304 39.2549 39.4554 39.6316 39.783 39.9095 40.0108 40.0869 40.1377 40.1631 37.353 37.3268 37.2745 37.196 37.0914 36.9607 36.8039 36.6213 36.4129 36.1791 35.9202 35.6368 35.3296 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resid norm 3.005729294791e+04 ||Ae||/||Ax|| 9.486627323288e-05 1 KSP preconditioned resid norm 5.352387062140e-07 true resid norm 8.438016085313e-07 ||Ae||/||Ax|| 2.663191062748e-15 1 KSP preconditioned resid norm 5.352387062140e-07 true resid norm 8.438016085313e-07 ||Ae||/||Ax|| 2.663191062748e-15 1 KSP preconditioned resid norm 5.352387062140e-07 true resid norm 8.438016085313e-07 ||Ae||/||Ax|| 2.663191062748e-15 Linear solve converged due to CONVERGED_RTOL Process [0] 71.0932 71.0721 71.0298 70.9666 70.8829 70.779 70.6555 70.5131 70.3525 70.1748 69.9809 69.7722 69.5501 69.3161 69.072 68.8197 68.5614 68.2993 68.0357 67.7734 67.515 67.2632 67.0208 66.7908 66.5759 66.3787 66.202 66.048 65.919 65.8166 65.7424 65.6974 65.6823 65.6974 65.7424 65.8166 65.919 66.048 66.202 66.3787 66.5759 66.7908 67.0208 67.2632 67.515 67.7734 68.0357 68.2993 68.5614 68.8197 69.072 69.3161 69.5501 69.7722 69.9809 70.1748 70.3525 70.5131 70.6555 70.779 70.8829 70.9666 71.0298 71.0721 71.0932 68.0729 68.0516 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||Ae||/||Ax|| 1.732619399736e-15 1 KSP preconditioned resid norm 2.416378524737e-07 true resid norm 7.075902174382e-07 ||Ae||/||Ax|| 1.732619399736e-15 1 KSP preconditioned resid norm 2.416378524737e-07 true resid norm 7.075902174382e-07 ||Ae||/||Ax|| 1.732619399736e-15 Linear solve converged due to CONVERGED_RTOL Process [0] 71.7852 71.7641 71.7219 71.6587 71.575 71.4712 71.3477 71.2053 71.0448 70.8671 70.6733 70.4646 70.2425 70.0086 69.7645 69.5123 69.2539 68.9918 68.7283 68.466 68.2076 67.9558 67.7135 67.4835 67.2685 67.0714 66.8947 66.7407 66.6117 66.5093 66.4351 66.3901 66.375 66.3901 66.4351 66.5093 66.6117 66.7407 66.8947 67.0714 67.2685 67.4835 67.7135 67.9558 68.2076 68.466 68.7283 68.9918 69.2539 69.5123 69.7645 70.0086 70.2425 70.4646 70.6733 70.8671 71.0448 71.2053 71.3477 71.4712 71.575 71.6587 71.7219 71.7641 71.7852 68.7648 68.7436 68.7011 68.6377 68.5536 68.4492 68.325 68.1818 68.0204 67.8415 67.6465 67.4364 67.2127 66.9769 66.7309 66.4765 66.2159 65.9514 65.6853 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9.372585274370e-07 ||Ae||/||Ax|| 2.294853794960e-15 1 KSP preconditioned resid norm 5.856729238698e-07 true resid norm 9.372585274370e-07 ||Ae||/||Ax|| 2.294853794960e-15 1 KSP preconditioned resid norm 5.856729238698e-07 true resid norm 9.372585274370e-07 ||Ae||/||Ax|| 2.294853794960e-15 1 KSP preconditioned resid norm 5.856729238698e-07 true resid norm 9.372585274370e-07 ||Ae||/||Ax|| 2.294853794960e-15 Linear solve converged due to CONVERGED_RTOL Process [0] 77.1459 77.1248 77.0825 77.0193 76.9355 76.8316 76.7081 76.5656 76.405 76.2272 76.0333 75.8246 75.6024 75.3683 75.1241 74.8718 74.6134 74.3512 74.0876 73.8252 73.5667 73.3148 73.0724 72.8424 72.6274 72.4302 72.2535 72.0995 71.9703 71.8679 71.7937 71.7487 71.7337 71.7487 71.7937 71.8679 71.9703 72.0995 72.2535 72.4302 72.6274 72.8424 73.0724 73.3148 73.5667 73.8252 74.0876 74.3512 74.6134 74.8718 75.1241 75.3683 75.6024 75.8246 76.0333 76.2272 76.405 76.5656 76.7081 76.8316 76.9355 77.0193 77.0825 77.1248 77.1459 74.1256 74.1043 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Writing inputfile to file: out.inp c_conv= 0.00E+00 c_visc= 6.07E+02 c_grav= 1.78E+02 c_st= 1.58E+03 ------------------------------------------- Start of time loop: L-s reinit converged after 10 steps with norm 1.716E-09 0 KSP preconditioned resid norm 3.168341703825e+08 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 0 KSP preconditioned resid norm 3.168341703825e+08 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 7.830661072700e-07 true resid norm 7.337644742621e-07 ||Ae||/||Ax|| 2.315925941246e-15 1 KSP preconditioned resid norm 7.830661072700e-07 true resid norm 7.337644742621e-07 ||Ae||/||Ax|| 2.315925941246e-15 Linear solve converged due to CONVERGED_RTOL Process [0] 66.5366 66.5153 66.473 66.4098 66.326 66.222 66.0984 65.9559 65.7952 65.6174 65.4234 65.2146 64.9923 64.7582 64.514 64.2616 64.0031 63.7408 63.4772 63.2148 62.9562 62.7043 62.4619 62.2317 62.0167 61.8195 61.6427 61.4887 61.3596 61.2572 61.1829 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resid norm 3.005729294791e+04 ||Ae||/||Ax|| 9.486627323288e-05 1 KSP preconditioned resid norm 5.352387062140e-07 true resid norm 8.438016085313e-07 ||Ae||/||Ax|| 2.663191062748e-15 1 KSP preconditioned resid norm 5.352387062140e-07 true resid norm 8.438016085313e-07 ||Ae||/||Ax|| 2.663191062748e-15 1 KSP preconditioned resid norm 5.352387062140e-07 true resid norm 8.438016085313e-07 ||Ae||/||Ax|| 2.663191062748e-15 Linear solve converged due to CONVERGED_RTOL Process [0] 71.0932 71.0721 71.0298 70.9666 70.8829 70.779 70.6555 70.5131 70.3525 70.1748 69.9809 69.7722 69.5501 69.3161 69.072 68.8197 68.5614 68.2993 68.0357 67.7734 67.515 67.2632 67.0208 66.7908 66.5759 66.3787 66.202 66.048 65.919 65.8166 65.7424 65.6974 65.6823 65.6974 65.7424 65.8166 65.919 66.048 66.202 66.3787 66.5759 66.7908 67.0208 67.2632 67.515 67.7734 68.0357 68.2993 68.5614 68.8197 69.072 69.3161 69.5501 69.7722 69.9809 70.1748 70.3525 70.5131 70.6555 70.779 70.8829 70.9666 71.0298 71.0721 71.0932 68.0729 68.0516 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||Ae||/||Ax|| 8.195006028572e-03 1 KSP preconditioned resid norm 3.346785854152e+06 true resid norm 3.346785854152e+06 ||Ae||/||Ax|| 8.195006028572e-03 1 KSP preconditioned resid norm 3.346785854152e+06 true resid norm 3.346785854152e+06 ||Ae||/||Ax|| 8.195006028572e-03 2 KSP preconditioned resid norm 4.820123849610e+03 true resid norm 4.820123849597e+03 ||Ae||/||Ax|| 1.180265058097e-05 2 KSP preconditioned resid norm 4.820123849610e+03 true resid norm 4.820123849597e+03 ||Ae||/||Ax|| 1.180265058097e-05 2 KSP preconditioned resid norm 4.820123849610e+03 true resid norm 4.820123849597e+03 ||Ae||/||Ax|| 1.180265058097e-05 2 KSP preconditioned resid norm 4.820123849610e+03 true resid norm 4.820123849597e+03 ||Ae||/||Ax|| 1.180265058097e-05 3 KSP preconditioned resid norm 1.466152207985e+01 true resid norm 1.466152208369e+01 ||Ae||/||Ax|| 3.590049292063e-08 3 KSP preconditioned resid norm 1.466152207985e+01 true resid norm 1.466152208369e+01 ||Ae||/||Ax|| 3.590049292063e-08 3 KSP preconditioned resid norm 1.466152207985e+01 true resid norm 1.466152208369e+01 ||Ae||/||Ax|| 3.590049292063e-08 3 KSP preconditioned resid norm 1.466152207985e+01 true resid norm 1.466152208369e+01 ||Ae||/||Ax|| 3.590049292063e-08 4 KSP preconditioned resid norm 1.116987751777e-01 true resid norm 1.116987932656e-01 ||Ae||/||Ax|| 2.735078741473e-10 4 KSP preconditioned resid norm 1.116987751777e-01 true resid norm 1.116987932656e-01 ||Ae||/||Ax|| 2.735078741473e-10 4 KSP preconditioned resid norm 1.116987751777e-01 true resid norm 1.116987932656e-01 ||Ae||/||Ax|| 2.735078741473e-10 4 KSP preconditioned resid norm 1.116987751777e-01 true resid norm 1.116987932656e-01 ||Ae||/||Ax|| 2.735078741473e-10 5 KSP preconditioned resid norm 8.016466601186e-05 true resid norm 8.013227122691e-05 ||Ae||/||Ax|| 1.962134640234e-13 5 KSP preconditioned resid norm 8.016466601186e-05 true resid norm 8.013227122691e-05 ||Ae||/||Ax|| 1.962134640234e-13 5 KSP preconditioned resid norm 8.016466601186e-05 true resid norm 8.013227122691e-05 ||Ae||/||Ax|| 1.962134640234e-13 5 KSP preconditioned resid norm 8.016466601186e-05 true resid norm 8.013227122691e-05 ||Ae||/||Ax|| 1.962134640234e-13 Linear solve converged due to CONVERGED_RTOL Process [0] 70.9845 70.9636 70.9217 70.859 70.776 70.673 70.5505 70.4092 70.25 70.0738 69.8816 69.6747 69.4545 69.2226 68.9807 68.7307 68.4748 68.2151 67.9542 67.6945 67.4387 67.1895 66.9498 66.7223 66.5098 66.3149 66.1403 65.9881 65.8606 65.7595 65.6862 65.6418 65.6269 65.6418 65.6862 65.7595 65.8606 65.9881 66.1403 66.3149 66.5098 66.7223 66.9498 67.1895 67.4387 67.6945 67.9542 68.2151 68.4748 68.7307 68.9807 69.2226 69.4545 69.6747 69.8816 70.0738 70.25 70.4092 70.5505 70.673 70.776 70.859 70.9217 70.9636 70.9845 67.9639 67.9429 67.9008 67.8378 67.7543 67.6508 67.5276 67.3856 67.2254 67.048 66.8546 66.6463 66.4245 66.1908 65.9469 65.6949 65.4367 65.1746 64.9111 64.6487 64.3901 64.1381 63.8956 63.6653 63.45 63.2526 63.0756 62.9214 62.7921 62.6895 62.6151 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9.516387654208e+05 true resid norm 9.516387654208e+05 ||Ae||/||Ax|| 2.340510427520e-03 1 KSP preconditioned resid norm 9.516387654208e+05 true resid norm 9.516387654208e+05 ||Ae||/||Ax|| 2.340510427520e-03 1 KSP preconditioned resid norm 9.516387654208e+05 true resid norm 9.516387654208e+05 ||Ae||/||Ax|| 2.340510427520e-03 2 KSP preconditioned resid norm 1.672012246723e+03 true resid norm 1.672012246751e+03 ||Ae||/||Ax|| 4.112234852823e-06 2 KSP preconditioned resid norm 1.672012246723e+03 true resid norm 1.672012246751e+03 ||Ae||/||Ax|| 4.112234852823e-06 2 KSP preconditioned resid norm 1.672012246723e+03 true resid norm 1.672012246751e+03 ||Ae||/||Ax|| 4.112234852823e-06 2 KSP preconditioned resid norm 1.672012246723e+03 true resid norm 1.672012246751e+03 ||Ae||/||Ax|| 4.112234852823e-06 2 KSP preconditioned resid norm 1.672012246723e+03 true resid norm 1.672012246751e+03 ||Ae||/||Ax|| 4.112234852823e-06 3 KSP preconditioned resid norm 9.105905260285e+00 true resid norm 9.105905236027e+00 ||Ae||/||Ax|| 2.239554222815e-08 3 KSP preconditioned resid norm 9.105905260285e+00 true resid norm 9.105905236027e+00 ||Ae||/||Ax|| 2.239554222815e-08 3 KSP preconditioned resid norm 9.105905260285e+00 true resid norm 9.105905236027e+00 ||Ae||/||Ax|| 2.239554222815e-08 3 KSP preconditioned resid norm 9.105905260285e+00 true resid norm 9.105905236027e+00 ||Ae||/||Ax|| 2.239554222815e-08 3 KSP preconditioned resid norm 9.105905260285e+00 true resid norm 9.105905236027e+00 ||Ae||/||Ax|| 2.239554222815e-08 4 KSP preconditioned resid norm 3.863456505538e-02 true resid norm 3.863455920924e-02 ||Ae||/||Ax|| 9.501986675783e-11 4 KSP preconditioned resid norm 3.863456505538e-02 true resid norm 3.863455920924e-02 ||Ae||/||Ax|| 9.501986675783e-11 4 KSP preconditioned resid norm 3.863456505538e-02 true resid norm 3.863455920924e-02 ||Ae||/||Ax|| 9.501986675783e-11 4 KSP preconditioned resid norm 3.863456505538e-02 true resid norm 3.863455920924e-02 ||Ae||/||Ax|| 9.501986675783e-11 4 KSP preconditioned resid norm 3.863456505538e-02 true resid norm 3.863455920924e-02 ||Ae||/||Ax|| 9.501986675783e-11 5 KSP preconditioned resid norm 3.774649063131e-05 true resid norm 3.774854002114e-05 ||Ae||/||Ax|| 9.284074456977e-14 5 KSP preconditioned resid norm 3.774649063131e-05 true resid norm 3.774854002114e-05 ||Ae||/||Ax|| 9.284074456977e-14 5 KSP preconditioned resid norm 3.774649063131e-05 true resid norm 3.774854002114e-05 ||Ae||/||Ax|| 9.284074456977e-14 5 KSP preconditioned resid norm 3.774649063131e-05 true resid norm 3.774854002114e-05 ||Ae||/||Ax|| 9.284074456977e-14 5 KSP preconditioned resid norm 3.774649063131e-05 true resid norm 3.774854002114e-05 ||Ae||/||Ax|| 9.284074456977e-14 Linear solve converged due to CONVERGED_RTOL Process [0] 72.7687 72.7477 72.7058 72.6432 72.5602 72.4572 72.3348 72.1937 72.0346 71.8585 71.6664 71.4597 71.2397 71.008 70.7663 70.5166 70.261 70.0017 69.741 69.4816 69.2261 68.9773 68.7379 68.5107 68.2985 68.104 67.9296 67.7777 67.6504 67.5495 67.4763 67.432 67.4171 67.432 67.4763 67.5495 67.6504 67.7777 67.9296 68.104 68.2985 68.5107 68.7379 68.9773 69.2261 69.4816 69.741 70.0017 70.261 70.5166 70.7663 71.008 71.2397 71.4597 71.6664 71.8585 72.0346 72.1937 72.3348 72.4572 72.5602 72.6432 72.7058 72.7477 72.7687 69.7481 69.7271 69.6849 69.622 69.5386 69.435 69.312 69.17 69.01 68.8327 68.6394 68.4313 68.2097 67.9762 67.7326 67.4808 67.2229 66.9611 66.6979 66.4358 66.1776 65.9259 65.6836 65.4537 65.2388 65.0417 64.8649 64.7109 64.5818 64.4794 64.4052 64.3602 64.3452 64.3602 64.4052 64.4794 64.5818 64.7109 64.8649 65.0417 65.2388 65.4537 65.6836 65.9259 66.1776 66.4358 66.6979 66.9611 67.2229 67.4808 67.7326 67.9762 68.2097 68.4313 68.6394 68.8327 69.01 69.17 69.312 69.435 69.5386 69.622 69.6849 69.7271 69.7481 66.749 66.7277 66.6852 66.6217 66.5374 66.4327 66.3083 66.1647 66.0028 65.8234 65.6275 65.4166 65.1918 64.9548 64.7073 64.4512 64.1887 63.922 63.6536 63.3861 63.1223 62.8649 62.6169 62.3813 62.161 61.9587 61.7772 61.6189 61.4861 61.3808 61.3044 61.2581 61.2426 61.2581 61.3044 61.3808 61.4861 61.6189 61.7772 61.9587 62.161 62.3813 62.6169 62.8649 63.1223 63.3861 63.6536 63.922 64.1887 64.4512 64.7073 64.9548 65.1918 65.4166 65.6275 65.8234 66.0028 66.1647 66.3083 66.4327 66.5374 66.6217 66.6852 66.7277 66.749 63.7716 63.75 63.7069 63.6423 63.5568 63.4505 63.3241 63.1781 63.0133 62.8306 62.6311 62.4158 62.1863 61.9439 61.6906 61.4281 61.1587 60.8846 60.6084 60.3327 60.0604 59.7944 59.5377 59.2935 59.0648 58.8546 58.6658 58.501 58.3626 58.2528 58.173 58.1247 58.1085 58.1247 58.173 58.2528 58.3626 58.501 58.6658 58.8546 59.0648 59.2935 59.5377 59.7944 60.0604 60.3327 60.6084 60.8846 61.1587 61.4281 61.6906 61.9439 62.1863 62.4158 62.6311 62.8306 63.0133 63.1781 63.3241 63.4505 63.5568 63.6423 63.7069 63.75 63.7716 60.8162 60.7942 60.7502 60.6844 60.5972 60.4888 60.3597 60.2106 60.0421 59.855 59.6505 59.4296 59.1937 58.9443 58.6832 58.4122 58.1335 57.8495 57.5627 57.2759 56.9921 56.7143 56.4458 56.1899 55.9498 55.7288 55.5299 55.3562 55.2102 55.0941 55.0098 54.9587 54.9416 54.9587 55.0098 55.0941 55.2102 55.3562 55.5299 55.7288 55.9498 56.1899 56.4458 56.7143 56.9921 57.2759 57.5627 57.8495 58.1335 58.4122 58.6832 58.9443 59.1937 59.4296 59.6505 59.855 60.0421 60.2106 60.3597 60.4888 60.5972 60.6844 60.7502 60.7942 60.8162 57.8831 57.8606 57.8156 57.7484 57.6591 57.548 57.4157 57.2627 57.0896 56.8972 56.6865 56.4586 56.2149 55.9566 55.6857 55.404 55.1137 54.8171 54.5169 54.2161 53.9176 53.6249 53.3412 53.0702 52.8154 52.5804 52.3686 52.1833 52.0273 51.9031 51.8129 51.7582 51.7398 51.7582 51.8129 51.9031 52.0273 52.1833 52.3686 52.5804 52.8154 53.0702 53.3412 53.6249 53.9176 54.2161 54.5169 54.8171 55.1137 55.404 55.6857 55.9566 56.2149 56.4586 56.6865 56.8972 57.0896 57.2627 57.4157 57.548 57.6591 57.7484 57.8156 57.8606 57.8831 54.9729 54.9499 54.9037 54.8347 54.743 54.6289 54.4928 54.3352 54.1567 53.958 53.74 53.5038 53.2506 52.9819 52.6992 52.4046 52.1001 51.7883 51.4719 51.1539 50.8374 50.5261 50.2237 49.934 49.661 49.4085 49.1805 48.9806 48.812 48.6777 48.58 48.5207 48.5008 48.5207 48.58 48.6777 48.812 48.9806 49.1805 49.4085 49.661 49.934 50.2237 50.5261 50.8374 51.1539 51.4719 51.7883 52.1001 52.4046 52.6992 52.9819 53.2506 53.5038 53.74 53.958 54.1567 54.3352 54.4928 54.6289 54.743 54.8347 54.9037 54.9499 54.9729 52.0862 52.0625 52.0151 51.9441 51.8497 51.7321 51.5918 51.429 51.2443 51.0384 50.8121 50.5663 50.3022 50.0212 49.7249 49.4151 49.0941 48.7643 48.4285 48.0899 47.752 47.4184 47.0933 46.7809 46.4856 46.2118 45.9639 45.746 45.562 45.4151 45.3081 45.2431 45.2213 45.2431 45.3081 45.4151 45.562 45.746 45.9639 46.2118 46.4856 46.7809 47.0933 47.4184 47.752 48.0899 48.4285 48.7643 49.0941 49.4151 49.7249 50.0212 50.3022 50.5663 50.8121 51.0384 51.2443 51.429 51.5918 51.7321 51.8497 51.9441 52.0151 52.0625 52.0862 49.2237 49.1992 49.1504 49.0773 48.9799 48.8585 48.7134 48.5449 48.3534 48.1395 47.9039 47.6473 47.371 47.0761 46.7642 46.4371 46.097 45.7464 45.3881 45.0254 44.6621 44.3021 43.95 43.6105 43.2884 42.9888 42.7168 42.4771 42.2742 42.1119 41.9937 41.9217 41.8975 41.9217 41.9937 42.1119 42.2742 42.4771 42.7168 42.9888 43.2884 43.6105 43.95 44.3021 44.6621 45.0254 45.3881 45.7464 46.097 46.4371 46.7642 47.0761 47.371 47.6473 47.9039 48.1395 48.3534 48.5449 48.7134 48.8585 48.9799 49.0773 49.1504 49.1992 49.2237 46.3859 46.3608 46.3104 46.235 46.1345 46.0091 45.8589 45.6842 45.4853 45.2627 45.0169 44.7485 44.4586 44.1483 43.819 43.4724 43.1106 42.7361 42.352 41.9615 41.5687 41.1779 40.794 40.4222 40.0683 39.7379 39.4368 39.1708 38.945 38.7642 38.6321 38.5517 38.5247 38.5517 38.6321 38.7642 38.945 39.1708 39.4368 39.7379 40.0683 40.4222 40.794 41.1779 41.5687 41.9615 42.352 42.7361 43.1106 43.4724 43.819 44.1483 44.4586 44.7485 45.0169 45.2627 45.4853 45.6842 45.8589 46.0091 46.1345 46.235 46.3104 46.3608 46.3859 43.5738 43.5479 43.496 43.4181 43.3144 43.1847 43.0292 42.8481 42.6414 42.4094 42.1527 41.8716 41.567 41.2398 40.8912 40.523 40.137 39.7358 39.3223 38.9001 38.4733 38.0466 37.6256 37.216 36.8242 36.4571 36.1213 35.8236 35.5703 35.3669 35.2182 35.1275 35.097 35.1275 35.2182 35.3669 35.5703 35.8236 36.1213 36.4571 36.8242 37.216 37.6256 38.0466 38.4733 38.9001 39.3223 39.7358 40.137 40.523 40.8912 41.2398 41.567 41.8716 42.1527 42.4094 42.6414 42.8481 43.0292 43.1847 43.3144 43.4181 43.496 43.5479 43.5738 40.788 40.7613 40.7079 40.6276 40.5206 40.3866 40.2257 40.0378 39.823 39.5814 39.3132 39.0186 38.6983 38.3529 37.9836 37.5916 37.179 36.7479 36.3015 35.8433 35.3777 34.9098 34.4455 33.9916 33.5553 33.1444 32.7671 32.4314 32.1448 31.9142 31.7452 31.6421 31.6075 31.6421 31.7452 31.9142 32.1448 32.4314 32.7671 33.1444 33.5553 33.9916 34.4455 34.9098 35.3777 35.8433 36.3015 36.7479 37.179 37.5916 37.9836 38.3529 38.6983 39.0186 39.3132 39.5814 39.823 40.0378 40.2257 40.3866 40.5206 40.6276 40.7079 40.7613 40.788 38.0294 38.002 37.947 37.8644 37.7541 37.6158 37.4495 37.2549 37.032 36.7805 36.5004 36.1918 35.855 35.4904 35.0988 34.6813 34.2396 33.7757 33.2927 32.794 32.2844 31.7692 31.255 30.7492 30.2604 29.7977 29.3707 28.9892 28.6624 28.3988 28.2054 28.0872 28.0475 28.0872 28.2054 28.3988 28.6624 28.9892 29.3707 29.7977 30.2604 30.7492 31.255 31.7692 32.2844 32.794 33.2927 33.7757 34.2396 34.6813 35.0988 35.4904 35.855 36.1918 36.5004 36.7805 37.032 37.2549 37.4495 37.6158 37.7541 37.8644 37.947 38.002 38.0294 35.2987 35.2705 35.2141 35.1293 35.0159 34.8736 34.702 34.5009 34.2699 34.0085 33.7165 33.3937 33.0399 32.6553 32.2403 31.7956 31.3226 30.823 30.2996 29.756 29.1967 28.6276 28.0558 27.4897 26.9391 26.4147 25.9282 25.4914 25.1159 24.8122 24.5891 24.4527 24.4069 24.4527 24.5891 24.8122 25.1159 25.4914 25.9282 26.4147 26.9391 27.4897 28.0558 28.6276 29.1967 29.756 30.2996 30.823 31.3226 31.7956 32.2403 32.6553 33.0399 33.3937 33.7165 34.0085 34.2699 34.5009 34.702 34.8736 35.0159 35.1293 35.2141 35.2705 35.2987 32.5966 32.5678 32.5102 32.4233 32.3071 32.161 31.9846 31.7773 31.5385 31.2676 30.964 30.627 30.2562 29.8512 29.4119 28.9388 28.4325 27.8945 27.3272 26.7338 26.119 25.4888 24.8508 24.2145 23.5911 22.9933 22.4351 21.9313 21.4965 21.1439 20.8846 20.7263 20.6731 20.7263 20.8846 21.1439 21.4965 21.9313 22.4351 22.9933 23.5911 24.2145 24.8508 25.4888 26.119 26.7338 27.3272 27.8945 28.4325 28.9388 29.4119 29.8512 30.2562 30.627 30.964 31.2676 31.5385 31.7773 31.9846 32.161 32.3071 32.4233 32.5102 32.5678 32.5966 29.9238 29.8945 29.8357 29.7472 29.6286 29.4792 29.2985 29.0856 28.8398 28.56 28.2453 27.8947 27.5071 27.0818 26.618 26.1156 25.5745 24.9958 24.3812 23.7334 23.057 22.3578 21.6441 20.9263 20.2171 19.5316 18.8868 18.3012 17.7935 17.3808 17.0775 16.893 16.8314 16.893 17.0775 17.3808 17.7935 18.3012 18.8868 19.5316 20.2171 20.9263 21.6441 22.3578 23.057 23.7334 24.3812 24.9958 25.5745 26.1156 26.618 27.0818 27.5071 27.8947 28.2453 28.56 28.8398 29.0856 29.2985 29.4792 29.6286 29.7472 29.8357 29.8945 29.9238 27.2808 27.2511 27.1916 27.1018 26.9812 26.8292 26.645 26.4275 26.1756 25.8879 25.5632 25.1998 24.7964 24.3514 23.8634 23.3315 22.7549 22.1337 21.4688 20.7622 20.0179 19.2416 18.4417 17.6293 16.819 16.0284 15.2784 14.5922 13.9939 13.5067 13.1498 12.935 12.8645 12.935 13.1498 13.5067 13.9939 14.5922 15.2784 16.0284 16.819 17.6293 18.4417 19.2416 20.0179 20.7622 21.4688 22.1337 22.7549 23.3315 23.8634 24.3514 24.7964 25.1998 25.5632 25.8879 26.1756 26.4275 26.645 26.8292 26.9812 27.1018 27.1916 27.2511 27.2808 24.668 24.6381 24.5781 24.4875 24.3658 24.212 24.0253 23.8043 23.5476 23.2535 22.9202 22.5457 22.1279 21.6645 21.1535 20.5927 19.9806 19.316 18.5986 17.8294 17.0113 16.1494 15.2518 14.3303 13.4008 12.4841 11.6053 10.7938 10.0814 9.50029 9.07794 8.83038 8.7543 8.83038 9.07794 9.50029 10.0814 10.7938 11.6053 12.4841 13.4008 14.3303 15.2518 16.1494 17.0113 17.8294 18.5986 19.316 19.9806 20.5927 21.1535 21.6645 22.1279 22.5457 22.9202 23.2535 23.5476 23.8043 24.0253 24.212 24.3658 24.4875 24.5781 24.6381 24.668 22.0856 22.0557 21.9956 21.9049 21.7828 21.6284 21.4404 21.2174 20.9576 20.6589 20.3191 19.9356 19.5056 19.0261 18.494 17.9062 17.2596 16.5518 15.7809 14.9463 14.0493 13.0935 12.0863 11.0393 9.96976 8.90121 7.86389 6.8946 6.03562 5.33262 4.8285 4.55164 4.48957 4.55164 4.8285 5.33262 6.03562 6.8946 7.86389 8.90121 9.96976 11.0393 12.0863 13.0935 14.0493 14.9463 15.7809 16.5518 17.2596 17.9062 18.494 19.0261 19.5056 19.9356 20.3191 20.6589 20.9576 21.2174 21.4404 21.6284 21.7828 21.9049 21.9956 22.0557 22.0856 19.5335 19.5039 19.4443 19.3542 19.2327 19.0788 18.8911 18.6678 18.407 18.1061 17.7624 17.3727 16.9336 16.4412 15.8912 15.2793 14.6009 13.8517 13.0279 12.1267 11.1468 10.0898 8.96107 7.77118 6.5377 5.28659 4.05339 2.88343 1.83144 0.962959 0.348276 0.0547373 0.0987876 0.0547373 0.348276 0.962959 1.83144 2.88343 4.05339 5.28659 6.5377 7.77118 8.96107 10.0898 11.1468 12.1267 13.0279 13.8517 14.6009 15.2793 15.8912 16.4412 16.9336 17.3727 17.7624 18.1061 18.407 18.6678 18.8911 19.0788 19.2327 19.3542 19.4443 19.5039 19.5335 17.0117 16.9826 16.9239 16.8352 16.7155 16.5636 16.3779 16.1565 15.897 15.5967 15.2523 14.8601 14.4158 13.9147 13.3513 12.7198 12.014 11.2274 10.3536 9.38683 8.32264 7.15903 5.89796 4.54735 3.12352 1.65379 0.178676 -1.24758 -2.55912 -3.66446 -4.45811 -4.78502 -4.20253 -4.78502 -4.45811 -3.66446 -2.55912 -1.24758 0.178676 1.65379 3.12352 4.54735 5.89796 7.15903 8.32264 9.38683 10.3536 11.2274 12.014 12.7198 13.3513 13.9147 14.4158 14.8601 15.2523 15.5967 15.897 16.1565 16.3779 16.5636 16.7155 16.8352 16.9239 16.9826 17.0117 14.5195 14.4912 14.4341 14.3477 14.231 14.0827 13.901 13.6838 13.4285 13.1321 12.7908 12.4003 11.9558 11.4513 10.8805 10.2358 9.5092 8.69163 7.77371 6.74594 5.59945 4.32721 2.92577 1.39788 -0.244044 -1.97356 -3.74567 -5.4951 -7.15909 -8.60843 -9.73865 -10.549 -7.23537 -10.549 -9.73865 -8.60843 -7.15909 -5.4951 -3.74567 -1.97356 -0.244044 1.39788 2.92577 4.32721 5.59945 6.74594 7.77371 8.69163 9.5092 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-285.102 -285.102 -285.102 -288.144 -288.143 -288.143 -288.143 -288.143 -288.143 -288.143 -288.142 -288.142 -288.142 -288.141 -288.141 -288.14 -288.14 -288.139 -288.139 -288.138 -288.138 -288.137 -288.137 -288.136 -288.136 -288.136 -288.135 -288.135 -288.134 -288.134 -288.134 -288.134 -288.134 -288.133 -288.133 -288.133 -288.133 -288.133 -288.134 -288.134 -288.134 -288.134 -288.134 -288.135 -288.135 -288.136 -288.136 -288.136 -288.137 -288.137 -288.138 -288.138 -288.139 -288.139 -288.14 -288.14 -288.141 -288.141 -288.142 -288.142 -288.142 -288.143 -288.143 -288.143 -288.143 -288.143 -288.143 -288.144 Time step 1 t=1.56074E-04 dt=1.561E-04 cfl=3.00E-01 cfl_v=9.48E-02 ------------------------------------------- c_conv= 2.54E+03 c_visc= 6.07E+02 c_grav= 1.78E+02 c_st= 5.03E+02 From knepley at gmail.com Sun Jun 17 09:18:33 2007 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 17 Jun 2007 09:18:33 -0500 Subject: Is it possible to build one Petsc that works for both C and C++? In-Reply-To: <686761.61517.qm@web36213.mail.mud.yahoo.com> References: <686761.61517.qm@web36213.mail.mud.yahoo.com> Message-ID: On 6/17/07, Shi Jin wrote: > Hi, > > I am learning the unstructured part of Petsc, which > naturally uses C++(at least the sample I am studying > is C++). On the other hand, my old Petsc codes are all > written in C. > I found that once I build the Petsc with C++, the old > C codes cannot be compiled since it is trying to use > mpicxx to compile the .c source files. However, I do This should be no problem. I do it all the time. Any C++ compiler can compile C just fine. Matt > see after the configuration stage that there is a > list: > C compiler: mpicc > C++ compiler: mpicxx > Fortran compiler: mpif77 > > Is it possible to instruct Petsc to use the > corresponding compiler for different source codes? > Thanks a lot. > PS. This is how I configured my Petsc-2.3.3-p3: > ./config/configure.py --with-cc=gcc --with-fc=g77 > --with-cxx=g++ --download-f-blas-lapack=1 > --download-mpich=1 --with-clanguage=cxx --with-sieve=1 > --download-boost=1 --download-chaco > --download-parmetis --download-fiat --download-generator > > > > ____________________________________________________________________________________ > Get the Yahoo! toolbar and be alerted to new email wherever you're surfing. > http://new.toolbar.yahoo.com/toolbar/features/mail/index.php > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From timothy.stitt at ichec.ie Sun Jun 17 10:33:02 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Sun, 17 Jun 2007 16:33:02 +0100 Subject: MatCreateMPIAIJ Pre-allocation Query Message-ID: <200706171633.02204.timothy.stitt@ichec.ie> Hi All, Currently I am using MatCreateMPIAIJ to create a distributed sparse matrix for use in my parallel sparse eigensolver. If I understand things correctly, it is important to specify the correct pre-allocation values for (o_nz,d_nz) or (o_nnz, d_nnz) respectively to obtain optimum memory usage per node. For information my matrix redistribution routine generates each row in the sparse matrix (associated with a given node) "on-the-fly" and then uses MatSetValues to apply the elements. My question is: does anyone have a standard code template for the calculating the d_nz or d_nnz values (along with o_nz or o_nnz respectively) so that optimum pre-allocation is obtained? Is there a simple way of determining if a given non-zero value in a row is part of the diagonal or off-diagonal regions for a given distributed topology? Any assistance gratefully received. Thanks in advance, Tim. -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From jinzishuai at yahoo.com Sun Jun 17 10:59:35 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Sun, 17 Jun 2007 08:59:35 -0700 (PDT) Subject: Is it possible to build one Petsc that works for both C and C++? In-Reply-To: Message-ID: <169129.20648.qm@web36208.mail.mud.yahoo.com> But this is what I got trying to compile my C petsc code with the C++ build: In file included from /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpi.h:1104, from spAF_incl.h:20, from spAF_analyt.h:11, from spAF_analyt.c:11: /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpicxx.h:26:2: error: #error "SEEK_SET is #defined but must not be for the C++ binding of MPI" /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpicxx.h:30:2: error: #error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpicxx.h:35:2: error: #error "SEEK_END is #defined but must not be for the C++ binding of MPI" make: *** [spAF_analyt.o] Error 1 Did you do anything special? I am using GCC. Thanks. Shi --- Matthew Knepley wrote: > On 6/17/07, Shi Jin wrote: > > Hi, > > > > I am learning the unstructured part of Petsc, > which > > naturally uses C++(at least the sample I am > studying > > is C++). On the other hand, my old Petsc codes are > all > > written in C. > > I found that once I build the Petsc with C++, the > old > > C codes cannot be compiled since it is trying to > use > > mpicxx to compile the .c source files. However, I > do > > This should be no problem. I do it all the time. Any > C++ > compiler can compile C just fine. > > Matt > > > see after the configuration stage that there is a > > list: > > C compiler: mpicc > > C++ compiler: mpicxx > > Fortran compiler: mpif77 > > > > Is it possible to instruct Petsc to use the > > corresponding compiler for different source > codes? > > Thanks a lot. > > PS. This is how I configured my Petsc-2.3.3-p3: > > ./config/configure.py --with-cc=gcc --with-fc=g77 > > --with-cxx=g++ --download-f-blas-lapack=1 > > --download-mpich=1 --with-clanguage=cxx > --with-sieve=1 > > --download-boost=1 --download-chaco > > --download-parmetis --download-fiat > --download-generator > > > > > > > > > ____________________________________________________________________________________ > > Get the Yahoo! toolbar and be alerted to new email > wherever you're surfing. > > > http://new.toolbar.yahoo.com/toolbar/features/mail/index.php > > > > > > > -- > What most experimenters take for granted before they > begin their > experiments is infinitely more interesting than any > results to which > their experiments lead. > -- Norbert Wiener > > ___________________________________________________________________________________ You snooze, you lose. Get messages ASAP with AutoCheck in the all-new Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_html.html From knepley at gmail.com Sun Jun 17 11:07:49 2007 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 17 Jun 2007 11:07:49 -0500 Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: <200706171633.02204.timothy.stitt@ichec.ie> References: <200706171633.02204.timothy.stitt@ichec.ie> Message-ID: On 6/17/07, Tim Stitt wrote: > Hi All, > > Currently I am using MatCreateMPIAIJ to create a distributed sparse matrix for > use in my parallel sparse eigensolver. If I understand things correctly, it > is important to specify the correct pre-allocation values for (o_nz,d_nz) or > (o_nnz, d_nnz) respectively to obtain optimum memory usage per node. > > For information my matrix redistribution routine generates each row in the > sparse matrix (associated with a given node) "on-the-fly" and then uses > MatSetValues to apply the elements. > > My question is: does anyone have a standard code template for the calculating > the d_nz or d_nnz values (along with o_nz or o_nnz respectively) so that > optimum pre-allocation is obtained? Is there a simple way of determining if a > given non-zero value in a row is part of the diagonal or off-diagonal regions > for a given distributed topology? > > Any assistance gratefully received. Basically, you run through the construction algorithm once to calculate d_nnz and o_nnz, and then again to set values. You can see my code for doing it in preallocateOperator() in src/dm/mesh/mesh.c. Matt > Thanks in advance, > > Tim. > > -- > Dr. Timothy Stitt > HPC Application Consultant - ICHEC (www.ichec.ie) > > Dublin Institute for Advanced Studies > 5 Merrion Square - Dublin 2 - Ireland > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From knepley at gmail.com Sun Jun 17 11:11:32 2007 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 17 Jun 2007 11:11:32 -0500 Subject: Is it possible to build one Petsc that works for both C and C++? In-Reply-To: <169129.20648.qm@web36208.mail.mud.yahoo.com> References: <169129.20648.qm@web36208.mail.mud.yahoo.com> Message-ID: This is an MPICH problem. From mpicxx.h: // There is a name conflict between stdio.h and the MPI C++ binding // with respect to the names SEEK_SET, SEEK_CUR, and SEEK_END. MPI // wants these in the MPI namespace, but stdio.h will #define these // to integer values. #undef'ing these can cause obscure problems // with other include files (such as iostream), so we instead use // #error to indicate a fatal error. Users can either #undef // the names before including mpi.h or include mpi.h *before* stdio.h // or iostream. #ifndef MPICH_IGNORE_CXX_SEEK #ifdef SEEK_SET #error "SEEK_SET is #defined but must not be for the C++ binding of MPI" //#undef SEEK_SET #endif #ifdef SEEK_CUR #error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" //#undef SEEK_CUR #endif #ifdef SEEK_END //#undef SEEK_END #error "SEEK_END is #defined but must not be for the C++ binding of MPI" #endif #endif I recommend not including stdio.h yourself. PETSc will do it. Matt On 6/17/07, Shi Jin wrote: > But this is what I got trying to compile my C petsc > code with the C++ build: > In file included from > /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpi.h:1104, > from spAF_incl.h:20, > from spAF_analyt.h:11, > from spAF_analyt.c:11: > /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpicxx.h:26:2: > error: #error "SEEK_SET is #defined but must not be > for the C++ binding of MPI" > /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpicxx.h:30:2: > error: #error "SEEK_CUR is #defined but must not be > for the C++ binding of MPI" > /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpicxx.h:35:2: > error: #error "SEEK_END is #defined but must not be > for the C++ binding of MPI" > make: *** [spAF_analyt.o] Error 1 > > Did you do anything special? I am using GCC. > Thanks. > > Shi > --- Matthew Knepley wrote: > > > On 6/17/07, Shi Jin wrote: > > > Hi, > > > > > > I am learning the unstructured part of Petsc, > > which > > > naturally uses C++(at least the sample I am > > studying > > > is C++). On the other hand, my old Petsc codes are > > all > > > written in C. > > > I found that once I build the Petsc with C++, the > > old > > > C codes cannot be compiled since it is trying to > > use > > > mpicxx to compile the .c source files. However, I > > do > > > > This should be no problem. I do it all the time. Any > > C++ > > compiler can compile C just fine. > > > > Matt > > > > > see after the configuration stage that there is a > > > list: > > > C compiler: mpicc > > > C++ compiler: mpicxx > > > Fortran compiler: mpif77 > > > > > > Is it possible to instruct Petsc to use the > > > corresponding compiler for different source > > codes? > > > Thanks a lot. > > > PS. This is how I configured my Petsc-2.3.3-p3: > > > ./config/configure.py --with-cc=gcc --with-fc=g77 > > > --with-cxx=g++ --download-f-blas-lapack=1 > > > --download-mpich=1 --with-clanguage=cxx > > --with-sieve=1 > > > --download-boost=1 --download-chaco > > > --download-parmetis --download-fiat > > --download-generator > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > Get the Yahoo! toolbar and be alerted to new email > > wherever you're surfing. > > > > > > http://new.toolbar.yahoo.com/toolbar/features/mail/index.php > > > > > > > > > > > > -- > > What most experimenters take for granted before they > > begin their > > experiments is infinitely more interesting than any > > results to which > > their experiments lead. > > -- Norbert Wiener > > > > > > > > ___________________________________________________________________________________ > You snooze, you lose. Get messages ASAP with AutoCheck > in the all-new Yahoo! Mail Beta. > http://advision.webevents.yahoo.com/mailbeta/newmail_html.html > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From bsmith at mcs.anl.gov Sun Jun 17 11:21:21 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sun, 17 Jun 2007 11:21:21 -0500 (CDT) Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: <200706171633.02204.timothy.stitt@ichec.ie> References: <200706171633.02204.timothy.stitt@ichec.ie> Message-ID: Tim, It is possible the macros MatPreallocateInitialize(), ... in petscmat.h are exactly what you need. Barry Take a look at DAGetMatrix2d_MPIAIJ() in src/dm/da/utils/fdda.c for an example of how they can be used. On Sun, 17 Jun 2007, Tim Stitt wrote: > Hi All, > > Currently I am using MatCreateMPIAIJ to create a distributed sparse matrix for > use in my parallel sparse eigensolver. If I understand things correctly, it > is important to specify the correct pre-allocation values for (o_nz,d_nz) or > (o_nnz, d_nnz) respectively to obtain optimum memory usage per node. > > For information my matrix redistribution routine generates each row in the > sparse matrix (associated with a given node) "on-the-fly" and then uses > MatSetValues to apply the elements. > > My question is: does anyone have a standard code template for the calculating > the d_nz or d_nnz values (along with o_nz or o_nnz respectively) so that > optimum pre-allocation is obtained? Is there a simple way of determining if a > given non-zero value in a row is part of the diagonal or off-diagonal regions > for a given distributed topology? > > Any assistance gratefully received. > > Thanks in advance, > > Tim. > > From jinzishuai at yahoo.com Sun Jun 17 11:22:54 2007 From: jinzishuai at yahoo.com (Shi Jin) Date: Sun, 17 Jun 2007 09:22:54 -0700 (PDT) Subject: Is it possible to build one Petsc that works for both C and C++? In-Reply-To: Message-ID: <20070617162254.11975.qmail@web36207.mail.mud.yahoo.com> Great! Thanks a lot! Shi --- Matthew Knepley wrote: > This is an MPICH problem. From mpicxx.h: > > // There is a name conflict between stdio.h and the > MPI C++ binding > // with respect to the names SEEK_SET, SEEK_CUR, and > SEEK_END. MPI > // wants these in the MPI namespace, but stdio.h > will #define these > // to integer values. #undef'ing these can cause > obscure problems > // with other include files (such as iostream), so > we instead use > // #error to indicate a fatal error. Users can > either #undef > // the names before including mpi.h or include mpi.h > *before* stdio.h > // or iostream. > > #ifndef MPICH_IGNORE_CXX_SEEK > #ifdef SEEK_SET > #error "SEEK_SET is #defined but must not be for the > C++ binding of MPI" > //#undef SEEK_SET > #endif > #ifdef SEEK_CUR > #error "SEEK_CUR is #defined but must not be for the > C++ binding of MPI" > //#undef SEEK_CUR > #endif > #ifdef SEEK_END > //#undef SEEK_END > #error "SEEK_END is #defined but must not be for the > C++ binding of MPI" > #endif > #endif > > I recommend not including stdio.h yourself. PETSc > will do it. > > Matt > > On 6/17/07, Shi Jin wrote: > > But this is what I got trying to compile my C > petsc > > code with the C++ build: > > In file included from > > > /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpi.h:1104, > > from spAF_incl.h:20, > > from spAF_analyt.h:11, > > from spAF_analyt.c:11: > > > /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpicxx.h:26:2: > > error: #error "SEEK_SET is #defined but must not > be > > for the C++ binding of MPI" > > > /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpicxx.h:30:2: > > error: #error "SEEK_CUR is #defined but must not > be > > for the C++ binding of MPI" > > > /mnt/200g/works/MyWork/PETSc/C++PETSc/petsc-2.3.3-p3/externalpackages/mpich2-1.0.5p4/linux-gnu-cxx-debug/include/mpicxx.h:35:2: > > error: #error "SEEK_END is #defined but must not > be > > for the C++ binding of MPI" > > make: *** [spAF_analyt.o] Error 1 > > > > Did you do anything special? I am using GCC. > > Thanks. > > > > Shi > > --- Matthew Knepley wrote: > > > > > On 6/17/07, Shi Jin > wrote: > > > > Hi, > > > > > > > > I am learning the unstructured part of Petsc, > > > which > > > > naturally uses C++(at least the sample I am > > > studying > > > > is C++). On the other hand, my old Petsc codes > are > > > all > > > > written in C. > > > > I found that once I build the Petsc with C++, > the > > > old > > > > C codes cannot be compiled since it is trying > to > > > use > > > > mpicxx to compile the .c source files. > However, I > > > do > > > > > > This should be no problem. I do it all the time. > Any > > > C++ > > > compiler can compile C just fine. > > > > > > Matt > > > > > > > see after the configuration stage that there > is a > > > > list: > > > > C compiler: mpicc > > > > C++ compiler: mpicxx > > > > Fortran compiler: mpif77 > > > > > > > > Is it possible to instruct Petsc to use the > > > > corresponding compiler for different source > > > codes? > > > > Thanks a lot. > > > > PS. This is how I configured my > Petsc-2.3.3-p3: > > > > ./config/configure.py --with-cc=gcc > --with-fc=g77 > > > > --with-cxx=g++ --download-f-blas-lapack=1 > > > > --download-mpich=1 --with-clanguage=cxx > > > --with-sieve=1 > > > > --download-boost=1 --download-chaco > > > > --download-parmetis --download-fiat > > > --download-generator > > > > > > > > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > > Get the Yahoo! toolbar and be alerted to new > email > > > wherever you're surfing. > > > > > > > > > > http://new.toolbar.yahoo.com/toolbar/features/mail/index.php > > > > > > > > > > > > > > > > > -- > > > What most experimenters take for granted before > they > > > begin their > > > experiments is infinitely more interesting than > any > > > results to which > > > their experiments lead. > > > -- Norbert Wiener > > > > > > > > > > > > > > > ___________________________________________________________________________________ > > You snooze, you lose. Get messages ASAP with > AutoCheck > > in the all-new Yahoo! Mail Beta. > > > http://advision.webevents.yahoo.com/mailbeta/newmail_html.html > > > > > > > -- > What most experimenters take for granted before they > begin their > experiments is infinitely more interesting than any > results to which > their experiments lead. > -- Norbert Wiener > > ____________________________________________________________________________________ Food fight? Enjoy some healthy debate in the Yahoo! Answers Food & Drink Q&A. http://answers.yahoo.com/dir/?link=list&sid=396545367 From timothy.stitt at ichec.ie Sun Jun 17 11:28:13 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Sun, 17 Jun 2007 17:28:13 +0100 Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: References: <200706171633.02204.timothy.stitt@ichec.ie> Message-ID: <200706171728.13496.timothy.stitt@ichec.ie> Thanks for that Matt...will check it out. Incidentally, I need to pass a 64-bit integer to MatCreateMPIAIJ. Do I need to rebuild PETSc using a 64-bit integer option switch? Tim. On Sunday 17 June 2007 17:07, Matthew Knepley wrote: > On 6/17/07, Tim Stitt wrote: > > Hi All, > > > > Currently I am using MatCreateMPIAIJ to create a distributed sparse > > matrix for use in my parallel sparse eigensolver. If I understand things > > correctly, it is important to specify the correct pre-allocation values > > for (o_nz,d_nz) or (o_nnz, d_nnz) respectively to obtain optimum memory > > usage per node. > > > > For information my matrix redistribution routine generates each row in > > the sparse matrix (associated with a given node) "on-the-fly" and then > > uses MatSetValues to apply the elements. > > > > My question is: does anyone have a standard code template for the > > calculating the d_nz or d_nnz values (along with o_nz or o_nnz > > respectively) so that optimum pre-allocation is obtained? Is there a > > simple way of determining if a given non-zero value in a row is part of > > the diagonal or off-diagonal regions for a given distributed topology? > > > > Any assistance gratefully received. > > Basically, you run through the construction algorithm once to calculate > d_nnz and o_nnz, and then again to set values. You can see my code for > doing it in preallocateOperator() in src/dm/mesh/mesh.c. > > Matt > > > Thanks in advance, > > > > Tim. > > > > -- > > Dr. Timothy Stitt > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > Dublin Institute for Advanced Studies > > 5 Merrion Square - Dublin 2 - Ireland > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From bsmith at mcs.anl.gov Sun Jun 17 11:33:43 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sun, 17 Jun 2007 11:33:43 -0500 (CDT) Subject: Setting tolerances for multigrid In-Reply-To: <1182070060.3606.116.camel@iept0415.ivt.ntnu.no> References: <200706141301.37757.timothy.stitt@ichec.ie> <200706141409.08369.timothy.stitt@ichec.ie> <1181835970.3606.62.camel@iept0415.ivt.ntnu.no> <1181894796.3606.67.camel@iept0415.ivt.ntnu.no> <1181901771.3606.78.camel@iept0415.ivt.ntnu.no> <1181927340.3606.93.camel@iept0415.ivt.ntnu.no> <1181983629.3606.109.camel@iept0415.ivt.ntnu.no> <1182070060.3606.116.camel@iept0415.ivt.ntnu.no> Message-ID: Switching this to petsc-amint Something is funky here. The results should be the same in both cases. They are both using gmres and lu, on the same problem. The linear systems should be solved in a single iteration in both cases (with lu as a direct solve). When the -pc_type lu is used then the multigrid is NOT used, just LU. Are you using matrix-free anywhere? At the start of the third linear solve the residual norms are slightly different. This means something else in your code (not in the linear solve) is doing something different in the two cases. Is the other part of the code using nlevels somewhere? Barry On Sun, 17 Jun 2007, Knut Erik Teigen wrote: > Ok, I've attached two files, one with > ./run -dmmg_galerkin -dmmg_nlevels 1 -ksp_type gmres -pc_type lu > -ksp_truemonitor -ksp_converged_reason > lev1 > > and one with > > ./run -dmmg_galerkin -dmmg_nlevels 2 -ksp_type gmres -pc_type lu > -mg_levels_1_ksp_type gmres -mg_levels_1_pc_type lu > -ksp_converged_reason -ksp_truemonitor > lev2 > > The relative residual is 1.e-12, and I am using > KSPSetInitialGuessNonzero. > I've also printed the solution, and if you diff the two files, you can > see that there is a large difference in the third step, e.g. 71.7852 vs. > 70.9845. This shouldn't happen, even with a true residual of 1.e-5? > > -Knut Erik- > > On Sat, 2007-06-16 at 16:56 -0500, Barry Smith wrote: > > > > On Sat, 16 Jun 2007, Knut Erik Teigen wrote: > > > > > On Fri, 2007-06-15 at 14:30 -0500, Barry Smith wrote: > > > > What happens if you run the two level with -ksp_rtol 1.e-12 > > > > > > The exact same thing happens. At the third time step, the solution with > > > two levels begin to deviate from the one with one level. > > > > > > > > > > > BTW: when you just change -dmmg_nlevels from 1 to 2 you are now > > > > solving a NEW problem that has twice as many points in each direction, > > > > this can also effect the time-stepping. You can use -dmmg_nlevels 2 > > > > -pc_type lu to compare with the -dmmg_nlevels 2 > > > > > > I forgot to mention that I adjust the coarsest level according to the > > > number of levels, so that the finest level always contains the same > > > amount of points. I.e. with one level it is 65x129, with two 33x65 and > > > so on. > > > > > > > > > > > Always verify things with a direct solver before using multigrid > > > > or any other iterative linear solver. Multigrid is ONLY an optimization > > > > (faster, less memory), debug BEFORE turning on the optimizations. > > > > > > Yes, I've already done this. With a direct solver, I get the same > > > solution as with one level. Since multigrid is only an optimization as > > > you mention, I don't understand why the solution should be different > > > when running with two or more levels as opposed to only one. > > > Here's the output when running with -pc_type lu. As you can see, with > > > two levels, suddenly more iterations are needed for the third step. > > > > > > -dmmg_nlevels 1 > > > Start of time loop: > > > L-s reinit converged after 10 steps with norm 1.716E-09 > > > 0 KSP preconditioned resid norm 1.366287028032e+04 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 3.325862387561e+02 true resid norm 8.783238319618e-07 ||Ae||/||Ax|| 2.772187832207e-15 > > > 2 KSP preconditioned resid norm 4.237324220037e-10 true resid norm 9.365968491320e-07 ||Ae||/||Ax|| 2.956110598807e-15 > > > Linear solve converged due to CONVERGED_RTOL > > 0 KSP preconditioned resid norm 1.366743784848e+04 true resid norm 3.168385551957e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 3.578541063222e+02 true resid norm 3.047639475331e-06 ||Ae||/||Ax|| 9.618903461571e-15 > > > 2 KSP preconditioned resid norm 2.490853654289e-10 true resid norm 2.047397542219e-06 ||Ae||/||Ax|| 6.461958333808e-15 > > > Linear solve converged due to CONVERGED_RTOL > > > 0 KSP preconditioned resid norm 1.373641039770e+04 true resid norm 4.083933364397e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 2.756300642422e+02 true resid norm 1.333942531534e-06 ||Ae||/||Ax|| 3.266318062786e-15 > > > 2 KSP preconditioned resid norm 1.967864218276e-09 true resid norm 4.708778143639e-06 ||Ae||/||Ax|| 1.153000728339e-14 > > > Linear solve converged due to CONVERGED_RTOL > > > > > > -dmmg_nlevels 2 > > > Start of time loop: > > > L-s reinit converged after 10 steps with norm 1.716E-09 > > > 0 KSP preconditioned resid norm 1.366287028032e+04 true resid norm 3.168341703825e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 3.325862387561e+02 true resid norm 8.783238319618e-07 ||Ae||/||Ax|| 2.772187832207e-15 > > > 2 KSP preconditioned resid norm 4.237324220037e-10 true resid norm 9.365968491320e-07 ||Ae||/||Ax|| 2.956110598807e-15 > > > Linear solve converged due to CONVERGED_RTOL > > > 0 KSP preconditioned resid norm 1.366743784848e+04 true resid norm 3.168385551957e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 3.578541063222e+02 true resid norm 3.047639475331e-06 ||Ae||/||Ax|| 9.618903461571e-15 > > > 2 KSP preconditioned resid norm 2.490853654289e-10 true resid norm 2.047397542219e-06 ||Ae||/||Ax|| 6.461958333808e-15 > > > Linear solve converged due to CONVERGED_RTOL > > > 0 KSP preconditioned resid norm 1.373641039770e+04 true resid norm 4.083933364397e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 2.826990181167e+02 true resid norm 3.621921471554e+07 ||Ae||/||Ax|| 8.868708542429e-02 > > > 2 KSP preconditioned resid norm 2.151728459050e+02 true resid norm 5.126312558070e+05 ||Ae||/||Ax|| 1.255239030774e-03 > > > 3 KSP preconditioned resid norm 9.420491033127e+01 true resid norm 7.221320422298e+02 ||Ae||/||Ax|| 1.768226799500e-06 > > > (...) > > > 118 KSP preconditioned resid norm 2.011348229632e-04 true resid norm 1.933530019765e-05 ||Ae||/||Ax|| 4.734479843920e-14 > > > 119 KSP preconditioned resid norm 1.002113384828e-04 true resid norm 1.933774400466e-05 ||Ae||/||Ax|| 4.735078239337e-14 > > > 120 KSP preconditioned resid norm 3.976002405523e-07 true resid norm 1.947236185243e-05 ||Ae||/||Ax|| 4.768041031762e-14 > > > Linear solve converged due to CONVERGED_RTOL > > > > > > > > > > The true residuals both me, they are very big at "convergence" 1.e-5? Are you using KSPSetInitialGuessNonzero() and > > using the previous solution as initial guess? > > > > Run with -ksp_type gmres -pc_type lu -ksp_monitor_true_residual. I bet the converged true residual is > > much better. Send the output. > > > > Barry > > > > > > > > > > > > > > > > > > > Barry > > > > > > > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > > > > > > > When running with those options I get this after the first timestep for > > > > > both one and two levels: > > > > > 159 KSP preconditioned resid norm 1.397494864058e-07 true resid norm > > > > > 4.996893774970e-02 ||Ae||/||Ax|| 1.577132216812e-10 > > > > > Linear solve converged due to CONVERGED_RTOL > > > > > > > > > > However, after the second timestep they start to get different. > > > > > With two levels the norm is actually lower, but still, the computation > > > > > diverges after about 6 time steps. With one level the computation runs > > > > > smoothly. Here are the numbers: > > > > > > > > > > -dmmg_nlevels 1 > > > > > 0 KSP preconditioned resid norm 1.674785901465e+02 > > > > > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > > > 1 KSP preconditioned resid norm 6.256839347623e+01 > > > > > true resid norm 4.220478752135e+07 ||Ae||/||Ax|| 1.033434774147e-01 > > > > > (...) > > > > > 159 KSP preconditioned resid norm 1.318896741223e-07 > > > > > true resid norm 5.104451971417e-02 ||Ae||/||Ax|| 1.249886204866e-10 > > > > > Linear solve converged due to CONVERGED_RTOL > > > > > > > > > > -dmmg_nlevels 2 > > > > > 0 KSP preconditioned resid norm 1.674785901465e+02 > > > > > true resid norm 4.083933362528e+08 ||Ae||/||Ax|| 1.000000000000e+00 > > > > > 1 KSP preconditioned resid norm 6.252455641723e+01 > > > > > true resid norm 5.561545924132e+07 ||Ae||/||Ax|| 1.361811134129e-01 > > > > > (...) > > > > > 159 KSP preconditioned resid norm 1.305901659826e-07 > > > > > true resid norm 4.297164043386e-02 ||Ae||/||Ax|| 1.052212086224e-10 > > > > > Linear solve converged due to CONVERGED_RTOL > > > > > > > > > > -Knut Erik- > > > > > > > > > > On Fri, 2007-06-15 at 10:10 -0500, Barry Smith wrote: > > > > > > You need to make sure the linear solvers are converging properly > > > > > > before even worrying about time-stepping. Run with -ksp_monitor_true_residual > > > > > > (-ksp_truemonitor on older versions of PETSc) and -ksp_converged_reason > > > > > > > > > > > > Barry > > > > > > > > > > > > > > > > > > On Fri, 15 Jun 2007, Knut Erik Teigen wrote: > > > > > > > > > > > > > The computation runs just fine with -dmmg_nlevels 1. > > > > > > > I use a grid of 65x129, with three levels, so that the coarsest grid is > > > > > > > 17x33. > > > > > > > I've diffed the solutions, and they are equal for the first two time > > > > > > > steps, but then they start to differ somewhat. Here is an excerpt: > > > > > > > -dmmg_nlevels 1: > > > > > > > 65.0427492820557 65.0216231814457 64.9793945321386 > > > > > > > -dmmg_nlevels 3: > > > > > > > 65.0920864319067 65.0711253401585 65.0292265582817 > > > > > > > > > > > > > > Using 2 or 4 levels produce the same result as 3 levels. > > > > > > > > > > > > > > -Knut Erik- > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Fri, 2007-06-15 at 10:21 +0200, Matthew Knepley wrote: > > > > > > > > This does not sound right to me. I think something must be > > > > > > > > configured incorrectly. All MG does is accelerate the solution > > > > > > > > of the fine grid problem. I think something must be wrong with > > > > > > > > the specification here. It is easy to check. Run with -dmmg_nlevels 1 > > > > > > > > which just solves on the fine grid. > > > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > > On 6/15/07, Knut Erik Teigen wrote: > > > > > > > > > Thanks, Matthew. It seems like the tolerances weren't my problem, > > > > > > > > > though. Even with a tolerance of 1e-10, the computation diverges after > > > > > > > > > only a few time steps when using multigrid. With ordinary linear > > > > > > > > > solvers, I can use a tolerance of 1e-4 and still get a satisfactory > > > > > > > > > solution. > > > > > > > > > Could it be that the Galerkin approximation for the coarser levels is > > > > > > > > > too inaccurate for my problem? > > > > > > > > > > > > > > > > > > -Knut Erik- > > > > > > > > > > > > > > > > > > On Thu, 2007-06-14 at 11:32 -0500, Matthew Knepley wrote: > > > > > > > > > > On 6/14/07, Knut Erik Teigen wrote: > > > > > > > > > > > Hello, > > > > > > > > > > > > > > > > > > > > > > How do I set the tolerances for the KSP solvers when using the > > > > > > > > > > > DMMG routines without using command line arguments? It seems that > > > > > > > > > > > I can use the argument -ksp_rtol on the command line, but in the code I > > > > > > > > > > > can't use KSPSetTolerances since I don't have access to the KSP solver > > > > > > > > > > > context? > > > > > > > > > > > > > > > > > > > > You can use DMMGGetKSP() for the finest level, and dmmg[level]->ksp for > > > > > > > > > > any others. > > > > > > > > > > > > > > > > > > > > > Also, I see there is a reference to the function DMMGSetUseGalerkin > > > > > > > > > > > in the source code, but I can't find the documentation for it. > > > > > > > > > > > Does this function not exist yet? Again I would like to use > > > > > > > > > > > -dmmg_galerkin, but setting it in the code instead of on the command > > > > > > > > > > > line. > > > > > > > > > > > > > > > > > > > > I think you want this: > > > > > > > > > > > > > > > > > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DA/DMMGSetUseGalerkinCoarse.html > > > > > > > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > > > Knut Erik Teigen > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From bsmith at mcs.anl.gov Sun Jun 17 11:36:04 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Sun, 17 Jun 2007 11:36:04 -0500 (CDT) Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: <200706171728.13496.timothy.stitt@ichec.ie> References: <200706171633.02204.timothy.stitt@ichec.ie> <200706171728.13496.timothy.stitt@ichec.ie> Message-ID: If your problem is so big that you need integers that represent numbers more than about 2 billion then yes you will need to rebuild PETSc. Barry You'll be the first PETSc user who solves a problem with more than 2 billion unknowns. On Sun, 17 Jun 2007, Tim Stitt wrote: > Thanks for that Matt...will check it out. > > Incidentally, I need to pass a 64-bit integer to MatCreateMPIAIJ. Do I need to > rebuild PETSc using a 64-bit integer option switch? > > Tim. > > On Sunday 17 June 2007 17:07, Matthew Knepley wrote: > > On 6/17/07, Tim Stitt wrote: > > > Hi All, > > > > > > Currently I am using MatCreateMPIAIJ to create a distributed sparse > > > matrix for use in my parallel sparse eigensolver. If I understand things > > > correctly, it is important to specify the correct pre-allocation values > > > for (o_nz,d_nz) or (o_nnz, d_nnz) respectively to obtain optimum memory > > > usage per node. > > > > > > For information my matrix redistribution routine generates each row in > > > the sparse matrix (associated with a given node) "on-the-fly" and then > > > uses MatSetValues to apply the elements. > > > > > > My question is: does anyone have a standard code template for the > > > calculating the d_nz or d_nnz values (along with o_nz or o_nnz > > > respectively) so that optimum pre-allocation is obtained? Is there a > > > simple way of determining if a given non-zero value in a row is part of > > > the diagonal or off-diagonal regions for a given distributed topology? > > > > > > Any assistance gratefully received. > > > > Basically, you run through the construction algorithm once to calculate > > d_nnz and o_nnz, and then again to set values. You can see my code for > > doing it in preallocateOperator() in src/dm/mesh/mesh.c. > > > > Matt > > > > > Thanks in advance, > > > > > > Tim. > > > > > > -- > > > Dr. Timothy Stitt > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > Dublin Institute for Advanced Studies > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > From timothy.stitt at ichec.ie Sun Jun 17 11:48:08 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Sun, 17 Jun 2007 17:48:08 +0100 Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: References: <200706171633.02204.timothy.stitt@ichec.ie> <200706171728.13496.timothy.stitt@ichec.ie> Message-ID: <200706171748.08649.timothy.stitt@ichec.ie> Actually my sparse matrix has >2^32 rows and columns hence the global row and column arguments need to be 64-bit. On Sunday 17 June 2007 17:36, Barry Smith wrote: > If your problem is so big that you need integers that represent numbers > more than about 2 billion then yes you will need to rebuild PETSc. > > Barry > > You'll be the first PETSc user who solves a problem with more than > 2 billion unknowns. > > On Sun, 17 Jun 2007, Tim Stitt wrote: > > Thanks for that Matt...will check it out. > > > > Incidentally, I need to pass a 64-bit integer to MatCreateMPIAIJ. Do I > > need to rebuild PETSc using a 64-bit integer option switch? > > > > Tim. > > > > On Sunday 17 June 2007 17:07, Matthew Knepley wrote: > > > On 6/17/07, Tim Stitt wrote: > > > > Hi All, > > > > > > > > Currently I am using MatCreateMPIAIJ to create a distributed sparse > > > > matrix for use in my parallel sparse eigensolver. If I understand > > > > things correctly, it is important to specify the correct > > > > pre-allocation values for (o_nz,d_nz) or (o_nnz, d_nnz) respectively > > > > to obtain optimum memory usage per node. > > > > > > > > For information my matrix redistribution routine generates each row > > > > in the sparse matrix (associated with a given node) "on-the-fly" and > > > > then uses MatSetValues to apply the elements. > > > > > > > > My question is: does anyone have a standard code template for the > > > > calculating the d_nz or d_nnz values (along with o_nz or o_nnz > > > > respectively) so that optimum pre-allocation is obtained? Is there a > > > > simple way of determining if a given non-zero value in a row is part > > > > of the diagonal or off-diagonal regions for a given distributed > > > > topology? > > > > > > > > Any assistance gratefully received. > > > > > > Basically, you run through the construction algorithm once to calculate > > > d_nnz and o_nnz, and then again to set values. You can see my code for > > > doing it in preallocateOperator() in src/dm/mesh/mesh.c. > > > > > > Matt > > > > > > > Thanks in advance, > > > > > > > > Tim. > > > > > > > > -- > > > > Dr. Timothy Stitt > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > Dublin Institute for Advanced Studies > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From knepley at gmail.com Sun Jun 17 11:54:03 2007 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 17 Jun 2007 11:54:03 -0500 Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: <200706171748.08649.timothy.stitt@ichec.ie> References: <200706171633.02204.timothy.stitt@ichec.ie> <200706171728.13496.timothy.stitt@ichec.ie> <200706171748.08649.timothy.stitt@ichec.ie> Message-ID: On 6/17/07, Tim Stitt wrote: > Actually my sparse matrix has >2^32 rows and columns hence the global row and > column arguments need to be 64-bit. Cool. What problem is that big? Matt > On Sunday 17 June 2007 17:36, Barry Smith wrote: > > If your problem is so big that you need integers that represent numbers > > more than about 2 billion then yes you will need to rebuild PETSc. > > > > Barry > > > > You'll be the first PETSc user who solves a problem with more than > > 2 billion unknowns. > > > > On Sun, 17 Jun 2007, Tim Stitt wrote: > > > Thanks for that Matt...will check it out. > > > > > > Incidentally, I need to pass a 64-bit integer to MatCreateMPIAIJ. Do I > > > need to rebuild PETSc using a 64-bit integer option switch? > > > > > > Tim. > > > > > > On Sunday 17 June 2007 17:07, Matthew Knepley wrote: > > > > On 6/17/07, Tim Stitt wrote: > > > > > Hi All, > > > > > > > > > > Currently I am using MatCreateMPIAIJ to create a distributed sparse > > > > > matrix for use in my parallel sparse eigensolver. If I understand > > > > > things correctly, it is important to specify the correct > > > > > pre-allocation values for (o_nz,d_nz) or (o_nnz, d_nnz) respectively > > > > > to obtain optimum memory usage per node. > > > > > > > > > > For information my matrix redistribution routine generates each row > > > > > in the sparse matrix (associated with a given node) "on-the-fly" and > > > > > then uses MatSetValues to apply the elements. > > > > > > > > > > My question is: does anyone have a standard code template for the > > > > > calculating the d_nz or d_nnz values (along with o_nz or o_nnz > > > > > respectively) so that optimum pre-allocation is obtained? Is there a > > > > > simple way of determining if a given non-zero value in a row is part > > > > > of the diagonal or off-diagonal regions for a given distributed > > > > > topology? > > > > > > > > > > Any assistance gratefully received. > > > > > > > > Basically, you run through the construction algorithm once to calculate > > > > d_nnz and o_nnz, and then again to set values. You can see my code for > > > > doing it in preallocateOperator() in src/dm/mesh/mesh.c. > > > > > > > > Matt > > > > > > > > > Thanks in advance, > > > > > > > > > > Tim. > > > > > > > > > > -- > > > > > Dr. Timothy Stitt > > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > > > Dublin Institute for Advanced Studies > > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > -- > Dr. Timothy Stitt > HPC Application Consultant - ICHEC (www.ichec.ie) > > Dublin Institute for Advanced Studies > 5 Merrion Square - Dublin 2 - Ireland > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From timothy.stitt at ichec.ie Sun Jun 17 12:12:17 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Sun, 17 Jun 2007 18:12:17 +0100 Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: References: <200706171633.02204.timothy.stitt@ichec.ie> <200706171748.08649.timothy.stitt@ichec.ie> Message-ID: <200706171812.17341.timothy.stitt@ichec.ie> Matt, We are investigating 32-qubit fault-tolerant quantum computation which results in 2^32 basis states and hence our large Hamiltonian matrix. I just ran into problems passing 2^32 in as the global row an column argument so I assumed I need to rebuild PETSc to accept 64-bit integers. Tim. On Sunday 17 June 2007 17:54, Matthew Knepley wrote: > On 6/17/07, Tim Stitt wrote: > > Actually my sparse matrix has >2^32 rows and columns hence the global row > > and column arguments need to be 64-bit. > > Cool. What problem is that big? > > Matt > > > On Sunday 17 June 2007 17:36, Barry Smith wrote: > > > If your problem is so big that you need integers that represent > > > numbers more than about 2 billion then yes you will need to rebuild > > > PETSc. > > > > > > Barry > > > > > > You'll be the first PETSc user who solves a problem with more than > > > 2 billion unknowns. > > > > > > On Sun, 17 Jun 2007, Tim Stitt wrote: > > > > Thanks for that Matt...will check it out. > > > > > > > > Incidentally, I need to pass a 64-bit integer to MatCreateMPIAIJ. Do > > > > I need to rebuild PETSc using a 64-bit integer option switch? > > > > > > > > Tim. > > > > > > > > On Sunday 17 June 2007 17:07, Matthew Knepley wrote: > > > > > On 6/17/07, Tim Stitt wrote: > > > > > > Hi All, > > > > > > > > > > > > Currently I am using MatCreateMPIAIJ to create a distributed > > > > > > sparse matrix for use in my parallel sparse eigensolver. If I > > > > > > understand things correctly, it is important to specify the > > > > > > correct pre-allocation values for (o_nz,d_nz) or (o_nnz, d_nnz) > > > > > > respectively to obtain optimum memory usage per node. > > > > > > > > > > > > For information my matrix redistribution routine generates each > > > > > > row in the sparse matrix (associated with a given node) > > > > > > "on-the-fly" and then uses MatSetValues to apply the elements. > > > > > > > > > > > > My question is: does anyone have a standard code template for the > > > > > > calculating the d_nz or d_nnz values (along with o_nz or o_nnz > > > > > > respectively) so that optimum pre-allocation is obtained? Is > > > > > > there a simple way of determining if a given non-zero value in a > > > > > > row is part of the diagonal or off-diagonal regions for a given > > > > > > distributed topology? > > > > > > > > > > > > Any assistance gratefully received. > > > > > > > > > > Basically, you run through the construction algorithm once to > > > > > calculate d_nnz and o_nnz, and then again to set values. You can > > > > > see my code for doing it in preallocateOperator() in > > > > > src/dm/mesh/mesh.c. > > > > > > > > > > Matt > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > Tim. > > > > > > > > > > > > -- > > > > > > Dr. Timothy Stitt > > > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > > > > > Dublin Institute for Advanced Studies > > > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 > > > > > > (mobile) > > > > -- > > Dr. Timothy Stitt > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > Dublin Institute for Advanced Studies > > 5 Merrion Square - Dublin 2 - Ireland > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From knepley at gmail.com Sun Jun 17 12:16:37 2007 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 17 Jun 2007 12:16:37 -0500 Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: <200706171812.17341.timothy.stitt@ichec.ie> References: <200706171633.02204.timothy.stitt@ichec.ie> <200706171748.08649.timothy.stitt@ichec.ie> <200706171812.17341.timothy.stitt@ichec.ie> Message-ID: On 6/17/07, Tim Stitt wrote: > Matt, > > We are investigating 32-qubit fault-tolerant quantum computation which results > in 2^32 basis states and hence our large Hamiltonian matrix. > > I just ran into problems passing 2^32 in as the global row an column argument > so I assumed I need to rebuild PETSc to accept 64-bit integers. Yes, reconfigure with --with-64-bit-indices and rebuild. You can do this in another arch if you want to keep your old build using --PETSC_ARCH= Matt > Tim. > > On Sunday 17 June 2007 17:54, Matthew Knepley wrote: > > On 6/17/07, Tim Stitt wrote: > > > Actually my sparse matrix has >2^32 rows and columns hence the global row > > > and column arguments need to be 64-bit. > > > > Cool. What problem is that big? > > > > Matt > > > > > On Sunday 17 June 2007 17:36, Barry Smith wrote: > > > > If your problem is so big that you need integers that represent > > > > numbers more than about 2 billion then yes you will need to rebuild > > > > PETSc. > > > > > > > > Barry > > > > > > > > You'll be the first PETSc user who solves a problem with more than > > > > 2 billion unknowns. > > > > > > > > On Sun, 17 Jun 2007, Tim Stitt wrote: > > > > > Thanks for that Matt...will check it out. > > > > > > > > > > Incidentally, I need to pass a 64-bit integer to MatCreateMPIAIJ. Do > > > > > I need to rebuild PETSc using a 64-bit integer option switch? > > > > > > > > > > Tim. > > > > > > > > > > On Sunday 17 June 2007 17:07, Matthew Knepley wrote: > > > > > > On 6/17/07, Tim Stitt wrote: > > > > > > > Hi All, > > > > > > > > > > > > > > Currently I am using MatCreateMPIAIJ to create a distributed > > > > > > > sparse matrix for use in my parallel sparse eigensolver. If I > > > > > > > understand things correctly, it is important to specify the > > > > > > > correct pre-allocation values for (o_nz,d_nz) or (o_nnz, d_nnz) > > > > > > > respectively to obtain optimum memory usage per node. > > > > > > > > > > > > > > For information my matrix redistribution routine generates each > > > > > > > row in the sparse matrix (associated with a given node) > > > > > > > "on-the-fly" and then uses MatSetValues to apply the elements. > > > > > > > > > > > > > > My question is: does anyone have a standard code template for the > > > > > > > calculating the d_nz or d_nnz values (along with o_nz or o_nnz > > > > > > > respectively) so that optimum pre-allocation is obtained? Is > > > > > > > there a simple way of determining if a given non-zero value in a > > > > > > > row is part of the diagonal or off-diagonal regions for a given > > > > > > > distributed topology? > > > > > > > > > > > > > > Any assistance gratefully received. > > > > > > > > > > > > Basically, you run through the construction algorithm once to > > > > > > calculate d_nnz and o_nnz, and then again to set values. You can > > > > > > see my code for doing it in preallocateOperator() in > > > > > > src/dm/mesh/mesh.c. > > > > > > > > > > > > Matt > > > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > > > Tim. > > > > > > > > > > > > > > -- > > > > > > > Dr. Timothy Stitt > > > > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > > > > > > > Dublin Institute for Advanced Studies > > > > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 > > > > > > > (mobile) > > > > > > -- > > > Dr. Timothy Stitt > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > Dublin Institute for Advanced Studies > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > -- > Dr. Timothy Stitt > HPC Application Consultant - ICHEC (www.ichec.ie) > > Dublin Institute for Advanced Studies > 5 Merrion Square - Dublin 2 - Ireland > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From timothy.stitt at ichec.ie Sun Jun 17 12:27:57 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Sun, 17 Jun 2007 18:27:57 +0100 Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: References: <200706171633.02204.timothy.stitt@ichec.ie> <200706171812.17341.timothy.stitt@ichec.ie> Message-ID: <200706171827.57347.timothy.stitt@ichec.ie> Cheers...perfect. On Sunday 17 June 2007 18:16, Matthew Knepley wrote: > On 6/17/07, Tim Stitt wrote: > > Matt, > > > > We are investigating 32-qubit fault-tolerant quantum computation which > > results in 2^32 basis states and hence our large Hamiltonian matrix. > > > > I just ran into problems passing 2^32 in as the global row an column > > argument so I assumed I need to rebuild PETSc to accept 64-bit integers. > > Yes, reconfigure with --with-64-bit-indices and rebuild. You can do > this in another > arch if you want to keep your old build using --PETSC_ARCH= > > Matt > > > Tim. > > > > On Sunday 17 June 2007 17:54, Matthew Knepley wrote: > > > On 6/17/07, Tim Stitt wrote: > > > > Actually my sparse matrix has >2^32 rows and columns hence the global > > > > row and column arguments need to be 64-bit. > > > > > > Cool. What problem is that big? > > > > > > Matt > > > > > > > On Sunday 17 June 2007 17:36, Barry Smith wrote: > > > > > If your problem is so big that you need integers that represent > > > > > numbers more than about 2 billion then yes you will need to rebuild > > > > > PETSc. > > > > > > > > > > Barry > > > > > > > > > > You'll be the first PETSc user who solves a problem with more than > > > > > 2 billion unknowns. > > > > > > > > > > On Sun, 17 Jun 2007, Tim Stitt wrote: > > > > > > Thanks for that Matt...will check it out. > > > > > > > > > > > > Incidentally, I need to pass a 64-bit integer to MatCreateMPIAIJ. > > > > > > Do I need to rebuild PETSc using a 64-bit integer option switch? > > > > > > > > > > > > Tim. > > > > > > > > > > > > On Sunday 17 June 2007 17:07, Matthew Knepley wrote: > > > > > > > On 6/17/07, Tim Stitt wrote: > > > > > > > > Hi All, > > > > > > > > > > > > > > > > Currently I am using MatCreateMPIAIJ to create a distributed > > > > > > > > sparse matrix for use in my parallel sparse eigensolver. If I > > > > > > > > understand things correctly, it is important to specify the > > > > > > > > correct pre-allocation values for (o_nz,d_nz) or (o_nnz, > > > > > > > > d_nnz) respectively to obtain optimum memory usage per node. > > > > > > > > > > > > > > > > For information my matrix redistribution routine generates > > > > > > > > each row in the sparse matrix (associated with a given node) > > > > > > > > "on-the-fly" and then uses MatSetValues to apply the > > > > > > > > elements. > > > > > > > > > > > > > > > > My question is: does anyone have a standard code template for > > > > > > > > the calculating the d_nz or d_nnz values (along with o_nz or > > > > > > > > o_nnz respectively) so that optimum pre-allocation is > > > > > > > > obtained? Is there a simple way of determining if a given > > > > > > > > non-zero value in a row is part of the diagonal or > > > > > > > > off-diagonal regions for a given distributed topology? > > > > > > > > > > > > > > > > Any assistance gratefully received. > > > > > > > > > > > > > > Basically, you run through the construction algorithm once to > > > > > > > calculate d_nnz and o_nnz, and then again to set values. You > > > > > > > can see my code for doing it in preallocateOperator() in > > > > > > > src/dm/mesh/mesh.c. > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > > > > > Tim. > > > > > > > > > > > > > > > > -- > > > > > > > > Dr. Timothy Stitt > > > > > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > > > > > > > > > Dublin Institute for Advanced Studies > > > > > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 > > > > > > > > (mobile) > > > > > > > > -- > > > > Dr. Timothy Stitt > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > Dublin Institute for Advanced Studies > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > > > -- > > Dr. Timothy Stitt > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > Dublin Institute for Advanced Studies > > 5 Merrion Square - Dublin 2 - Ireland > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From timothy.stitt at ichec.ie Sun Jun 17 12:50:01 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Sun, 17 Jun 2007 18:50:01 +0100 Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: <200706171827.57347.timothy.stitt@ichec.ie> References: <200706171633.02204.timothy.stitt@ichec.ie> <200706171827.57347.timothy.stitt@ichec.ie> Message-ID: <200706171850.01431.timothy.stitt@ichec.ie> Matt, I am getting a lot of warnings regarding incompatible pointer types when compiling with that option. Here is an example: ziscoloringf90.c: In function `iscoloringgetisf90_': ziscoloringf90.c:20: warning: passing arg 2 of `ISColoringGetIS' from incompatible pointer type Is this a problem? Tim. On Sunday 17 June 2007 18:27, Tim Stitt wrote: > Cheers...perfect. > > On Sunday 17 June 2007 18:16, Matthew Knepley wrote: > > On 6/17/07, Tim Stitt wrote: > > > Matt, > > > > > > We are investigating 32-qubit fault-tolerant quantum computation which > > > results in 2^32 basis states and hence our large Hamiltonian matrix. > > > > > > I just ran into problems passing 2^32 in as the global row an column > > > argument so I assumed I need to rebuild PETSc to accept 64-bit > > > integers. > > > > Yes, reconfigure with --with-64-bit-indices and rebuild. You can do > > this in another > > arch if you want to keep your old build using --PETSC_ARCH= > name> > > > > Matt > > > > > Tim. > > > > > > On Sunday 17 June 2007 17:54, Matthew Knepley wrote: > > > > On 6/17/07, Tim Stitt wrote: > > > > > Actually my sparse matrix has >2^32 rows and columns hence the > > > > > global row and column arguments need to be 64-bit. > > > > > > > > Cool. What problem is that big? > > > > > > > > Matt > > > > > > > > > On Sunday 17 June 2007 17:36, Barry Smith wrote: > > > > > > If your problem is so big that you need integers that represent > > > > > > numbers more than about 2 billion then yes you will need to > > > > > > rebuild PETSc. > > > > > > > > > > > > Barry > > > > > > > > > > > > You'll be the first PETSc user who solves a problem with more > > > > > > than 2 billion unknowns. > > > > > > > > > > > > On Sun, 17 Jun 2007, Tim Stitt wrote: > > > > > > > Thanks for that Matt...will check it out. > > > > > > > > > > > > > > Incidentally, I need to pass a 64-bit integer to > > > > > > > MatCreateMPIAIJ. Do I need to rebuild PETSc using a 64-bit > > > > > > > integer option switch? > > > > > > > > > > > > > > Tim. > > > > > > > > > > > > > > On Sunday 17 June 2007 17:07, Matthew Knepley wrote: > > > > > > > > On 6/17/07, Tim Stitt wrote: > > > > > > > > > Hi All, > > > > > > > > > > > > > > > > > > Currently I am using MatCreateMPIAIJ to create a > > > > > > > > > distributed sparse matrix for use in my parallel sparse > > > > > > > > > eigensolver. If I understand things correctly, it is > > > > > > > > > important to specify the correct pre-allocation values for > > > > > > > > > (o_nz,d_nz) or (o_nnz, d_nnz) respectively to obtain > > > > > > > > > optimum memory usage per node. > > > > > > > > > > > > > > > > > > For information my matrix redistribution routine generates > > > > > > > > > each row in the sparse matrix (associated with a given > > > > > > > > > node) "on-the-fly" and then uses MatSetValues to apply the > > > > > > > > > elements. > > > > > > > > > > > > > > > > > > My question is: does anyone have a standard code template > > > > > > > > > for the calculating the d_nz or d_nnz values (along with > > > > > > > > > o_nz or o_nnz respectively) so that optimum pre-allocation > > > > > > > > > is obtained? Is there a simple way of determining if a > > > > > > > > > given non-zero value in a row is part of the diagonal or > > > > > > > > > off-diagonal regions for a given distributed topology? > > > > > > > > > > > > > > > > > > Any assistance gratefully received. > > > > > > > > > > > > > > > > Basically, you run through the construction algorithm once to > > > > > > > > calculate d_nnz and o_nnz, and then again to set values. You > > > > > > > > can see my code for doing it in preallocateOperator() in > > > > > > > > src/dm/mesh/mesh.c. > > > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > > > > > > > Tim. > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Dr. Timothy Stitt > > > > > > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > > > > > > > > > > > Dublin Institute for Advanced Studies > > > > > > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > > > > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / > > > > > > > > > +353-874195427 (mobile) > > > > > > > > > > -- > > > > > Dr. Timothy Stitt > > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > > > Dublin Institute for Advanced Studies > > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 > > > > > (mobile) > > > > > > -- > > > Dr. Timothy Stitt > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > Dublin Institute for Advanced Studies > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From timothy.stitt at ichec.ie Sun Jun 17 12:55:23 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Sun, 17 Jun 2007 18:55:23 +0100 Subject: MatCreateMPIAIJ Pre-allocation Query In-Reply-To: <200706171827.57347.timothy.stitt@ichec.ie> References: <200706171633.02204.timothy.stitt@ichec.ie> <200706171827.57347.timothy.stitt@ichec.ie> Message-ID: <200706171855.23182.timothy.stitt@ichec.ie> Matt, Also at the end of the configure I get the following error: characteristic.c:253: error: conflicting types for `CharacteristicSetVelocityInterpolation' /ichec/home/staff/tstitt/builds/petsc/src/contrib/semiLagrange/characteristic.h:47: error: previous declaration of `CharacteristicSetVelocityInterpolation' characteristic.c:268: error: conflicting types for `CharacteristicSetVelocityInterpolationLocal' /ichec/home/staff/tstitt/builds/petsc/src/contrib/semiLagrange/characteristic.h:48: error: previous declaration of `CharacteristicSetVelocityInterpolationLocal' characteristic.c:283: error: conflicting types for `CharacteristicSetFieldInterpolation' /ichec/home/staff/tstitt/builds/petsc/src/contrib/semiLagrange/characteristic.h:49: error: previous declaration of `CharacteristicSetFieldInterpolation' characteristic.c:302: error: conflicting types for `CharacteristicSetFieldInterpolationLocal' /ichec/home/staff/tstitt/builds/petsc/src/contrib/semiLagrange/characteristic.h:50: error: previous declaration of `CharacteristicSetFieldInterpolationLocal'characteristic.c: In function `CharacteristicSolve': characteristic.c:347: warning: passing arg 2 of `DAGetNeighborsRank' from incompatible pointer type characteristic.c: At top level: characteristic.c:732: error: conflicting types for `HeapSort' characteristic.c:17: error: previous declaration of `HeapSort' characteristic.c:769: error: conflicting types for `SiftDown' characteristic.c:18: error: previous declaration of `SiftDown' /usr/bin/ar: 'characteristic.o': No such file This breaks the build. Tim. On Sunday 17 June 2007 18:27, Tim Stitt wrote: > Cheers...perfect. > > On Sunday 17 June 2007 18:16, Matthew Knepley wrote: > > On 6/17/07, Tim Stitt wrote: > > > Matt, > > > > > > We are investigating 32-qubit fault-tolerant quantum computation which > > > results in 2^32 basis states and hence our large Hamiltonian matrix. > > > > > > I just ran into problems passing 2^32 in as the global row an column > > > argument so I assumed I need to rebuild PETSc to accept 64-bit > > > integers. > > > > Yes, reconfigure with --with-64-bit-indices and rebuild. You can do > > this in another > > arch if you want to keep your old build using --PETSC_ARCH= > name> > > > > Matt > > > > > Tim. > > > > > > On Sunday 17 June 2007 17:54, Matthew Knepley wrote: > > > > On 6/17/07, Tim Stitt wrote: > > > > > Actually my sparse matrix has >2^32 rows and columns hence the > > > > > global row and column arguments need to be 64-bit. > > > > > > > > Cool. What problem is that big? > > > > > > > > Matt > > > > > > > > > On Sunday 17 June 2007 17:36, Barry Smith wrote: > > > > > > If your problem is so big that you need integers that represent > > > > > > numbers more than about 2 billion then yes you will need to > > > > > > rebuild PETSc. > > > > > > > > > > > > Barry > > > > > > > > > > > > You'll be the first PETSc user who solves a problem with more > > > > > > than 2 billion unknowns. > > > > > > > > > > > > On Sun, 17 Jun 2007, Tim Stitt wrote: > > > > > > > Thanks for that Matt...will check it out. > > > > > > > > > > > > > > Incidentally, I need to pass a 64-bit integer to > > > > > > > MatCreateMPIAIJ. Do I need to rebuild PETSc using a 64-bit > > > > > > > integer option switch? > > > > > > > > > > > > > > Tim. > > > > > > > > > > > > > > On Sunday 17 June 2007 17:07, Matthew Knepley wrote: > > > > > > > > On 6/17/07, Tim Stitt wrote: > > > > > > > > > Hi All, > > > > > > > > > > > > > > > > > > Currently I am using MatCreateMPIAIJ to create a > > > > > > > > > distributed sparse matrix for use in my parallel sparse > > > > > > > > > eigensolver. If I understand things correctly, it is > > > > > > > > > important to specify the correct pre-allocation values for > > > > > > > > > (o_nz,d_nz) or (o_nnz, d_nnz) respectively to obtain > > > > > > > > > optimum memory usage per node. > > > > > > > > > > > > > > > > > > For information my matrix redistribution routine generates > > > > > > > > > each row in the sparse matrix (associated with a given > > > > > > > > > node) "on-the-fly" and then uses MatSetValues to apply the > > > > > > > > > elements. > > > > > > > > > > > > > > > > > > My question is: does anyone have a standard code template > > > > > > > > > for the calculating the d_nz or d_nnz values (along with > > > > > > > > > o_nz or o_nnz respectively) so that optimum pre-allocation > > > > > > > > > is obtained? Is there a simple way of determining if a > > > > > > > > > given non-zero value in a row is part of the diagonal or > > > > > > > > > off-diagonal regions for a given distributed topology? > > > > > > > > > > > > > > > > > > Any assistance gratefully received. > > > > > > > > > > > > > > > > Basically, you run through the construction algorithm once to > > > > > > > > calculate d_nnz and o_nnz, and then again to set values. You > > > > > > > > can see my code for doing it in preallocateOperator() in > > > > > > > > src/dm/mesh/mesh.c. > > > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > > > > > > > Tim. > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Dr. Timothy Stitt > > > > > > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > > > > > > > > > > > Dublin Institute for Advanced Studies > > > > > > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > > > > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / > > > > > > > > > +353-874195427 (mobile) > > > > > > > > > > -- > > > > > Dr. Timothy Stitt > > > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > > > > > Dublin Institute for Advanced Studies > > > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 > > > > > (mobile) > > > > > > -- > > > Dr. Timothy Stitt > > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > > > Dublin Institute for Advanced Studies > > > 5 Merrion Square - Dublin 2 - Ireland > > > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From zonexo at gmail.com Sun Jun 17 21:40:44 2007 From: zonexo at gmail.com (Ben Tay) Date: Mon, 18 Jun 2007 10:40:44 +0800 Subject: KSPSetTolerances and processors size In-Reply-To: References: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> Message-ID: <804ab5d40706171940r69615610wb978e2c2582da265@mail.gmail.com> Yes, the no. of pt is always 64. Btw, here's the output with KSPSetTolerances = 1.0e-8 using 1 to 8 processors 1: 0 64 0 KSP preconditioned resid norm 5.509130713952e+01 true resid norm 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 6.561453237357e+00 true resid norm 8.697577384386e+00 ||Ae||/||Ax|| 2.549285554017e-01 2 KSP preconditioned resid norm 1.208347069756e+00 true resid norm 7.425376743449e+00 ||Ae||/||Ax|| 2.176399798315e-01 3 KSP preconditioned resid norm 3.386218089799e-01 true resid norm 7.347207820518e+00 ||Ae||/||Ax|| 2.153488256722e-01 4 KSP preconditioned resid norm 3.296482144730e-01 true resid norm 7.745880291985e+00 ||Ae||/||Ax|| 2.270340332579e-01 5 KSP preconditioned resid norm 3.145738742595e-01 true resid norm 7.547707467510e+00 ||Ae||/||Ax|| 2.212255293918e-01 6 KSP preconditioned resid norm 1.643048266097e-01 true resid norm 4.306709238860e+00 ||Ae||/||Ax|| 1.262309165273e-01 7 KSP preconditioned resid norm 6.078974689223e-02 true resid norm 4.482652283996e+00 ||Ae||/||Ax|| 1.313878590122e-01 8 KSP preconditioned resid norm 6.054372794034e-02 true resid norm 4.355614139989e+00 ||Ae||/||Ax|| 1.276643335865e-01 9 KSP preconditioned resid norm 5.867972436189e-02 true resid norm 4.233715997285e+00 ||Ae||/||Ax|| 1.240914631132e-01 10 KSP preconditioned resid norm 2.168073622951e-02 true resid norm 2.086394899960e+00 ||Ae||/||Ax|| 6.115284915993e-02 11 KSP preconditioned resid norm 1.139327427516e-02 true resid norm 2.155289979633e+00 ||Ae||/||Ax|| 6.317218424133e-02 12 KSP preconditioned resid norm 1.088027785149e-02 true resid norm 1.991898557592e+00 ||Ae||/||Ax|| 5.838313352696e-02 13 KSP preconditioned resid norm 1.072820075665e-02 true resid norm 1.942479796672e+00 ||Ae||/||Ax|| 5.693465508586e-02 14 KSP preconditioned resid norm 3.781319329677e-03 true resid norm 9.806622346091e-01 ||Ae||/||Ax|| 2.874349899487e-02 15 KSP preconditioned resid norm 2.314101409645e-03 true resid norm 7.976384924484e-01 ||Ae||/||Ax|| 2.337901919420e-02 16 KSP preconditioned resid norm 2.293131061139e-03 true resid norm 7.897410852774e-01 ||Ae||/||Ax|| 2.314754386348e-02 17 KSP preconditioned resid norm 2.117223511336e-03 true resid norm 6.782416967980e-01 ||Ae||/||Ax|| 1.987946393996e-02 18 KSP preconditioned resid norm 7.524359734379e-05 true resid norm 9.092345849564e-04 ||Ae||/||Ax|| 2.664993354130e-05 19 KSP preconditioned resid norm 5.494325808096e-07 true resid norm 7.001916128345e-06 ||Ae||/||Ax|| 2.052282244533e-07 2: 0 32 32 64 0 KSP preconditioned resid norm 4.902369798248e+01 true resid norm 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 8.253504641663e+00 true resid norm 1.259698849910e+01 ||Ae||/||Ax|| 3.692214439222e-01 2 KSP preconditioned resid norm 3.797891005886e+00 true resid norm 1.195333867118e+01 ||Ae||/||Ax|| 3.503558778495e-01 3 KSP preconditioned resid norm 2.578365901732e+00 true resid norm 1.159420670971e+01 ||Ae||/||Ax|| 3.398296142602e-01 4 KSP preconditioned resid norm 1.568196901288e+00 true resid norm 9.963750299049e+00 ||Ae||/||Ax|| 2.920404565390e-01 5 KSP preconditioned resid norm 1.317764005274e+00 true resid norm 9.066502566015e+00 ||Ae||/||Ax|| 2.657418611589e-01 6 KSP preconditioned resid norm 6.023727405584e-01 true resid norm 8.058099054033e+00 ||Ae||/||Ax|| 2.361852571517e-01 7 KSP preconditioned resid norm 4.957651340342e-02 true resid norm 7.520037445249e+00 ||Ae||/||Ax|| 2.204145128879e-01 8 KSP preconditioned resid norm 2.449473557300e-02 true resid norm 7.475057378184e+00 ||Ae||/||Ax|| 2.190961338713e-01 9 KSP preconditioned resid norm 2.361338376271e-02 true resid norm 7.217194046579e+00 ||Ae||/||Ax|| 2.115380836566e-01 10 KSP preconditioned resid norm 2.307344735925e-02 true resid norm 7.205616297960e+00 ||Ae||/||Ax|| 2.111987364338e-01 11 KSP preconditioned resid norm 1.934171008299e-02 true resid norm 5.261866236257e+00 ||Ae||/||Ax|| 1.542268495057e-01 12 KSP preconditioned resid norm 5.190847895073e-03 true resid norm 4.466349759791e+00 ||Ae||/||Ax|| 1.309100272251e-01 13 KSP preconditioned resid norm 4.871871781446e-03 true resid norm 4.194634080458e+00 ||Ae||/||Ax|| 1.229459606177e-01 14 KSP preconditioned resid norm 4.823921505423e-03 true resid norm 4.173223968428e+00 ||Ae||/||Ax|| 1.223184239268e-01 15 KSP preconditioned resid norm 4.701199647155e-03 true resid norm 3.957555688130e+00 ||Ae||/||Ax|| 1.159971230964e-01 16 KSP preconditioned resid norm 1.035300954721e-03 true resid norm 2.196668371922e+00 ||Ae||/||Ax|| 6.438499710918e-02 17 KSP preconditioned resid norm 8.832653700092e-04 true resid norm 1.916576324421e+00 ||Ae||/||Ax|| 5.617541668313e-02 18 KSP preconditioned resid norm 8.703924311133e-04 true resid norm 1.916104922195e+00 ||Ae||/||Ax|| 5.616159974502e-02 19 KSP preconditioned resid norm 8.698960956884e-04 true resid norm 1.913670720373e+00 ||Ae||/||Ax|| 5.609025257250e-02 20 KSP preconditioned resid norm 3.690946760360e-04 true resid norm 7.994885772359e-01 ||Ae||/||Ax|| 2.343324572435e-02 21 KSP preconditioned resid norm 2.023100555576e-04 true resid norm 8.179025108455e-01 ||Ae||/||Ax|| 2.397296354311e-02 22 KSP preconditioned resid norm 1.833817790776e-04 true resid norm 7.636868289475e-01 ||Ae||/||Ax|| 2.238388593499e-02 23 KSP preconditioned resid norm 1.833460480641e-04 true resid norm 7.634428328860e-01 ||Ae||/||Ax|| 2.237673433855e-02 24 KSP preconditioned resid norm 1.340284902298e-04 true resid norm 4.038942687674e-01 ||Ae||/||Ax|| 1.183826000292e-02 25 KSP preconditioned resid norm 1.120073985756e-06 true resid norm 6.289062400618e-04 ||Ae||/||Ax|| 1.843342716903e-05 26 KSP preconditioned resid norm 1.681823992311e-07 true resid norm 7.113523745896e-04 ||Ae||/||Ax|| 2.084994766028e-05 4: 16 32 48 64 0 16 32 48 0 KSP preconditioned resid norm 4.414786383499e+01 true resid norm 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 7.579678467669e+00 true resid norm 1.423835009315e+01 ||Ae||/||Ax|| 4.173302357811e-01 2 KSP preconditioned resid norm 2.972753009220e+00 true resid norm 1.290812750005e+01 ||Ae||/||Ax|| 3.783410197001e-01 3 KSP preconditioned resid norm 1.347960602345e+00 true resid norm 1.173368275935e+01 ||Ae||/||Ax|| 3.439176983641e-01 4 KSP preconditioned resid norm 1.111052862809e+00 true resid norm 1.106221549565e+01 ||Ae||/||Ax|| 3.242367950541e-01 5 KSP preconditioned resid norm 9.872224937494e-01 true resid norm 1.005157038653e+01 ||Ae||/||Ax|| 2.946144891744e-01 6 KSP preconditioned resid norm 7.251219493841e-01 true resid norm 9.007852893929e+00 ||Ae||/||Ax|| 2.640228219921e-01 7 KSP preconditioned resid norm 5.925185640664e-01 true resid norm 8.104036732737e+00 ||Ae||/||Ax|| 2.375317040476e-01 8 KSP preconditioned resid norm 3.381465672631e-01 true resid norm 7.256440004925e+00 ||Ae||/||Ax|| 2.126883942574e-01 9 KSP preconditioned resid norm 1.647154013552e-01 true resid norm 7.263797232535e+00 ||Ae||/||Ax|| 2.129040367661e-01 10 KSP preconditioned resid norm 7.697425793821e-02 true resid norm 7.155391777961e+00 ||Ae||/||Ax|| 2.097266409567e-01 11 KSP preconditioned resid norm 3.477770299629e-02 true resid norm 7.127853631055e+00 ||Ae||/||Ax|| 2.089194897583e-01 12 KSP preconditioned resid norm 2.573627666614e-02 true resid norm 7.088156599392e+00 ||Ae||/||Ax|| 2.077559580657e-01 13 KSP preconditioned resid norm 2.221352319865e-02 true resid norm 7.093825972365e+00 ||Ae||/||Ax|| 2.079221290577e-01 14 KSP preconditioned resid norm 2.093106984691e-02 true resid norm 7.062268285770e+00 ||Ae||/||Ax|| 2.069971639669e-01 15 KSP preconditioned resid norm 2.034509930217e-02 true resid norm 7.031405865561e+00 ||Ae||/||Ax|| 2.060925773386e-01 16 KSP preconditioned resid norm 2.029393080560e-02 true resid norm 7.008984378537e+00 ||Ae||/||Ax|| 2.054353969487e-01 17 KSP preconditioned resid norm 1.587358534265e-02 true resid norm 4.635842103718e+00 ||Ae||/||Ax|| 1.358778977572e-01 18 KSP preconditioned resid norm 1.055491860699e-02 true resid norm 3.773993858722e+00 ||Ae||/||Ax|| 1.106168718000e-01 19 KSP preconditioned resid norm 5.655638925006e-03 true resid norm 4.203919883144e+00 ||Ae||/||Ax|| 1.232181302299e-01 20 KSP preconditioned resid norm 4.767909232406e-03 true resid norm 4.121869307404e+00 ||Ae||/||Ax|| 1.208132036833e-01 21 KSP preconditioned resid norm 4.648572929978e-03 true resid norm 4.076834878296e+00 ||Ae||/||Ax|| 1.194932312992e-01 22 KSP preconditioned resid norm 4.638216815872e-03 true resid norm 4.058874907114e+00 ||Ae||/||Ax|| 1.189668192529e-01 23 KSP preconditioned resid norm 1.851801714075e-03 true resid norm 2.017702443794e+00 ||Ae||/||Ax|| 5.913945303323e-02 24 KSP preconditioned resid norm 9.594251508173e-04 true resid norm 2.065135975225e+00 ||Ae||/||Ax|| 6.052974381317e-02 25 KSP preconditioned resid norm 8.609050236229e-04 true resid norm 1.901663497990e+00 ||Ae||/||Ax|| 5.573831734719e-02 26 KSP preconditioned resid norm 8.607029066323e-04 true resid norm 1.901221069645e+00 ||Ae||/||Ax|| 5.572534964205e-02 27 KSP preconditioned resid norm 6.010429111401e-04 true resid norm 1.025962923033e+00 ||Ae||/||Ax|| 3.007127551793e-02 28 KSP preconditioned resid norm 2.036565987243e-04 true resid norm 8.385451121270e-01 ||Ae||/||Ax|| 2.457800426788e-02 29 KSP preconditioned resid norm 1.822673355787e-04 true resid norm 7.604317104951e-01 ||Ae||/||Ax|| 2.228847745421e-02 30 KSP preconditioned resid norm 1.821718775413e-04 true resid norm 7.603850665982e-01 ||Ae||/||Ax|| 2.228711030785e-02 31 KSP preconditioned resid norm 1.821716333573e-04 true resid norm 7.603829685457e-01 ||Ae||/||Ax|| 2.228704881332e-02 32 KSP preconditioned resid norm 1.821699115817e-04 true resid norm 7.603675572467e-01 ||Ae||/||Ax|| 2.228659710360e-02 33 KSP preconditioned resid norm 1.821688824892e-04 true resid norm 7.603562690023e-01 ||Ae||/||Ax|| 2.228626624183e-02 34 KSP preconditioned resid norm 1.821630228019e-04 true resid norm 7.603023835619e-01 ||Ae||/||Ax|| 2.228468684370e-02 35 KSP preconditioned resid norm 1.821590039577e-04 true resid norm 7.602690723682e-01 ||Ae||/||Ax|| 2.228371048280e-02 36 KSP preconditioned resid norm 1.821524946900e-04 true resid norm 7.602091695035e-01 ||Ae||/||Ax|| 2.228195471219e-02 37 KSP preconditioned resid norm 1.821431139881e-04 true resid norm 7.601164961025e-01 ||Ae||/||Ax|| 2.227923842750e-02 38 KSP preconditioned resid norm 1.819830193376e-04 true resid norm 7.586612864086e-01 ||Ae||/||Ax|| 2.223658580268e-02 39 KSP preconditioned resid norm 1.805931315815e-04 true resid norm 7.461275848519e-01 ||Ae||/||Ax|| 2.186921931768e-02 40 KSP preconditioned resid norm 1.797867614957e-04 true resid norm 7.389658088801e-01 ||Ae||/||Ax|| 2.165930555412e-02 41 KSP preconditioned resid norm 1.745605892795e-04 true resid norm 6.931550391508e-01 ||Ae||/||Ax|| 2.031657839772e-02 42 KSP preconditioned resid norm 1.178557773010e-04 true resid norm 2.926903648063e-01 ||Ae||/||Ax|| 8.578840817675e-03 43 KSP preconditioned resid norm 1.050152183416e-04 true resid norm 2.292356889576e-01 ||Ae||/||Ax|| 6.718965575103e-03 44 KSP preconditioned resid norm 1.029381823671e-04 true resid norm 2.202321585214e-01 ||Ae||/||Ax|| 6.455069445620e-03 45 KSP preconditioned resid norm 1.027399702486e-04 true resid norm 2.193939014098e-01 ||Ae||/||Ax|| 6.430499882731e-03 46 KSP preconditioned resid norm 1.025133937710e-04 true resid norm 2.184172674053e-01 ||Ae||/||Ax|| 6.401874452348e-03 47 KSP preconditioned resid norm 1.022602748747e-04 true resid norm 2.173181596557e-01 ||Ae||/||Ax|| 6.369659280415e-03 48 KSP preconditioned resid norm 1.015807260074e-04 true resid norm 2.146198575471e-01 ||Ae||/||Ax|| 6.290571250704e-03 49 KSP preconditioned resid norm 1.009993195316e-04 true resid norm 2.123571445648e-01 ||Ae||/||Ax|| 6.224250466607e-03 50 KSP preconditioned resid norm 8.525591342593e-05 true resid norm 1.568093042422e-01 ||Ae||/||Ax|| 4.596126902620e-03 51 KSP preconditioned resid norm 7.202973331289e-05 true resid norm 1.261481404121e-01 ||Ae||/||Ax|| 3.697439158127e-03 52 KSP preconditioned resid norm 7.198664751553e-05 true resid norm 1.260630320549e-01 ||Ae||/||Ax|| 3.694944607104e-03 53 KSP preconditioned resid norm 7.008311686197e-05 true resid norm 1.247964964786e-01 ||Ae||/||Ax|| 3.657822076247e-03 54 KSP preconditioned resid norm 4.135565734370e-05 true resid norm 4.973246177429e-02 ||Ae||/||Ax|| 1.457673105553e-03 55 KSP preconditioned resid norm 8.048037215745e-06 true resid norm 1.643447807384e-02 ||Ae||/||Ax|| 4.816993938640e-04 56 KSP preconditioned resid norm 8.026216400683e-06 true resid norm 1.641852860727e-02 ||Ae||/||Ax|| 4.812319103004e-04 57 KSP preconditioned resid norm 7.995005443726e-06 true resid norm 1.649949772958e-02 ||Ae||/||Ax|| 4.836051391283e-04 58 KSP preconditioned resid norm 6.919240358793e-06 true resid norm 1.238969532520e-02 ||Ae||/||Ax|| 3.631456199274e-04 59 KSP preconditioned resid norm 2.303987118188e-07 true resid norm 1.408145188438e-05 ||Ae||/||Ax|| 4.127315030605e-07 8: 0 8 8 16 48 56 40 48 16 24 24 32 56 64 32 40 0 KSP preconditioned resid norm 4.299803638671e+01 true resid norm 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 9.603727351867e+00 true resid norm 1.922897810349e+01 ||Ae||/||Ax|| 5.636070129797e-01 2 KSP preconditioned resid norm 2.931835632556e+00 true resid norm 1.355792423218e+01 ||Ae||/||Ax|| 3.973867533457e-01 3 KSP preconditioned resid norm 1.314351599619e+00 true resid norm 9.882281425137e+00 ||Ae||/||Ax|| 2.896525798443e-01 4 KSP preconditioned resid norm 8.218956530484e-01 true resid norm 9.318760482806e+00 ||Ae||/||Ax|| 2.731356150140e-01 5 KSP preconditioned resid norm 6.895693486764e-01 true resid norm 9.360126907217e+00 ||Ae||/||Ax|| 2.743480770998e-01 6 KSP preconditioned resid norm 6.138748402770e-01 true resid norm 9.020243051395e+00 ||Ae||/||Ax|| 2.643859811575e-01 7 KSP preconditioned resid norm 5.265342569996e-01 true resid norm 8.781477094899e+00 ||Ae||/||Ax|| 2.573876806333e-01 8 KSP preconditioned resid norm 4.403325671754e-01 true resid norm 8.314776073768e+00 ||Ae||/||Ax|| 2.437085362160e-01 9 KSP preconditioned resid norm 2.353592633657e-01 true resid norm 7.347976506279e+00 ||Ae||/||Ax|| 2.153713560783e-01 10 KSP preconditioned resid norm 8.943808926292e-02 true resid norm 6.972332890712e+00 ||Ae||/||Ax|| 2.043611310432e-01 11 KSP preconditioned resid norm 5.930469791557e-02 true resid norm 6.957386646797e+00 ||Ae||/||Ax|| 2.039230522310e-01 12 KSP preconditioned resid norm 5.283812047599e-02 true resid norm 6.981023245883e+00 ||Ae||/||Ax|| 2.046158479134e-01 13 KSP preconditioned resid norm 3.665176395384e-02 true resid norm 6.992078556546e+00 ||Ae||/||Ax|| 2.049398823258e-01 14 KSP preconditioned resid norm 2.516790937741e-02 true resid norm 6.949891196404e+00 ||Ae||/||Ax|| 2.037033583718e-01 15 KSP preconditioned resid norm 2.192690814272e-02 true resid norm 6.927621207906e+00 ||Ae||/||Ax|| 2.030506184483e-01 16 KSP preconditioned resid norm 2.058802964863e-02 true resid norm 6.919125260713e+00 ||Ae||/||Ax|| 2.028015997332e-01 17 KSP preconditioned resid norm 1.984533974458e-02 true resid norm 6.853733693988e+00 ||Ae||/||Ax|| 2.008849536484e-01 18 KSP preconditioned resid norm 1.958243371255e-02 true resid norm 6.766030769290e+00 ||Ae||/||Ax|| 1.983143550887e-01 19 KSP preconditioned resid norm 1.874262002187e-02 true resid norm 6.323230908702e+00 ||Ae||/||Ax|| 1.853357607281e-01 20 KSP preconditioned resid norm 1.754461572091e-02 true resid norm 5.538708901675e+00 ||Ae||/||Ax|| 1.623411895857e-01 21 KSP preconditioned resid norm 1.184321475064e-02 true resid norm 3.839931686898e+00 ||Ae||/||Ax|| 1.125495289688e-01 22 KSP preconditioned resid norm 1.070434172478e-02 true resid norm 3.754159266432e+00 ||Ae||/||Ax|| 1.100355140568e-01 23 KSP preconditioned resid norm 8.011880009497e-03 true resid norm 3.937870836170e+00 ||Ae||/||Ax|| 1.154201542864e-01 24 KSP preconditioned resid norm 5.573761552253e-03 true resid norm 4.205066407359e+00 ||Ae||/||Ax|| 1.232517351924e-01 25 KSP preconditioned resid norm 4.810675543540e-03 true resid norm 4.069723693466e+00 ||Ae||/||Ax|| 1.192848003769e-01 26 KSP preconditioned resid norm 4.647944860704e-03 true resid norm 4.044329745280e+00 ||Ae||/||Ax|| 1.185404962746e-01 27 KSP preconditioned resid norm 4.606926939804e-03 true resid norm 4.039416044569e+00 ||Ae||/||Ax|| 1.183964742593e-01 28 KSP preconditioned resid norm 4.606174352197e-03 true resid norm 4.038658488893e+00 ||Ae||/||Ax|| 1.183742700792e-01 29 KSP preconditioned resid norm 4.604980580071e-03 true resid norm 4.034721549326e+00 ||Ae||/||Ax|| 1.182588772207e-01 30 KSP preconditioned resid norm 4.551931835395e-03 true resid norm 3.942692013899e+00 ||Ae||/||Ax|| 1.155614644259e-01 31 KSP preconditioned resid norm 4.534435621643e-03 true resid norm 3.940744976447e+00 ||Ae||/||Ax|| 1.155043961846e-01 32 KSP preconditioned resid norm 4.533889403959e-03 true resid norm 3.940661031251e+00 ||Ae||/||Ax|| 1.155019357261e-01 33 KSP preconditioned resid norm 4.533315616020e-03 true resid norm 3.940962366962e+00 ||Ae||/||Ax|| 1.155107679646e-01 34 KSP preconditioned resid norm 4.533098107272e-03 true resid norm 3.940998854473e+00 ||Ae||/||Ax|| 1.155118374243e-01 35 KSP preconditioned resid norm 4.531113895054e-03 true resid norm 3.939900266217e+00 ||Ae||/||Ax|| 1.154796374789e-01 36 KSP preconditioned resid norm 4.530789523555e-03 true resid norm 3.939483356865e+00 ||Ae||/||Ax|| 1.154674177430e-01 37 KSP preconditioned resid norm 4.530789514003e-03 true resid norm 3.939490762772e+00 ||Ae||/||Ax|| 1.154676348123e-01 38 KSP preconditioned resid norm 4.530624961751e-03 true resid norm 3.937889462104e+00 ||Ae||/||Ax|| 1.154207002179e-01 39 KSP preconditioned resid norm 4.517785703071e-03 true resid norm 3.927441577896e+00 ||Ae||/||Ax|| 1.151144696539e-01 40 KSP preconditioned resid norm 4.508890400648e-03 true resid norm 3.919421029911e+00 ||Ae||/||Ax|| 1.148793850297e-01 41 KSP preconditioned resid norm 4.508823049754e-03 true resid norm 3.920408845458e+00 ||Ae||/||Ax|| 1.149083381943e-01 42 KSP preconditioned resid norm 4.504581641358e-03 true resid norm 3.910936323861e+00 ||Ae||/||Ax|| 1.146306957958e-01 43 KSP preconditioned resid norm 4.496299729031e-03 true resid norm 3.892573202489e+00 ||Ae||/||Ax|| 1.140924672987e-01 44 KSP preconditioned resid norm 4.327165698785e-03 true resid norm 3.499303379330e+00 ||Ae||/||Ax|| 1.025656129265e-01 45 KSP preconditioned resid norm 3.860049921599e-03 true resid norm 2.642394407576e+00 ||Ae||/||Ax|| 7.744935852298e-02 46 KSP preconditioned resid norm 3.813681936798e-03 true resid norm 2.561643926848e+00 ||Ae||/||Ax|| 7.508253814415e-02 47 KSP preconditioned resid norm 3.811608329841e-03 true resid norm 2.553393452252e+00 ||Ae||/||Ax|| 7.484071430319e-02 48 KSP preconditioned resid norm 3.805700908518e-03 true resid norm 2.559614961583e+00 ||Ae||/||Ax|| 7.502306857451e-02 49 KSP preconditioned resid norm 3.783124026053e-03 true resid norm 2.523808739092e+00 ||Ae||/||Ax|| 7.397357764494e-02 50 KSP preconditioned resid norm 3.777662131381e-03 true resid norm 2.516105834856e+00 ||Ae||/||Ax|| 7.374780325255e-02 51 KSP preconditioned resid norm 3.710923429451e-03 true resid norm 2.426657981798e+00 ||Ae||/||Ax|| 7.112606032852e-02 52 KSP preconditioned resid norm 3.604808013597e-03 true resid norm 2.303594181107e+00 ||Ae||/||Ax|| 6.751902407624e-02 53 KSP preconditioned resid norm 3.513880489788e-03 true resid norm 2.188212014004e+00 ||Ae||/||Ax|| 6.413713876742e-02 54 KSP preconditioned resid norm 3.320184202285e-03 true resid norm 1.978987642137e+00 ||Ae||/||Ax|| 5.800471079148e-02 55 KSP preconditioned resid norm 2.195662794099e-03 true resid norm 1.448538675887e+00 ||Ae||/||Ax|| 4.245709532291e-02 56 KSP preconditioned resid norm 9.077826763324e-04 true resid norm 1.628573968470e+00 ||Ae||/||Ax|| 4.773398278607e-02 57 KSP preconditioned resid norm 7.602131391716e-04 true resid norm 1.659109675600e+00 ||Ae||/||Ax|| 4.862899335772e-02 58 KSP preconditioned resid norm 7.450227847936e-04 true resid norm 1.651479746174e+00 ||Ae||/||Ax|| 4.840535787852e-02 59 KSP preconditioned resid norm 7.410161195392e-04 true resid norm 1.649502155114e+00 ||Ae||/||Ax|| 4.834739410196e-02 60 KSP preconditioned resid norm 7.399447579004e-04 true resid norm 1.648188611058e+00 ||Ae||/||Ax|| 4.830889373871e-02 61 KSP preconditioned resid norm 7.399146825366e-04 true resid norm 1.648156339888e+00 ||Ae||/||Ax|| 4.830794786121e-02 62 KSP preconditioned resid norm 7.399119217730e-04 true resid norm 1.648143662498e+00 ||Ae||/||Ax|| 4.830757628317e-02 63 KSP preconditioned resid norm 7.399115190929e-04 true resid norm 1.648149747433e+00 ||Ae||/||Ax|| 4.830775463441e-02 64 KSP preconditioned resid norm 7.398927702838e-04 true resid norm 1.648083443482e+00 ||Ae||/||Ax|| 4.830581124607e-02 65 KSP preconditioned resid norm 7.398398384099e-04 true resid norm 1.647873653551e+00 ||Ae||/||Ax|| 4.829966224141e-02 66 KSP preconditioned resid norm 7.398251502315e-04 true resid norm 1.647783674785e+00 ||Ae||/||Ax|| 4.829702493725e-02 67 KSP preconditioned resid norm 7.398217631044e-04 true resid norm 1.647733028046e+00 ||Ae||/||Ax|| 4.829554046641e-02 68 KSP preconditioned resid norm 7.398045634717e-04 true resid norm 1.647630453201e+00 ||Ae||/||Ax|| 4.829253396748e-02 69 KSP preconditioned resid norm 7.397586859381e-04 true resid norm 1.647387302132e+00 ||Ae||/||Ax|| 4.828540713804e-02 70 KSP preconditioned resid norm 7.396782241138e-04 true resid norm 1.646889429724e+00 ||Ae||/||Ax|| 4.827081435109e-02 71 KSP preconditioned resid norm 7.395189566969e-04 true resid norm 1.646041167917e+00 ||Ae||/||Ax|| 4.824595154763e-02 72 KSP preconditioned resid norm 7.391300711199e-04 true resid norm 1.643970513576e+00 ||Ae||/||Ax|| 4.818526005889e-02 73 KSP preconditioned resid norm 7.367639912300e-04 true resid norm 1.631221838831e+00 ||Ae||/||Ax|| 4.781159264642e-02 74 KSP preconditioned resid norm 7.075386327019e-04 true resid norm 1.473482203196e+00 ||Ae||/||Ax|| 4.318819745660e-02 75 KSP preconditioned resid norm 6.769663644505e-04 true resid norm 1.324870886213e+00 ||Ae||/||Ax|| 3.883235597562e-02 76 KSP preconditioned resid norm 6.510062346881e-04 true resid norm 1.209103850108e+00 ||Ae||/||Ax|| 3.543919004296e-02 77 KSP preconditioned resid norm 6.416005299115e-04 true resid norm 1.174343461999e+00 ||Ae||/||Ax|| 3.442035282725e-02 78 KSP preconditioned resid norm 6.269785791288e-04 true resid norm 1.115598946804e+00 ||Ae||/||Ax|| 3.269853378102e-02 79 KSP preconditioned resid norm 6.143599514076e-04 true resid norm 1.060258719301e+00 ||Ae||/||Ax|| 3.107649540993e-02 80 KSP preconditioned resid norm 6.118239459355e-04 true resid norm 1.049506356947e+00 ||Ae||/||Ax|| 3.076134050174e-02 81 KSP preconditioned resid norm 6.112876406857e-04 true resid norm 1.046662765401e+00 ||Ae||/||Ax|| 3.067799399581e-02 82 KSP preconditioned resid norm 6.092506607543e-04 true resid norm 1.042978389425e+00 ||Ae||/||Ax|| 3.057000385056e-02 83 KSP preconditioned resid norm 6.081618319409e-04 true resid norm 1.040456343908e+00 ||Ae||/||Ax|| 3.049608195349e-02 84 KSP preconditioned resid norm 6.071647595071e-04 true resid norm 1.037276486552e+00 ||Ae||/||Ax|| 3.040287939761e-02 85 KSP preconditioned resid norm 5.795095806265e-04 true resid norm 9.478301874350e-01 ||Ae||/||Ax|| 2.778118202003e-02 86 KSP preconditioned resid norm 4.787555615154e-04 true resid norm 6.865840307207e-01 ||Ae||/||Ax|| 2.012398020485e-02 87 KSP preconditioned resid norm 4.213257765496e-04 true resid norm 5.905989111727e-01 ||Ae||/||Ax|| 1.731062807413e-02 88 KSP preconditioned resid norm 4.123977761693e-04 true resid norm 5.807815859857e-01 ||Ae||/||Ax|| 1.702287938076e-02 89 KSP preconditioned resid norm 4.115095902916e-04 true resid norm 5.798345338457e-01 ||Ae||/||Ax|| 1.699512100354e-02 90 KSP preconditioned resid norm 4.108801176214e-04 true resid norm 5.793647424755e-01 ||Ae||/||Ax|| 1.698135128008e-02 91 KSP preconditioned resid norm 4.108190755084e-04 true resid norm 5.791872846528e-01 ||Ae||/||Ax|| 1.697614993902e-02 92 KSP preconditioned resid norm 4.108155029469e-04 true resid norm 5.791926093107e-01 ||Ae||/||Ax|| 1.697630600631e-02 93 KSP preconditioned resid norm 4.107643215473e-04 true resid norm 5.790565420549e-01 ||Ae||/||Ax|| 1.697231783496e-02 94 KSP preconditioned resid norm 4.107470285220e-04 true resid norm 5.790043835353e-01 ||Ae||/||Ax|| 1.697078905338e-02 95 KSP preconditioned resid norm 4.106027433097e-04 true resid norm 5.788370547615e-01 ||Ae||/||Ax|| 1.696588459773e-02 96 KSP preconditioned resid norm 4.105373219087e-04 true resid norm 5.787406622632e-01 ||Ae||/||Ax|| 1.696305930521e-02 97 KSP preconditioned resid norm 4.101903272161e-04 true resid norm 5.782775654139e-01 ||Ae||/||Ax|| 1.694948580013e-02 98 KSP preconditioned resid norm 4.099747390001e-04 true resid norm 5.779940033737e-01 ||Ae||/||Ax|| 1.694117451319e-02 99 KSP preconditioned resid norm 4.096326465608e-04 true resid norm 5.776176495203e-01 ||Ae||/||Ax|| 1.693014347088e-02 100 KSP preconditioned resid norm 4.092060802411e-04 true resid norm 5.770662599556e-01 ||Ae||/||Ax|| 1.691398208030e-02 101 KSP preconditioned resid norm 4.086261522954e-04 true resid norm 5.762792914356e-01 ||Ae||/||Ax|| 1.689091580114e-02 102 KSP preconditioned resid norm 4.071887041444e-04 true resid norm 5.745955672588e-01 ||Ae||/||Ax|| 1.684156534950e-02 103 KSP preconditioned resid norm 4.011719381813e-04 true resid norm 5.677078870256e-01 ||Ae||/||Ax|| 1.663968541279e-02 104 KSP preconditioned resid norm 3.731483912664e-04 true resid norm 5.390066307155e-01 ||Ae||/||Ax|| 1.579844313509e-02 105 KSP preconditioned resid norm 3.578740957934e-04 true resid norm 5.257995151776e-01 ||Ae||/||Ax|| 1.541133868792e-02 106 KSP preconditioned resid norm 3.563978076795e-04 true resid norm 5.245622816931e-01 ||Ae||/||Ax|| 1.537507501000e-02 107 KSP preconditioned resid norm 3.563405850927e-04 true resid norm 5.245065876166e-01 ||Ae||/||Ax|| 1.537344260021e-02 108 KSP preconditioned resid norm 3.563078476870e-04 true resid norm 5.244228510017e-01 ||Ae||/||Ax|| 1.537098825536e-02 109 KSP preconditioned resid norm 3.560224342942e-04 true resid norm 5.239210281149e-01 ||Ae||/||Ax|| 1.535627967872e-02 110 KSP preconditioned resid norm 3.545467903925e-04 true resid norm 5.214874571494e-01 ||Ae||/||Ax|| 1.528495099680e-02 111 KSP preconditioned resid norm 3.508567045265e-04 true resid norm 5.149689537524e-01 ||Ae||/||Ax|| 1.509389174191e-02 112 KSP preconditioned resid norm 3.416224689711e-04 true resid norm 5.002948544039e-01 ||Ae||/||Ax|| 1.466378956709e-02 113 KSP preconditioned resid norm 3.284537883016e-04 true resid norm 4.816353969094e-01 ||Ae||/||Ax|| 1.411687537093e-02 114 KSP preconditioned resid norm 2.844770402668e-04 true resid norm 4.208829442864e-01 ||Ae||/||Ax|| 1.233620308717e-02 115 KSP preconditioned resid norm 1.888979430188e-04 true resid norm 3.277232690461e-01 ||Ae||/||Ax|| 9.605665561473e-03 116 KSP preconditioned resid norm 1.493428151783e-04 true resid norm 3.046255632247e-01 ||Ae||/||Ax|| 8.928664999373e-03 117 KSP preconditioned resid norm 1.204726650252e-04 true resid norm 2.943808888272e-01 ||Ae||/||Ax|| 8.628390574747e-03 118 KSP preconditioned resid norm 1.150878696433e-04 true resid norm 2.926063341945e-01 ||Ae||/||Ax|| 8.576377855687e-03 119 KSP preconditioned resid norm 1.148200624778e-04 true resid norm 2.924882027350e-01 ||Ae||/||Ax|| 8.572915387810e-03 120 KSP preconditioned resid norm 1.147090901833e-04 true resid norm 2.923355388243e-01 ||Ae||/||Ax|| 8.568440763612e-03 121 KSP preconditioned resid norm 1.147086480772e-04 true resid norm 2.923340459246e-01 ||Ae||/||Ax|| 8.568397006283e-03 122 KSP preconditioned resid norm 1.147074345772e-04 true resid norm 2.923297850377e-01 ||Ae||/||Ax|| 8.568272118432e-03 123 KSP preconditioned resid norm 1.147065243614e-04 true resid norm 2.923248091878e-01 ||Ae||/||Ax|| 8.568126274805e-03 124 KSP preconditioned resid norm 1.147026092967e-04 true resid norm 2.923061694175e-01 ||Ae||/||Ax|| 8.567579937648e-03 125 KSP preconditioned resid norm 1.146860466801e-04 true resid norm 2.922477898898e-01 ||Ae||/||Ax|| 8.565868816492e-03 126 KSP preconditioned resid norm 1.146751149250e-04 true resid norm 2.922025269642e-01 ||Ae||/||Ax|| 8.564542146810e-03 127 KSP preconditioned resid norm 1.146656275932e-04 true resid norm 2.921534168032e-01 ||Ae||/||Ax|| 8.563102713521e-03 128 KSP preconditioned resid norm 1.146540738338e-04 true resid norm 2.921052187869e-01 ||Ae||/||Ax|| 8.561690015466e-03 129 KSP preconditioned resid norm 1.146317629504e-04 true resid norm 2.920356909505e-01 ||Ae||/||Ax|| 8.559652134098e-03 130 KSP preconditioned resid norm 1.145852824725e-04 true resid norm 2.918498699830e-01 ||Ae||/||Ax|| 8.554205666799e-03 131 KSP preconditioned resid norm 1.144841413764e-04 true resid norm 2.914417917651e-01 ||Ae||/||Ax|| 8.542244774013e-03 132 KSP preconditioned resid norm 1.142937917430e-04 true resid norm 2.906644453652e-01 ||Ae||/||Ax|| 8.519460522031e-03 133 KSP preconditioned resid norm 1.130548110220e-04 true resid norm 2.857679871300e-01 ||Ae||/||Ax|| 8.375943888683e-03 134 KSP preconditioned resid norm 1.057276349053e-04 true resid norm 2.589611976549e-01 ||Ae||/||Ax|| 7.590228992013e-03 135 KSP preconditioned resid norm 9.871511526536e-05 true resid norm 2.357745100216e-01 ||Ae||/||Ax|| 6.910620346794e-03 136 KSP preconditioned resid norm 8.312274984506e-05 true resid norm 1.934235830959e-01 ||Ae||/||Ax|| 5.669302202216e-03 137 KSP preconditioned resid norm 8.145220568973e-05 true resid norm 1.897472689905e-01 ||Ae||/||Ax|| 5.561548352763e-03 138 KSP preconditioned resid norm 8.089429792995e-05 true resid norm 1.885182459383e-01 ||Ae||/||Ax|| 5.525525325038e-03 139 KSP preconditioned resid norm 8.078248026168e-05 true resid norm 1.882859034386e-01 ||Ae||/||Ax|| 5.518715297926e-03 140 KSP preconditioned resid norm 8.058519490339e-05 true resid norm 1.878082979467e-01 ||Ae||/||Ax|| 5.504716540256e-03 141 KSP preconditioned resid norm 8.053553569122e-05 true resid norm 1.876391443962e-01 ||Ae||/||Ax|| 5.499758599862e-03 142 KSP preconditioned resid norm 8.053100220065e-05 true resid norm 1.876118055046e-01 ||Ae||/||Ax|| 5.498957288895e-03 143 KSP preconditioned resid norm 8.047535876508e-05 true resid norm 1.874565005127e-01 ||Ae||/||Ax|| 5.494405253830e-03 144 KSP preconditioned resid norm 7.996745286426e-05 true resid norm 1.855927278450e-01 ||Ae||/||Ax|| 5.439777527882e-03 145 KSP preconditioned resid norm 7.850097439778e-05 true resid norm 1.797120423955e-01 ||Ae||/||Ax|| 5.267412904933e-03 146 KSP preconditioned resid norm 7.712267640033e-05 true resid norm 1.745638681335e-01 ||Ae||/||Ax|| 5.116518400685e-03 147 KSP preconditioned resid norm 7.704640842904e-05 true resid norm 1.743102871574e-01 ||Ae||/||Ax|| 5.109085867572e-03 148 KSP preconditioned resid norm 7.702851816825e-05 true resid norm 1.742055406542e-01 ||Ae||/||Ax|| 5.106015716707e-03 149 KSP preconditioned resid norm 7.701945656908e-05 true resid norm 1.741740928683e-01 ||Ae||/||Ax|| 5.105093972837e-03 150 KSP preconditioned resid norm 7.626884365698e-05 true resid norm 1.719730645601e-01 ||Ae||/||Ax|| 5.040581184712e-03 151 KSP preconditioned resid norm 7.599607213302e-05 true resid norm 1.710277105380e-01 ||Ae||/||Ax|| 5.012872579826e-03 152 KSP preconditioned resid norm 7.598836518420e-05 true resid norm 1.709843924190e-01 ||Ae||/||Ax|| 5.011602912996e-03 153 KSP preconditioned resid norm 7.598568634564e-05 true resid norm 1.709611115829e-01 ||Ae||/||Ax|| 5.010920544833e-03 154 KSP preconditioned resid norm 7.594895134427e-05 true resid norm 1.708815153643e-01 ||Ae||/||Ax|| 5.008587556218e-03 155 KSP preconditioned resid norm 7.592875515541e-05 true resid norm 1.708598854441e-01 ||Ae||/||Ax|| 5.007953576885e-03 156 KSP preconditioned resid norm 7.592230757916e-05 true resid norm 1.708647514467e-01 ||Ae||/||Ax|| 5.008096200855e-03 157 KSP preconditioned resid norm 7.592153907587e-05 true resid norm 1.708599956105e-01 ||Ae||/||Ax|| 5.007956805893e-03 158 KSP preconditioned resid norm 7.592125192899e-05 true resid norm 1.708571037991e-01 ||Ae||/||Ax|| 5.007872046050e-03 159 KSP preconditioned resid norm 7.592054253568e-05 true resid norm 1.708534374643e-01 ||Ae||/||Ax|| 5.007764584696e-03 160 KSP preconditioned resid norm 7.591877965155e-05 true resid norm 1.708609734601e-01 ||Ae||/||Ax|| 5.007985466952e-03 161 KSP preconditioned resid norm 7.591547091588e-05 true resid norm 1.708731663098e-01 ||Ae||/||Ax|| 5.008342842969e-03 162 KSP preconditioned resid norm 7.590728066868e-05 true resid norm 1.708460548271e-01 ||Ae||/||Ax|| 5.007548197426e-03 163 KSP preconditioned resid norm 7.590604125401e-05 true resid norm 1.708258151094e-01 ||Ae||/||Ax|| 5.006954965336e-03 164 KSP preconditioned resid norm 7.575601456397e-05 true resid norm 1.699569477792e-01 ||Ae||/||Ax|| 4.981488207924e-03 165 KSP preconditioned resid norm 7.496358459267e-05 true resid norm 1.652638635963e-01 ||Ae||/||Ax|| 4.843932527965e-03 166 KSP preconditioned resid norm 7.371383740852e-05 true resid norm 1.570097101150e-01 ||Ae||/||Ax|| 4.602000857792e-03 167 KSP preconditioned resid norm 7.260492934217e-05 true resid norm 1.490904744222e-01 ||Ae||/||Ax|| 4.369885726665e-03 168 KSP preconditioned resid norm 6.960471930917e-05 true resid norm 1.313687271003e-01 ||Ae||/||Ax|| 3.850456091918e-03 169 KSP preconditioned resid norm 6.058742425563e-05 true resid norm 8.237807014788e-02 ||Ae||/||Ax|| 2.414525504226e-03 170 KSP preconditioned resid norm 5.796590184916e-05 true resid norm 6.844108072714e-02 ||Ae||/||Ax|| 2.006028238532e-03 171 KSP preconditioned resid norm 5.659281816236e-05 true resid norm 6.155606294805e-02 ||Ae||/||Ax|| 1.804226339134e-03 172 KSP preconditioned resid norm 5.599468691024e-05 true resid norm 6.027302651902e-02 ||Ae||/||Ax|| 1.766620163422e-03 173 KSP preconditioned resid norm 5.572484068824e-05 true resid norm 5.976567742033e-02 ||Ae||/||Ax|| 1.751749611877e-03 174 KSP preconditioned resid norm 5.489265229891e-05 true resid norm 5.808169027841e-02 ||Ae||/||Ax|| 1.702391452653e-03 175 KSP preconditioned resid norm 5.322512449517e-05 true resid norm 5.402659090376e-02 ||Ae||/||Ax|| 1.583535295368e-03 176 KSP preconditioned resid norm 4.847307773229e-05 true resid norm 4.170357201893e-02 ||Ae||/||Ax|| 1.222343981551e-03 177 KSP preconditioned resid norm 3.600405920790e-05 true resid norm 2.320103054648e-02 ||Ae||/||Ax|| 6.800290402316e-04 178 KSP preconditioned resid norm 2.399058700709e-05 true resid norm 2.289697274620e-02 ||Ae||/||Ax|| 6.711170165315e-04 179 KSP preconditioned resid norm 2.089274123649e-05 true resid norm 2.349444820543e-02 ||Ae||/||Ax|| 6.886291982548e-04 180 KSP preconditioned resid norm 2.061041323531e-05 true resid norm 2.360266912827e-02 ||Ae||/||Ax|| 6.918011853849e-04 181 KSP preconditioned resid norm 2.060670303994e-05 true resid norm 2.360086641678e-02 ||Ae||/||Ax|| 6.917483473798e-04 182 KSP preconditioned resid norm 2.060654081035e-05 true resid norm 2.360068375355e-02 ||Ae||/||Ax|| 6.917429934668e-04 183 KSP preconditioned resid norm 2.060649196076e-05 true resid norm 2.360043425312e-02 ||Ae||/||Ax|| 6.917356805358e-04 184 KSP preconditioned resid norm 2.060634884895e-05 true resid norm 2.360026575587e-02 ||Ae||/||Ax|| 6.917307418316e-04 185 KSP preconditioned resid norm 2.060447413038e-05 true resid norm 2.359634071259e-02 ||Ae||/||Ax|| 6.916156976570e-04 186 KSP preconditioned resid norm 2.060255598650e-05 true resid norm 2.359221445514e-02 ||Ae||/||Ax|| 6.914947558354e-04 187 KSP preconditioned resid norm 2.057964076755e-05 true resid norm 2.354289672964e-02 ||Ae||/||Ax|| 6.900492387722e-04 188 KSP preconditioned resid norm 2.049253617466e-05 true resid norm 2.333501704133e-02 ||Ae||/||Ax|| 6.839562238674e-04 189 KSP preconditioned resid norm 2.040326487567e-05 true resid norm 2.314464127396e-02 ||Ae||/||Ax|| 6.783762540420e-04 190 KSP preconditioned resid norm 2.036166574338e-05 true resid norm 2.305811696778e-02 ||Ae||/||Ax|| 6.758402011382e-04 191 KSP preconditioned resid norm 2.029257268551e-05 true resid norm 2.288536790482e-02 ||Ae||/||Ax|| 6.707768752117e-04 192 KSP preconditioned resid norm 2.019062061590e-05 true resid norm 2.266350980459e-02 ||Ae||/||Ax|| 6.642741489358e-04 193 KSP preconditioned resid norm 2.009806404940e-05 true resid norm 2.248035988873e-02 ||Ae||/||Ax|| 6.589059709469e-04 194 KSP preconditioned resid norm 1.858828207261e-05 true resid norm 1.943356782067e-02 ||Ae||/||Ax|| 5.696035978615e-04 195 KSP preconditioned resid norm 1.794572927242e-05 true resid norm 1.813018510105e-02 ||Ae||/||Ax|| 5.314010663790e-04 196 KSP preconditioned resid norm 1.697409251441e-05 true resid norm 1.633874057399e-02 ||Ae||/||Ax|| 4.788932995398e-04 197 KSP preconditioned resid norm 1.662567023921e-05 true resid norm 1.574930995992e-02 ||Ae||/||Ax|| 4.616169145977e-04 198 KSP preconditioned resid norm 1.632913689748e-05 true resid norm 1.528536784108e-02 ||Ae||/||Ax|| 4.480186344193e-04 199 KSP preconditioned resid norm 1.602212706226e-05 true resid norm 1.487806028555e-02 ||Ae||/||Ax|| 4.360803299761e-04 200 KSP preconditioned resid norm 1.598585516281e-05 true resid norm 1.482432854003e-02 ||Ae||/||Ax|| 4.345054366856e-04 201 KSP preconditioned resid norm 1.598384641464e-05 true resid norm 1.481028866520e-02 ||Ae||/||Ax|| 4.340939238184e-04 202 KSP preconditioned resid norm 1.595854650059e-05 true resid norm 1.487748733370e-02 ||Ae||/||Ax|| 4.360635365884e-04 203 KSP preconditioned resid norm 1.582982523503e-05 true resid norm 1.478598116058e-02 ||Ae||/||Ax|| 4.333814636970e-04 204 KSP preconditioned resid norm 1.515519370048e-05 true resid norm 1.366768101741e-02 ||Ae||/||Ax|| 4.006037570546e-04 205 KSP preconditioned resid norm 1.299464666840e-05 true resid norm 1.016769800126e-02 ||Ae||/||Ax|| 2.980182237728e-04 206 KSP preconditioned resid norm 2.696783682868e-06 true resid norm 1.287176432531e-03 ||Ae||/||Ax|| 3.772752043360e-05 207 KSP preconditioned resid norm 7.605459742619e-07 true resid norm 1.108935910729e-03 ||Ae||/||Ax|| 3.250323823078e-05 208 KSP preconditioned resid norm 4.320742115795e-07 true resid norm 1.112610809460e-03 ||Ae||/||Ax|| 3.261095059519e-05 209 KSP preconditioned resid norm 2.742804824767e-07 true resid norm 1.110429131777e-03 ||Ae||/||Ax|| 3.254700497957e-05 Hope it helps. Thanks On 6/17/07, Barry Smith wrote: > > > Ben, > > > On Sat, 16 Jun 2007, Ben Tay wrote: > > > Hi, > > > > I am trying to use PETSc to solve my poisson eqn. In the past, when I'm > not > > using MPI, I set KSPSetTolerances to 1.0e-5. This seems to be good > enuff. > > > > Now, I'm trying to use PETSc with MPI to solve the eqn. I am using a > very > > small no. of pts, only 16x4. On 1 processor, the ans is the same as the > one > > without MPI. However, on 2 processors, I found that I've to increase the > > KSPSetTolerances to 1.0e-6, else those grid pts on the edge will be > > different. On 4 processors, KSPSetTolerances has to be decreased to > 1.0e-7. > > On 8 processors, when KSPSetTolerances is 1.0e-8, the difference of the > last > > pt between 1 and 8 processors is about 3%. > > > > Are you using the same number of grid points when changing the number of > processors? > > Run the cases with -ksp_monitor_true_residual and send us ALL the > output. > > Barry > > > > > May I know why this is so? Also, does this happens only on very small > grids? > > Does it happen on large grids as well? I usually solve grids with approx > > 20000 to 55000 pts. > > > > Thank you. > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zonexo at gmail.com Sun Jun 17 21:44:41 2007 From: zonexo at gmail.com (Ben Tay) Date: Mon, 18 Jun 2007 10:44:41 +0800 Subject: KSPSetTolerances and processors size In-Reply-To: References: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> Message-ID: <804ab5d40706171944s21ccd6able03542b0895e9b08@mail.gmail.com> Oh btw, here's the output when KSPSetTolerances = 1.0e-5. 1: 0 KSP preconditioned resid norm 5.509130713952e+01 true resid norm 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 6.561453237357e+00 true resid norm 8.697577384386e+00 ||Ae||/||Ax|| 2.549285554017e-01 2 KSP preconditioned resid norm 1.208347069756e+00 true resid norm 7.425376743449e+00 ||Ae||/||Ax|| 2.176399798315e-01 3 KSP preconditioned resid norm 3.386218089799e-01 true resid norm 7.347207820518e+00 ||Ae||/||Ax|| 2.153488256722e-01 4 KSP preconditioned resid norm 3.296482144730e-01 true resid norm 7.745880291985e+00 ||Ae||/||Ax|| 2.270340332579e-01 5 KSP preconditioned resid norm 3.145738742595e-01 true resid norm 7.547707467510e+00 ||Ae||/||Ax|| 2.212255293918e-01 6 KSP preconditioned resid norm 1.643048266097e-01 true resid norm 4.306709238860e+00 ||Ae||/||Ax|| 1.262309165273e-01 7 KSP preconditioned resid norm 6.078974689223e-02 true resid norm 4.482652283996e+00 ||Ae||/||Ax|| 1.313878590122e-01 8 KSP preconditioned resid norm 6.054372794034e-02 true resid norm 4.355614139989e+00 ||Ae||/||Ax|| 1.276643335865e-01 9 KSP preconditioned resid norm 5.867972436189e-02 true resid norm 4.233715997285e+00 ||Ae||/||Ax|| 1.240914631132e-01 10 KSP preconditioned resid norm 2.168073622951e-02 true resid norm 2.086394899960e+00 ||Ae||/||Ax|| 6.115284915993e-02 11 KSP preconditioned resid norm 1.139327427516e-02 true resid norm 2.155289979633e+00 ||Ae||/||Ax|| 6.317218424133e-02 12 KSP preconditioned resid norm 1.088027785149e-02 true resid norm 1.991898557592e+00 ||Ae||/||Ax|| 5.838313352696e-02 13 KSP preconditioned resid norm 1.072820075665e-02 true resid norm 1.942479796672e+00 ||Ae||/||Ax|| 5.693465508586e-02 14 KSP preconditioned resid norm 3.781319329677e-03 true resid norm 9.806622346091e-01 ||Ae||/||Ax|| 2.874349899487e-02 15 KSP preconditioned resid norm 2.314101409645e-03 true resid norm 7.976384924484e-01 ||Ae||/||Ax|| 2.337901919420e-02 16 KSP preconditioned resid norm 2.293131061139e-03 true resid norm 7.897410852774e-01 ||Ae||/||Ax|| 2.314754386348e-02 17 KSP preconditioned resid norm 2.117223511336e-03 true resid norm 6.782416967980e-01 ||Ae||/||Ax|| 1.987946393996e-02 18 KSP preconditioned resid norm 7.524359734379e-05 true resid norm 9.092345849564e-04 ||Ae||/||Ax|| 2.664993354130e-05 2: 0 32 32 64 0 KSP preconditioned resid norm 4.902369798248e+01 true resid norm 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 8.253504641663e+00 true resid norm 1.259698849910e+01 ||Ae||/||Ax|| 3.692214439222e-01 2 KSP preconditioned resid norm 3.797891005886e+00 true resid norm 1.195333867118e+01 ||Ae||/||Ax|| 3.503558778495e-01 3 KSP preconditioned resid norm 2.578365901732e+00 true resid norm 1.159420670971e+01 ||Ae||/||Ax|| 3.398296142602e-01 4 KSP preconditioned resid norm 1.568196901288e+00 true resid norm 9.963750299049e+00 ||Ae||/||Ax|| 2.920404565390e-01 5 KSP preconditioned resid norm 1.317764005274e+00 true resid norm 9.066502566015e+00 ||Ae||/||Ax|| 2.657418611589e-01 6 KSP preconditioned resid norm 6.023727405584e-01 true resid norm 8.058099054033e+00 ||Ae||/||Ax|| 2.361852571517e-01 7 KSP preconditioned resid norm 4.957651340342e-02 true resid norm 7.520037445249e+00 ||Ae||/||Ax|| 2.204145128879e-01 8 KSP preconditioned resid norm 2.449473557300e-02 true resid norm 7.475057378184e+00 ||Ae||/||Ax|| 2.190961338713e-01 9 KSP preconditioned resid norm 2.361338376271e-02 true resid norm 7.217194046579e+00 ||Ae||/||Ax|| 2.115380836566e-01 10 KSP preconditioned resid norm 2.307344735925e-02 true resid norm 7.205616297960e+00 ||Ae||/||Ax|| 2.111987364338e-01 11 KSP preconditioned resid norm 1.934171008299e-02 true resid norm 5.261866236257e+00 ||Ae||/||Ax|| 1.542268495057e-01 12 KSP preconditioned resid norm 5.190847895073e-03 true resid norm 4.466349759791e+00 ||Ae||/||Ax|| 1.309100272251e-01 13 KSP preconditioned resid norm 4.871871781446e-03 true resid norm 4.194634080458e+00 ||Ae||/||Ax|| 1.229459606177e-01 14 KSP preconditioned resid norm 4.823921505423e-03 true resid norm 4.173223968428e+00 ||Ae||/||Ax|| 1.223184239268e-01 15 KSP preconditioned resid norm 4.701199647155e-03 true resid norm 3.957555688130e+00 ||Ae||/||Ax|| 1.159971230964e-01 16 KSP preconditioned resid norm 1.035300954721e-03 true resid norm 2.196668371922e+00 ||Ae||/||Ax|| 6.438499710918e-02 17 KSP preconditioned resid norm 8.832653700092e-04 true resid norm 1.916576324421e+00 ||Ae||/||Ax|| 5.617541668313e-02 18 KSP preconditioned resid norm 8.703924311133e-04 true resid norm 1.916104922195e+00 ||Ae||/||Ax|| 5.616159974502e-02 19 KSP preconditioned resid norm 8.698960956884e-04 true resid norm 1.913670720373e+00 ||Ae||/||Ax|| 5.609025257250e-02 20 KSP preconditioned resid norm 3.690946760360e-04 true resid norm 7.994885772359e-01 ||Ae||/||Ax|| 2.343324572435e-02 4: 0 16 32 48 48 64 0 KSP preconditioned resid norm 4.414786383499e+01 true resid norm 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 7.579678467669e+00 true resid norm 1.423835009315e+01 ||Ae||/||Ax|| 4.173302357811e-01 2 KSP preconditioned resid norm 2.972753009220e+00 true resid norm 1.290812750005e+01 ||Ae||/||Ax|| 3.783410197001e-01 3 KSP preconditioned resid norm 1.347960602345e+00 true resid norm 1.173368275935e+01 ||Ae||/||Ax|| 3.439176983641e-01 4 KSP preconditioned resid norm 1.111052862809e+00 true resid norm 1.106221549565e+01 ||Ae||/||Ax|| 3.242367950541e-01 5 KSP preconditioned resid norm 9.872224937494e-01 true resid norm 1.005157038653e+01 ||Ae||/||Ax|| 2.946144891744e-01 6 KSP preconditioned resid norm 7.251219493841e-01 true resid norm 9.007852893929e+00 ||Ae||/||Ax|| 2.640228219921e-01 7 KSP preconditioned resid norm 5.925185640664e-01 true resid norm 8.104036732737e+00 ||Ae||/||Ax|| 2.375317040476e-01 8 KSP preconditioned resid norm 3.381465672631e-01 true resid norm 7.256440004925e+00 ||Ae||/||Ax|| 2.126883942574e-01 9 KSP preconditioned resid norm 1.647154013552e-01 true resid norm 7.263797232535e+00 ||Ae||/||Ax|| 2.129040367661e-01 10 KSP preconditioned resid norm 7.697425793821e-02 true resid norm 7.155391777961e+00 ||Ae||/||Ax|| 2.097266409567e-01 11 KSP preconditioned resid norm 3.477770299629e-02 true resid norm 7.127853631055e+00 ||Ae||/||Ax|| 2.089194897583e-01 12 KSP preconditioned resid norm 2.573627666614e-02 true resid norm 7.088156599392e+00 ||Ae||/||Ax|| 2.077559580657e-01 13 KSP preconditioned resid norm 2.221352319865e-02 true resid norm 7.093825972365e+00 ||Ae||/||Ax|| 2.079221290577e-01 14 KSP preconditioned resid norm 2.093106984691e-02 true resid norm 7.062268285770e+00 ||Ae||/||Ax|| 2.069971639669e-01 15 KSP preconditioned resid norm 2.034509930217e-02 true resid norm 7.031405865561e+00 ||Ae||/||Ax|| 2.060925773386e-01 16 KSP preconditioned resid norm 2.029393080560e-02 true resid norm 7.008984378537e+00 ||Ae||/||Ax|| 2.054353969487e-01 17 KSP preconditioned resid norm 1.587358534265e-02 true resid norm 4.635842103718e+00 ||Ae||/||Ax|| 1.358778977572e-01 18 KSP preconditioned resid norm 1.055491860699e-02 true resid norm 3.773993858722e+00 ||Ae||/||Ax|| 1.106168718000e-01 19 KSP preconditioned resid norm 5.655638925006e-03 true resid norm 4.203919883144e+00 ||Ae||/||Ax|| 1.232181302299e-01 20 KSP preconditioned resid norm 4.767909232406e-03 true resid norm 4.121869307404e+00 ||Ae||/||Ax|| 1.208132036833e-01 21 KSP preconditioned resid norm 4.648572929978e-03 true resid norm 4.076834878296e+00 ||Ae||/||Ax|| 1.194932312992e-01 22 KSP preconditioned resid norm 4.638216815872e-03 true resid norm 4.058874907114e+00 ||Ae||/||Ax|| 1.189668192529e-01 23 KSP preconditioned resid norm 1.851801714075e-03 true resid norm 2.017702443794e+00 ||Ae||/||Ax|| 5.913945303323e-02 24 KSP preconditioned resid norm 9.594251508173e-04 true resid norm 2.065135975225e+00 ||Ae||/||Ax|| 6.052974381317e-02 25 KSP preconditioned resid norm 8.609050236229e-04 true resid norm 1.901663497990e+00 ||Ae||/||Ax|| 5.573831734719e-02 26 KSP preconditioned resid norm 8.607029066323e-04 true resid norm 1.901221069645e+00 ||Ae||/||Ax|| 5.572534964205e-02 27 KSP preconditioned resid norm 6.010429111401e-04 true resid norm 1.025962923033e+00 ||Ae||/||Ax|| 3.007127551793e-02 28 KSP preconditioned resid norm 2.036565987243e-04 true resid norm 8.385451121270e-01 ||Ae||/||Ax|| 2.457800426788e-02 8: 8 16 24 32 56 64 16 24 48 56 0 8 32 40 40 48 0 KSP preconditioned resid norm 4.299803638671e+01 true resid norm 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 1 KSP preconditioned resid norm 9.603727351867e+00 true resid norm 1.922897810349e+01 ||Ae||/||Ax|| 5.636070129797e-01 2 KSP preconditioned resid norm 2.931835632556e+00 true resid norm 1.355792423218e+01 ||Ae||/||Ax|| 3.973867533457e-01 3 KSP preconditioned resid norm 1.314351599619e+00 true resid norm 9.882281425137e+00 ||Ae||/||Ax|| 2.896525798443e-01 4 KSP preconditioned resid norm 8.218956530484e-01 true resid norm 9.318760482806e+00 ||Ae||/||Ax|| 2.731356150140e-01 5 KSP preconditioned resid norm 6.895693486764e-01 true resid norm 9.360126907217e+00 ||Ae||/||Ax|| 2.743480770998e-01 6 KSP preconditioned resid norm 6.138748402770e-01 true resid norm 9.020243051395e+00 ||Ae||/||Ax|| 2.643859811575e-01 7 KSP preconditioned resid norm 5.265342569996e-01 true resid norm 8.781477094899e+00 ||Ae||/||Ax|| 2.573876806333e-01 8 KSP preconditioned resid norm 4.403325671754e-01 true resid norm 8.314776073768e+00 ||Ae||/||Ax|| 2.437085362160e-01 9 KSP preconditioned resid norm 2.353592633657e-01 true resid norm 7.347976506279e+00 ||Ae||/||Ax|| 2.153713560783e-01 10 KSP preconditioned resid norm 8.943808926292e-02 true resid norm 6.972332890712e+00 ||Ae||/||Ax|| 2.043611310432e-01 11 KSP preconditioned resid norm 5.930469791557e-02 true resid norm 6.957386646797e+00 ||Ae||/||Ax|| 2.039230522310e-01 12 KSP preconditioned resid norm 5.283812047599e-02 true resid norm 6.981023245883e+00 ||Ae||/||Ax|| 2.046158479134e-01 13 KSP preconditioned resid norm 3.665176395384e-02 true resid norm 6.992078556546e+00 ||Ae||/||Ax|| 2.049398823258e-01 14 KSP preconditioned resid norm 2.516790937741e-02 true resid norm 6.949891196404e+00 ||Ae||/||Ax|| 2.037033583718e-01 15 KSP preconditioned resid norm 2.192690814272e-02 true resid norm 6.927621207906e+00 ||Ae||/||Ax|| 2.030506184483e-01 16 KSP preconditioned resid norm 2.058802964863e-02 true resid norm 6.919125260713e+00 ||Ae||/||Ax|| 2.028015997332e-01 17 KSP preconditioned resid norm 1.984533974458e-02 true resid norm 6.853733693988e+00 ||Ae||/||Ax|| 2.008849536484e-01 18 KSP preconditioned resid norm 1.958243371255e-02 true resid norm 6.766030769290e+00 ||Ae||/||Ax|| 1.983143550887e-01 19 KSP preconditioned resid norm 1.874262002187e-02 true resid norm 6.323230908702e+00 ||Ae||/||Ax|| 1.853357607281e-01 20 KSP preconditioned resid norm 1.754461572091e-02 true resid norm 5.538708901675e+00 ||Ae||/||Ax|| 1.623411895857e-01 21 KSP preconditioned resid norm 1.184321475064e-02 true resid norm 3.839931686898e+00 ||Ae||/||Ax|| 1.125495289688e-01 22 KSP preconditioned resid norm 1.070434172478e-02 true resid norm 3.754159266432e+00 ||Ae||/||Ax|| 1.100355140568e-01 23 KSP preconditioned resid norm 8.011880009497e-03 true resid norm 3.937870836170e+00 ||Ae||/||Ax|| 1.154201542864e-01 24 KSP preconditioned resid norm 5.573761552253e-03 true resid norm 4.205066407359e+00 ||Ae||/||Ax|| 1.232517351924e-01 25 KSP preconditioned resid norm 4.810675543540e-03 true resid norm 4.069723693466e+00 ||Ae||/||Ax|| 1.192848003769e-01 26 KSP preconditioned resid norm 4.647944860704e-03 true resid norm 4.044329745280e+00 ||Ae||/||Ax|| 1.185404962746e-01 27 KSP preconditioned resid norm 4.606926939804e-03 true resid norm 4.039416044569e+00 ||Ae||/||Ax|| 1.183964742593e-01 28 KSP preconditioned resid norm 4.606174352197e-03 true resid norm 4.038658488893e+00 ||Ae||/||Ax|| 1.183742700792e-01 29 KSP preconditioned resid norm 4.604980580071e-03 true resid norm 4.034721549326e+00 ||Ae||/||Ax|| 1.182588772207e-01 30 KSP preconditioned resid norm 4.551931835395e-03 true resid norm 3.942692013899e+00 ||Ae||/||Ax|| 1.155614644259e-01 31 KSP preconditioned resid norm 4.534435621643e-03 true resid norm 3.940744976447e+00 ||Ae||/||Ax|| 1.155043961846e-01 32 KSP preconditioned resid norm 4.533889403959e-03 true resid norm 3.940661031251e+00 ||Ae||/||Ax|| 1.155019357261e-01 33 KSP preconditioned resid norm 4.533315616020e-03 true resid norm 3.940962366962e+00 ||Ae||/||Ax|| 1.155107679646e-01 34 KSP preconditioned resid norm 4.533098107272e-03 true resid norm 3.940998854473e+00 ||Ae||/||Ax|| 1.155118374243e-01 35 KSP preconditioned resid norm 4.531113895054e-03 true resid norm 3.939900266217e+00 ||Ae||/||Ax|| 1.154796374789e-01 36 KSP preconditioned resid norm 4.530789523555e-03 true resid norm 3.939483356865e+00 ||Ae||/||Ax|| 1.154674177430e-01 37 KSP preconditioned resid norm 4.530789514003e-03 true resid norm 3.939490762772e+00 ||Ae||/||Ax|| 1.154676348123e-01 38 KSP preconditioned resid norm 4.530624961751e-03 true resid norm 3.937889462104e+00 ||Ae||/||Ax|| 1.154207002179e-01 39 KSP preconditioned resid norm 4.517785703071e-03 true resid norm 3.927441577896e+00 ||Ae||/||Ax|| 1.151144696539e-01 40 KSP preconditioned resid norm 4.508890400648e-03 true resid norm 3.919421029911e+00 ||Ae||/||Ax|| 1.148793850297e-01 41 KSP preconditioned resid norm 4.508823049754e-03 true resid norm 3.920408845458e+00 ||Ae||/||Ax|| 1.149083381943e-01 42 KSP preconditioned resid norm 4.504581641358e-03 true resid norm 3.910936323861e+00 ||Ae||/||Ax|| 1.146306957958e-01 43 KSP preconditioned resid norm 4.496299729031e-03 true resid norm 3.892573202489e+00 ||Ae||/||Ax|| 1.140924672987e-01 44 KSP preconditioned resid norm 4.327165698785e-03 true resid norm 3.499303379330e+00 ||Ae||/||Ax|| 1.025656129265e-01 45 KSP preconditioned resid norm 3.860049921599e-03 true resid norm 2.642394407576e+00 ||Ae||/||Ax|| 7.744935852298e-02 46 KSP preconditioned resid norm 3.813681936798e-03 true resid norm 2.561643926848e+00 ||Ae||/||Ax|| 7.508253814415e-02 47 KSP preconditioned resid norm 3.811608329841e-03 true resid norm 2.553393452252e+00 ||Ae||/||Ax|| 7.484071430319e-02 48 KSP preconditioned resid norm 3.805700908518e-03 true resid norm 2.559614961583e+00 ||Ae||/||Ax|| 7.502306857451e-02 49 KSP preconditioned resid norm 3.783124026053e-03 true resid norm 2.523808739092e+00 ||Ae||/||Ax|| 7.397357764494e-02 50 KSP preconditioned resid norm 3.777662131381e-03 true resid norm 2.516105834856e+00 ||Ae||/||Ax|| 7.374780325255e-02 51 KSP preconditioned resid norm 3.710923429451e-03 true resid norm 2.426657981798e+00 ||Ae||/||Ax|| 7.112606032852e-02 52 KSP preconditioned resid norm 3.604808013597e-03 true resid norm 2.303594181107e+00 ||Ae||/||Ax|| 6.751902407624e-02 53 KSP preconditioned resid norm 3.513880489788e-03 true resid norm 2.188212014004e+00 ||Ae||/||Ax|| 6.413713876742e-02 54 KSP preconditioned resid norm 3.320184202285e-03 true resid norm 1.978987642137e+00 ||Ae||/||Ax|| 5.800471079148e-02 55 KSP preconditioned resid norm 2.195662794099e-03 true resid norm 1.448538675887e+00 ||Ae||/||Ax|| 4.245709532291e-02 56 KSP preconditioned resid norm 9.077826763324e-04 true resid norm 1.628573968470e+00 ||Ae||/||Ax|| 4.773398278607e-02 57 KSP preconditioned resid norm 7.602131391716e-04 true resid norm 1.659109675600e+00 ||Ae||/||Ax|| 4.862899335772e-02 58 KSP preconditioned resid norm 7.450227847936e-04 true resid norm 1.651479746174e+00 ||Ae||/||Ax|| 4.840535787852e-02 59 KSP preconditioned resid norm 7.410161195392e-04 true resid norm 1.649502155114e+00 ||Ae||/||Ax|| 4.834739410196e-02 60 KSP preconditioned resid norm 7.399447579004e-04 true resid norm 1.648188611058e+00 ||Ae||/||Ax|| 4.830889373871e-02 61 KSP preconditioned resid norm 7.399146825366e-04 true resid norm 1.648156339888e+00 ||Ae||/||Ax|| 4.830794786121e-02 62 KSP preconditioned resid norm 7.399119217730e-04 true resid norm 1.648143662498e+00 ||Ae||/||Ax|| 4.830757628317e-02 63 KSP preconditioned resid norm 7.399115190929e-04 true resid norm 1.648149747433e+00 ||Ae||/||Ax|| 4.830775463441e-02 64 KSP preconditioned resid norm 7.398927702838e-04 true resid norm 1.648083443482e+00 ||Ae||/||Ax|| 4.830581124607e-02 65 KSP preconditioned resid norm 7.398398384099e-04 true resid norm 1.647873653551e+00 ||Ae||/||Ax|| 4.829966224141e-02 66 KSP preconditioned resid norm 7.398251502315e-04 true resid norm 1.647783674785e+00 ||Ae||/||Ax|| 4.829702493725e-02 67 KSP preconditioned resid norm 7.398217631044e-04 true resid norm 1.647733028046e+00 ||Ae||/||Ax|| 4.829554046641e-02 68 KSP preconditioned resid norm 7.398045634717e-04 true resid norm 1.647630453201e+00 ||Ae||/||Ax|| 4.829253396748e-02 69 KSP preconditioned resid norm 7.397586859381e-04 true resid norm 1.647387302132e+00 ||Ae||/||Ax|| 4.828540713804e-02 70 KSP preconditioned resid norm 7.396782241138e-04 true resid norm 1.646889429724e+00 ||Ae||/||Ax|| 4.827081435109e-02 71 KSP preconditioned resid norm 7.395189566969e-04 true resid norm 1.646041167917e+00 ||Ae||/||Ax|| 4.824595154763e-02 72 KSP preconditioned resid norm 7.391300711199e-04 true resid norm 1.643970513576e+00 ||Ae||/||Ax|| 4.818526005889e-02 73 KSP preconditioned resid norm 7.367639912300e-04 true resid norm 1.631221838831e+00 ||Ae||/||Ax|| 4.781159264642e-02 74 KSP preconditioned resid norm 7.075386327019e-04 true resid norm 1.473482203196e+00 ||Ae||/||Ax|| 4.318819745660e-02 75 KSP preconditioned resid norm 6.769663644505e-04 true resid norm 1.324870886213e+00 ||Ae||/||Ax|| 3.883235597562e-02 76 KSP preconditioned resid norm 6.510062346881e-04 true resid norm 1.209103850108e+00 ||Ae||/||Ax|| 3.543919004296e-02 77 KSP preconditioned resid norm 6.416005299115e-04 true resid norm 1.174343461999e+00 ||Ae||/||Ax|| 3.442035282725e-02 78 KSP preconditioned resid norm 6.269785791288e-04 true resid norm 1.115598946804e+00 ||Ae||/||Ax|| 3.269853378102e-02 79 KSP preconditioned resid norm 6.143599514076e-04 true resid norm 1.060258719301e+00 ||Ae||/||Ax|| 3.107649540993e-02 80 KSP preconditioned resid norm 6.118239459355e-04 true resid norm 1.049506356947e+00 ||Ae||/||Ax|| 3.076134050174e-02 81 KSP preconditioned resid norm 6.112876406857e-04 true resid norm 1.046662765401e+00 ||Ae||/||Ax|| 3.067799399581e-02 82 KSP preconditioned resid norm 6.092506607543e-04 true resid norm 1.042978389425e+00 ||Ae||/||Ax|| 3.057000385056e-02 83 KSP preconditioned resid norm 6.081618319409e-04 true resid norm 1.040456343908e+00 ||Ae||/||Ax|| 3.049608195349e-02 84 KSP preconditioned resid norm 6.071647595071e-04 true resid norm 1.037276486552e+00 ||Ae||/||Ax|| 3.040287939761e-02 85 KSP preconditioned resid norm 5.795095806265e-04 true resid norm 9.478301874350e-01 ||Ae||/||Ax|| 2.778118202003e-02 86 KSP preconditioned resid norm 4.787555615154e-04 true resid norm 6.865840307207e-01 ||Ae||/||Ax|| 2.012398020485e-02 87 KSP preconditioned resid norm 4.213257765496e-04 true resid norm 5.905989111727e-01 ||Ae||/||Ax|| 1.731062807413e-02 It seems that the no. of lines is much lesser compared to the eariler case when KSPSetTolerances = 1.0e-8 Thanks again On 6/17/07, Barry Smith wrote: > > > Ben, > > > On Sat, 16 Jun 2007, Ben Tay wrote: > > > Hi, > > > > I am trying to use PETSc to solve my poisson eqn. In the past, when I'm > not > > using MPI, I set KSPSetTolerances to 1.0e-5. This seems to be good > enuff. > > > > Now, I'm trying to use PETSc with MPI to solve the eqn. I am using a > very > > small no. of pts, only 16x4. On 1 processor, the ans is the same as the > one > > without MPI. However, on 2 processors, I found that I've to increase the > > KSPSetTolerances to 1.0e-6, else those grid pts on the edge will be > > different. On 4 processors, KSPSetTolerances has to be decreased to > 1.0e-7. > > On 8 processors, when KSPSetTolerances is 1.0e-8, the difference of the > last > > pt between 1 and 8 processors is about 3%. > > > > Are you using the same number of grid points when changing the number of > processors? > > Run the cases with -ksp_monitor_true_residual and send us ALL the > output. > > Barry > > > > > May I know why this is so? Also, does this happens only on very small > grids? > > Does it happen on large grids as well? I usually solve grids with approx > > 20000 to 55000 pts. > > > > Thank you. > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Mon Jun 18 16:02:04 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Mon, 18 Jun 2007 16:02:04 -0500 (CDT) Subject: KSPSetTolerances and processors size In-Reply-To: <804ab5d40706171944s21ccd6able03542b0895e9b08@mail.gmail.com> References: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> <804ab5d40706171944s21ccd6able03542b0895e9b08@mail.gmail.com> Message-ID: Note that with 8 processors and a rtol of 1.e-5 the TRUE residual norm is only 1.e-2 at the end while with one process it is 1.e-5. The preconditioner is not working well with 8 processes, thought the preconditioned residual norm is small the true residual norm is not. What KSP are you using? If gmres try using -ksp_type fgmres if cg try adding -ksp_norm_type unpreconditioned Is the matrix symmetric? Do you expect/want it to be symmetric? Barry On Mon, 18 Jun 2007, Ben Tay wrote: > Oh btw, here's the output when KSPSetTolerances = 1.0e-5. > > > 1: > > 0 KSP preconditioned resid norm 5.509130713952e+01 true resid norm > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 6.561453237357e+00 true resid norm > 8.697577384386e+00 ||Ae||/||Ax|| 2.549285554017e-01 > 2 KSP preconditioned resid norm 1.208347069756e+00 true resid norm > 7.425376743449e+00 ||Ae||/||Ax|| 2.176399798315e-01 > 3 KSP preconditioned resid norm 3.386218089799e-01 true resid norm > 7.347207820518e+00 ||Ae||/||Ax|| 2.153488256722e-01 > 4 KSP preconditioned resid norm 3.296482144730e-01 true resid norm > 7.745880291985e+00 ||Ae||/||Ax|| 2.270340332579e-01 > 5 KSP preconditioned resid norm 3.145738742595e-01 true resid norm > 7.547707467510e+00 ||Ae||/||Ax|| 2.212255293918e-01 > 6 KSP preconditioned resid norm 1.643048266097e-01 true resid norm > 4.306709238860e+00 ||Ae||/||Ax|| 1.262309165273e-01 > 7 KSP preconditioned resid norm 6.078974689223e-02 true resid norm > 4.482652283996e+00 ||Ae||/||Ax|| 1.313878590122e-01 > 8 KSP preconditioned resid norm 6.054372794034e-02 true resid norm > 4.355614139989e+00 ||Ae||/||Ax|| 1.276643335865e-01 > 9 KSP preconditioned resid norm 5.867972436189e-02 true resid norm > 4.233715997285e+00 ||Ae||/||Ax|| 1.240914631132e-01 > 10 KSP preconditioned resid norm 2.168073622951e-02 true resid norm > 2.086394899960e+00 ||Ae||/||Ax|| 6.115284915993e-02 > 11 KSP preconditioned resid norm 1.139327427516e-02 true resid norm > 2.155289979633e+00 ||Ae||/||Ax|| 6.317218424133e-02 > 12 KSP preconditioned resid norm 1.088027785149e-02 true resid norm > 1.991898557592e+00 ||Ae||/||Ax|| 5.838313352696e-02 > 13 KSP preconditioned resid norm 1.072820075665e-02 true resid norm > 1.942479796672e+00 ||Ae||/||Ax|| 5.693465508586e-02 > 14 KSP preconditioned resid norm 3.781319329677e-03 true resid norm > 9.806622346091e-01 ||Ae||/||Ax|| 2.874349899487e-02 > 15 KSP preconditioned resid norm 2.314101409645e-03 true resid norm > 7.976384924484e-01 ||Ae||/||Ax|| 2.337901919420e-02 > 16 KSP preconditioned resid norm 2.293131061139e-03 true resid norm > 7.897410852774e-01 ||Ae||/||Ax|| 2.314754386348e-02 > 17 KSP preconditioned resid norm 2.117223511336e-03 true resid norm > 6.782416967980e-01 ||Ae||/||Ax|| 1.987946393996e-02 > 18 KSP preconditioned resid norm 7.524359734379e-05 true resid norm > 9.092345849564e-04 ||Ae||/||Ax|| 2.664993354130e-05 > > 2: > > 0 32 > 32 64 > 0 KSP preconditioned resid norm 4.902369798248e+01 true resid norm > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 8.253504641663e+00 true resid norm > 1.259698849910e+01 ||Ae||/||Ax|| 3.692214439222e-01 > 2 KSP preconditioned resid norm 3.797891005886e+00 true resid norm > 1.195333867118e+01 ||Ae||/||Ax|| 3.503558778495e-01 > 3 KSP preconditioned resid norm 2.578365901732e+00 true resid norm > 1.159420670971e+01 ||Ae||/||Ax|| 3.398296142602e-01 > 4 KSP preconditioned resid norm 1.568196901288e+00 true resid norm > 9.963750299049e+00 ||Ae||/||Ax|| 2.920404565390e-01 > 5 KSP preconditioned resid norm 1.317764005274e+00 true resid norm > 9.066502566015e+00 ||Ae||/||Ax|| 2.657418611589e-01 > 6 KSP preconditioned resid norm 6.023727405584e-01 true resid norm > 8.058099054033e+00 ||Ae||/||Ax|| 2.361852571517e-01 > 7 KSP preconditioned resid norm 4.957651340342e-02 true resid norm > 7.520037445249e+00 ||Ae||/||Ax|| 2.204145128879e-01 > 8 KSP preconditioned resid norm 2.449473557300e-02 true resid norm > 7.475057378184e+00 ||Ae||/||Ax|| 2.190961338713e-01 > 9 KSP preconditioned resid norm 2.361338376271e-02 true resid norm > 7.217194046579e+00 ||Ae||/||Ax|| 2.115380836566e-01 > 10 KSP preconditioned resid norm 2.307344735925e-02 true resid norm > 7.205616297960e+00 ||Ae||/||Ax|| 2.111987364338e-01 > 11 KSP preconditioned resid norm 1.934171008299e-02 true resid norm > 5.261866236257e+00 ||Ae||/||Ax|| 1.542268495057e-01 > 12 KSP preconditioned resid norm 5.190847895073e-03 true resid norm > 4.466349759791e+00 ||Ae||/||Ax|| 1.309100272251e-01 > 13 KSP preconditioned resid norm 4.871871781446e-03 true resid norm > 4.194634080458e+00 ||Ae||/||Ax|| 1.229459606177e-01 > 14 KSP preconditioned resid norm 4.823921505423e-03 true resid norm > 4.173223968428e+00 ||Ae||/||Ax|| 1.223184239268e-01 > 15 KSP preconditioned resid norm 4.701199647155e-03 true resid norm > 3.957555688130e+00 ||Ae||/||Ax|| 1.159971230964e-01 > 16 KSP preconditioned resid norm 1.035300954721e-03 true resid norm > 2.196668371922e+00 ||Ae||/||Ax|| 6.438499710918e-02 > 17 KSP preconditioned resid norm 8.832653700092e-04 true resid norm > 1.916576324421e+00 ||Ae||/||Ax|| 5.617541668313e-02 > 18 KSP preconditioned resid norm 8.703924311133e-04 true resid norm > 1.916104922195e+00 ||Ae||/||Ax|| 5.616159974502e-02 > 19 KSP preconditioned resid norm 8.698960956884e-04 true resid norm > 1.913670720373e+00 ||Ae||/||Ax|| 5.609025257250e-02 > 20 KSP preconditioned resid norm 3.690946760360e-04 true resid norm > 7.994885772359e-01 ||Ae||/||Ax|| 2.343324572435e-02 > > 4: > > 0 16 > 32 48 > 48 64 > 0 KSP preconditioned resid norm 4.414786383499e+01 true resid norm > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 7.579678467669e+00 true resid norm > 1.423835009315e+01 ||Ae||/||Ax|| 4.173302357811e-01 > 2 KSP preconditioned resid norm 2.972753009220e+00 true resid norm > 1.290812750005e+01 ||Ae||/||Ax|| 3.783410197001e-01 > 3 KSP preconditioned resid norm 1.347960602345e+00 true resid norm > 1.173368275935e+01 ||Ae||/||Ax|| 3.439176983641e-01 > 4 KSP preconditioned resid norm 1.111052862809e+00 true resid norm > 1.106221549565e+01 ||Ae||/||Ax|| 3.242367950541e-01 > 5 KSP preconditioned resid norm 9.872224937494e-01 true resid norm > 1.005157038653e+01 ||Ae||/||Ax|| 2.946144891744e-01 > 6 KSP preconditioned resid norm 7.251219493841e-01 true resid norm > 9.007852893929e+00 ||Ae||/||Ax|| 2.640228219921e-01 > 7 KSP preconditioned resid norm 5.925185640664e-01 true resid norm > 8.104036732737e+00 ||Ae||/||Ax|| 2.375317040476e-01 > 8 KSP preconditioned resid norm 3.381465672631e-01 true resid norm > 7.256440004925e+00 ||Ae||/||Ax|| 2.126883942574e-01 > 9 KSP preconditioned resid norm 1.647154013552e-01 true resid norm > 7.263797232535e+00 ||Ae||/||Ax|| 2.129040367661e-01 > 10 KSP preconditioned resid norm 7.697425793821e-02 true resid norm > 7.155391777961e+00 ||Ae||/||Ax|| 2.097266409567e-01 > 11 KSP preconditioned resid norm 3.477770299629e-02 true resid norm > 7.127853631055e+00 ||Ae||/||Ax|| 2.089194897583e-01 > 12 KSP preconditioned resid norm 2.573627666614e-02 true resid norm > 7.088156599392e+00 ||Ae||/||Ax|| 2.077559580657e-01 > 13 KSP preconditioned resid norm 2.221352319865e-02 true resid norm > 7.093825972365e+00 ||Ae||/||Ax|| 2.079221290577e-01 > 14 KSP preconditioned resid norm 2.093106984691e-02 true resid norm > 7.062268285770e+00 ||Ae||/||Ax|| 2.069971639669e-01 > 15 KSP preconditioned resid norm 2.034509930217e-02 true resid norm > 7.031405865561e+00 ||Ae||/||Ax|| 2.060925773386e-01 > 16 KSP preconditioned resid norm 2.029393080560e-02 true resid norm > 7.008984378537e+00 ||Ae||/||Ax|| 2.054353969487e-01 > 17 KSP preconditioned resid norm 1.587358534265e-02 true resid norm > 4.635842103718e+00 ||Ae||/||Ax|| 1.358778977572e-01 > 18 KSP preconditioned resid norm 1.055491860699e-02 true resid norm > 3.773993858722e+00 ||Ae||/||Ax|| 1.106168718000e-01 > 19 KSP preconditioned resid norm 5.655638925006e-03 true resid norm > 4.203919883144e+00 ||Ae||/||Ax|| 1.232181302299e-01 > 20 KSP preconditioned resid norm 4.767909232406e-03 true resid norm > 4.121869307404e+00 ||Ae||/||Ax|| 1.208132036833e-01 > 21 KSP preconditioned resid norm 4.648572929978e-03 true resid norm > 4.076834878296e+00 ||Ae||/||Ax|| 1.194932312992e-01 > 22 KSP preconditioned resid norm 4.638216815872e-03 true resid norm > 4.058874907114e+00 ||Ae||/||Ax|| 1.189668192529e-01 > 23 KSP preconditioned resid norm 1.851801714075e-03 true resid norm > 2.017702443794e+00 ||Ae||/||Ax|| 5.913945303323e-02 > 24 KSP preconditioned resid norm 9.594251508173e-04 true resid norm > 2.065135975225e+00 ||Ae||/||Ax|| 6.052974381317e-02 > 25 KSP preconditioned resid norm 8.609050236229e-04 true resid norm > 1.901663497990e+00 ||Ae||/||Ax|| 5.573831734719e-02 > 26 KSP preconditioned resid norm 8.607029066323e-04 true resid norm > 1.901221069645e+00 ||Ae||/||Ax|| 5.572534964205e-02 > 27 KSP preconditioned resid norm 6.010429111401e-04 true resid norm > 1.025962923033e+00 ||Ae||/||Ax|| 3.007127551793e-02 > 28 KSP preconditioned resid norm 2.036565987243e-04 true resid norm > 8.385451121270e-01 ||Ae||/||Ax|| 2.457800426788e-02 > > 8: > > 8 16 > 24 32 > 56 64 > 16 24 > 48 56 > 0 8 > 32 40 > 40 48 > 0 KSP preconditioned resid norm 4.299803638671e+01 true resid norm > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > 1 KSP preconditioned resid norm 9.603727351867e+00 true resid norm > 1.922897810349e+01 ||Ae||/||Ax|| 5.636070129797e-01 > 2 KSP preconditioned resid norm 2.931835632556e+00 true resid norm > 1.355792423218e+01 ||Ae||/||Ax|| 3.973867533457e-01 > 3 KSP preconditioned resid norm 1.314351599619e+00 true resid norm > 9.882281425137e+00 ||Ae||/||Ax|| 2.896525798443e-01 > 4 KSP preconditioned resid norm 8.218956530484e-01 true resid norm > 9.318760482806e+00 ||Ae||/||Ax|| 2.731356150140e-01 > 5 KSP preconditioned resid norm 6.895693486764e-01 true resid norm > 9.360126907217e+00 ||Ae||/||Ax|| 2.743480770998e-01 > 6 KSP preconditioned resid norm 6.138748402770e-01 true resid norm > 9.020243051395e+00 ||Ae||/||Ax|| 2.643859811575e-01 > 7 KSP preconditioned resid norm 5.265342569996e-01 true resid norm > 8.781477094899e+00 ||Ae||/||Ax|| 2.573876806333e-01 > 8 KSP preconditioned resid norm 4.403325671754e-01 true resid norm > 8.314776073768e+00 ||Ae||/||Ax|| 2.437085362160e-01 > 9 KSP preconditioned resid norm 2.353592633657e-01 true resid norm > 7.347976506279e+00 ||Ae||/||Ax|| 2.153713560783e-01 > 10 KSP preconditioned resid norm 8.943808926292e-02 true resid norm > 6.972332890712e+00 ||Ae||/||Ax|| 2.043611310432e-01 > 11 KSP preconditioned resid norm 5.930469791557e-02 true resid norm > 6.957386646797e+00 ||Ae||/||Ax|| 2.039230522310e-01 > 12 KSP preconditioned resid norm 5.283812047599e-02 true resid norm > 6.981023245883e+00 ||Ae||/||Ax|| 2.046158479134e-01 > 13 KSP preconditioned resid norm 3.665176395384e-02 true resid norm > 6.992078556546e+00 ||Ae||/||Ax|| 2.049398823258e-01 > 14 KSP preconditioned resid norm 2.516790937741e-02 true resid norm > 6.949891196404e+00 ||Ae||/||Ax|| 2.037033583718e-01 > 15 KSP preconditioned resid norm 2.192690814272e-02 true resid norm > 6.927621207906e+00 ||Ae||/||Ax|| 2.030506184483e-01 > 16 KSP preconditioned resid norm 2.058802964863e-02 true resid norm > 6.919125260713e+00 ||Ae||/||Ax|| 2.028015997332e-01 > 17 KSP preconditioned resid norm 1.984533974458e-02 true resid norm > 6.853733693988e+00 ||Ae||/||Ax|| 2.008849536484e-01 > 18 KSP preconditioned resid norm 1.958243371255e-02 true resid norm > 6.766030769290e+00 ||Ae||/||Ax|| 1.983143550887e-01 > 19 KSP preconditioned resid norm 1.874262002187e-02 true resid norm > 6.323230908702e+00 ||Ae||/||Ax|| 1.853357607281e-01 > 20 KSP preconditioned resid norm 1.754461572091e-02 true resid norm > 5.538708901675e+00 ||Ae||/||Ax|| 1.623411895857e-01 > 21 KSP preconditioned resid norm 1.184321475064e-02 true resid norm > 3.839931686898e+00 ||Ae||/||Ax|| 1.125495289688e-01 > 22 KSP preconditioned resid norm 1.070434172478e-02 true resid norm > 3.754159266432e+00 ||Ae||/||Ax|| 1.100355140568e-01 > 23 KSP preconditioned resid norm 8.011880009497e-03 true resid norm > 3.937870836170e+00 ||Ae||/||Ax|| 1.154201542864e-01 > 24 KSP preconditioned resid norm 5.573761552253e-03 true resid norm > 4.205066407359e+00 ||Ae||/||Ax|| 1.232517351924e-01 > 25 KSP preconditioned resid norm 4.810675543540e-03 true resid norm > 4.069723693466e+00 ||Ae||/||Ax|| 1.192848003769e-01 > 26 KSP preconditioned resid norm 4.647944860704e-03 true resid norm > 4.044329745280e+00 ||Ae||/||Ax|| 1.185404962746e-01 > 27 KSP preconditioned resid norm 4.606926939804e-03 true resid norm > 4.039416044569e+00 ||Ae||/||Ax|| 1.183964742593e-01 > 28 KSP preconditioned resid norm 4.606174352197e-03 true resid norm > 4.038658488893e+00 ||Ae||/||Ax|| 1.183742700792e-01 > 29 KSP preconditioned resid norm 4.604980580071e-03 true resid norm > 4.034721549326e+00 ||Ae||/||Ax|| 1.182588772207e-01 > 30 KSP preconditioned resid norm 4.551931835395e-03 true resid norm > 3.942692013899e+00 ||Ae||/||Ax|| 1.155614644259e-01 > 31 KSP preconditioned resid norm 4.534435621643e-03 true resid norm > 3.940744976447e+00 ||Ae||/||Ax|| 1.155043961846e-01 > 32 KSP preconditioned resid norm 4.533889403959e-03 true resid norm > 3.940661031251e+00 ||Ae||/||Ax|| 1.155019357261e-01 > 33 KSP preconditioned resid norm 4.533315616020e-03 true resid norm > 3.940962366962e+00 ||Ae||/||Ax|| 1.155107679646e-01 > 34 KSP preconditioned resid norm 4.533098107272e-03 true resid norm > 3.940998854473e+00 ||Ae||/||Ax|| 1.155118374243e-01 > 35 KSP preconditioned resid norm 4.531113895054e-03 true resid norm > 3.939900266217e+00 ||Ae||/||Ax|| 1.154796374789e-01 > 36 KSP preconditioned resid norm 4.530789523555e-03 true resid norm > 3.939483356865e+00 ||Ae||/||Ax|| 1.154674177430e-01 > 37 KSP preconditioned resid norm 4.530789514003e-03 true resid norm > 3.939490762772e+00 ||Ae||/||Ax|| 1.154676348123e-01 > 38 KSP preconditioned resid norm 4.530624961751e-03 true resid norm > 3.937889462104e+00 ||Ae||/||Ax|| 1.154207002179e-01 > 39 KSP preconditioned resid norm 4.517785703071e-03 true resid norm > 3.927441577896e+00 ||Ae||/||Ax|| 1.151144696539e-01 > 40 KSP preconditioned resid norm 4.508890400648e-03 true resid norm > 3.919421029911e+00 ||Ae||/||Ax|| 1.148793850297e-01 > 41 KSP preconditioned resid norm 4.508823049754e-03 true resid norm > 3.920408845458e+00 ||Ae||/||Ax|| 1.149083381943e-01 > 42 KSP preconditioned resid norm 4.504581641358e-03 true resid norm > 3.910936323861e+00 ||Ae||/||Ax|| 1.146306957958e-01 > 43 KSP preconditioned resid norm 4.496299729031e-03 true resid norm > 3.892573202489e+00 ||Ae||/||Ax|| 1.140924672987e-01 > 44 KSP preconditioned resid norm 4.327165698785e-03 true resid norm > 3.499303379330e+00 ||Ae||/||Ax|| 1.025656129265e-01 > 45 KSP preconditioned resid norm 3.860049921599e-03 true resid norm > 2.642394407576e+00 ||Ae||/||Ax|| 7.744935852298e-02 > 46 KSP preconditioned resid norm 3.813681936798e-03 true resid norm > 2.561643926848e+00 ||Ae||/||Ax|| 7.508253814415e-02 > 47 KSP preconditioned resid norm 3.811608329841e-03 true resid norm > 2.553393452252e+00 ||Ae||/||Ax|| 7.484071430319e-02 > 48 KSP preconditioned resid norm 3.805700908518e-03 true resid norm > 2.559614961583e+00 ||Ae||/||Ax|| 7.502306857451e-02 > 49 KSP preconditioned resid norm 3.783124026053e-03 true resid norm > 2.523808739092e+00 ||Ae||/||Ax|| 7.397357764494e-02 > 50 KSP preconditioned resid norm 3.777662131381e-03 true resid norm > 2.516105834856e+00 ||Ae||/||Ax|| 7.374780325255e-02 > 51 KSP preconditioned resid norm 3.710923429451e-03 true resid norm > 2.426657981798e+00 ||Ae||/||Ax|| 7.112606032852e-02 > 52 KSP preconditioned resid norm 3.604808013597e-03 true resid norm > 2.303594181107e+00 ||Ae||/||Ax|| 6.751902407624e-02 > 53 KSP preconditioned resid norm 3.513880489788e-03 true resid norm > 2.188212014004e+00 ||Ae||/||Ax|| 6.413713876742e-02 > 54 KSP preconditioned resid norm 3.320184202285e-03 true resid norm > 1.978987642137e+00 ||Ae||/||Ax|| 5.800471079148e-02 > 55 KSP preconditioned resid norm 2.195662794099e-03 true resid norm > 1.448538675887e+00 ||Ae||/||Ax|| 4.245709532291e-02 > 56 KSP preconditioned resid norm 9.077826763324e-04 true resid norm > 1.628573968470e+00 ||Ae||/||Ax|| 4.773398278607e-02 > 57 KSP preconditioned resid norm 7.602131391716e-04 true resid norm > 1.659109675600e+00 ||Ae||/||Ax|| 4.862899335772e-02 > 58 KSP preconditioned resid norm 7.450227847936e-04 true resid norm > 1.651479746174e+00 ||Ae||/||Ax|| 4.840535787852e-02 > 59 KSP preconditioned resid norm 7.410161195392e-04 true resid norm > 1.649502155114e+00 ||Ae||/||Ax|| 4.834739410196e-02 > 60 KSP preconditioned resid norm 7.399447579004e-04 true resid norm > 1.648188611058e+00 ||Ae||/||Ax|| 4.830889373871e-02 > 61 KSP preconditioned resid norm 7.399146825366e-04 true resid norm > 1.648156339888e+00 ||Ae||/||Ax|| 4.830794786121e-02 > 62 KSP preconditioned resid norm 7.399119217730e-04 true resid norm > 1.648143662498e+00 ||Ae||/||Ax|| 4.830757628317e-02 > 63 KSP preconditioned resid norm 7.399115190929e-04 true resid norm > 1.648149747433e+00 ||Ae||/||Ax|| 4.830775463441e-02 > 64 KSP preconditioned resid norm 7.398927702838e-04 true resid norm > 1.648083443482e+00 ||Ae||/||Ax|| 4.830581124607e-02 > 65 KSP preconditioned resid norm 7.398398384099e-04 true resid norm > 1.647873653551e+00 ||Ae||/||Ax|| 4.829966224141e-02 > 66 KSP preconditioned resid norm 7.398251502315e-04 true resid norm > 1.647783674785e+00 ||Ae||/||Ax|| 4.829702493725e-02 > 67 KSP preconditioned resid norm 7.398217631044e-04 true resid norm > 1.647733028046e+00 ||Ae||/||Ax|| 4.829554046641e-02 > 68 KSP preconditioned resid norm 7.398045634717e-04 true resid norm > 1.647630453201e+00 ||Ae||/||Ax|| 4.829253396748e-02 > 69 KSP preconditioned resid norm 7.397586859381e-04 true resid norm > 1.647387302132e+00 ||Ae||/||Ax|| 4.828540713804e-02 > 70 KSP preconditioned resid norm 7.396782241138e-04 true resid norm > 1.646889429724e+00 ||Ae||/||Ax|| 4.827081435109e-02 > 71 KSP preconditioned resid norm 7.395189566969e-04 true resid norm > 1.646041167917e+00 ||Ae||/||Ax|| 4.824595154763e-02 > 72 KSP preconditioned resid norm 7.391300711199e-04 true resid norm > 1.643970513576e+00 ||Ae||/||Ax|| 4.818526005889e-02 > 73 KSP preconditioned resid norm 7.367639912300e-04 true resid norm > 1.631221838831e+00 ||Ae||/||Ax|| 4.781159264642e-02 > 74 KSP preconditioned resid norm 7.075386327019e-04 true resid norm > 1.473482203196e+00 ||Ae||/||Ax|| 4.318819745660e-02 > 75 KSP preconditioned resid norm 6.769663644505e-04 true resid norm > 1.324870886213e+00 ||Ae||/||Ax|| 3.883235597562e-02 > 76 KSP preconditioned resid norm 6.510062346881e-04 true resid norm > 1.209103850108e+00 ||Ae||/||Ax|| 3.543919004296e-02 > 77 KSP preconditioned resid norm 6.416005299115e-04 true resid norm > 1.174343461999e+00 ||Ae||/||Ax|| 3.442035282725e-02 > 78 KSP preconditioned resid norm 6.269785791288e-04 true resid norm > 1.115598946804e+00 ||Ae||/||Ax|| 3.269853378102e-02 > 79 KSP preconditioned resid norm 6.143599514076e-04 true resid norm > 1.060258719301e+00 ||Ae||/||Ax|| 3.107649540993e-02 > 80 KSP preconditioned resid norm 6.118239459355e-04 true resid norm > 1.049506356947e+00 ||Ae||/||Ax|| 3.076134050174e-02 > 81 KSP preconditioned resid norm 6.112876406857e-04 true resid norm > 1.046662765401e+00 ||Ae||/||Ax|| 3.067799399581e-02 > 82 KSP preconditioned resid norm 6.092506607543e-04 true resid norm > 1.042978389425e+00 ||Ae||/||Ax|| 3.057000385056e-02 > 83 KSP preconditioned resid norm 6.081618319409e-04 true resid norm > 1.040456343908e+00 ||Ae||/||Ax|| 3.049608195349e-02 > 84 KSP preconditioned resid norm 6.071647595071e-04 true resid norm > 1.037276486552e+00 ||Ae||/||Ax|| 3.040287939761e-02 > 85 KSP preconditioned resid norm 5.795095806265e-04 true resid norm > 9.478301874350e-01 ||Ae||/||Ax|| 2.778118202003e-02 > 86 KSP preconditioned resid norm 4.787555615154e-04 true resid norm > 6.865840307207e-01 ||Ae||/||Ax|| 2.012398020485e-02 > 87 KSP preconditioned resid norm 4.213257765496e-04 true resid norm > 5.905989111727e-01 ||Ae||/||Ax|| 1.731062807413e-02 > > It seems that the no. of lines is much lesser compared to the eariler case > when KSPSetTolerances = 1.0e-8 > > Thanks again > > > > On 6/17/07, Barry Smith wrote: > > > > > > Ben, > > > > > > On Sat, 16 Jun 2007, Ben Tay wrote: > > > > > Hi, > > > > > > I am trying to use PETSc to solve my poisson eqn. In the past, when I'm > > not > > > using MPI, I set KSPSetTolerances to 1.0e-5. This seems to be good > > enuff. > > > > > > Now, I'm trying to use PETSc with MPI to solve the eqn. I am using a > > very > > > small no. of pts, only 16x4. On 1 processor, the ans is the same as the > > one > > > without MPI. However, on 2 processors, I found that I've to increase the > > > KSPSetTolerances to 1.0e-6, else those grid pts on the edge will be > > > different. On 4 processors, KSPSetTolerances has to be decreased to > > 1.0e-7. > > > On 8 processors, when KSPSetTolerances is 1.0e-8, the difference of the > > last > > > pt between 1 and 8 processors is about 3%. > > > > > > > Are you using the same number of grid points when changing the number of > > processors? > > > > Run the cases with -ksp_monitor_true_residual and send us ALL the > > output. > > > > Barry > > > > > > > > > May I know why this is so? Also, does this happens only on very small > > grids? > > > Does it happen on large grids as well? I usually solve grids with approx > > > 20000 to 55000 pts. > > > > > > Thank you. > > > > > > > > From zonexo at gmail.com Mon Jun 18 22:14:29 2007 From: zonexo at gmail.com (Ben Tay) Date: Tue, 19 Jun 2007 11:14:29 +0800 Subject: KSPSetTolerances and processors size In-Reply-To: References: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> <804ab5d40706171944s21ccd6able03542b0895e9b08@mail.gmail.com> Message-ID: <804ab5d40706182014r224c6b21p95f0f2a8dc40fcf5@mail.gmail.com> Hi, I've just tested with -ksp_type fgmres with rtol of 1.e-5 with 8 proceesors. It 's much better, although the last value still has some difference at .638e-2 and .635e-2. The original one was done with the default precon and solver. Btw, if I use hypre as the precond then the value with 1 or 8 processors is the same. So am I right to say that the problem is due to the precon? What is the best way to ensure that my results are correct? I found that if I use the default precond and solver and did not use call KSPSetTolerances(ksp,tol,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_INTEGER,ierr) to set the tolerence to 1.e-8 when using 8 processors, I 'll get incorrect results. How can I avoid this? Thanks On 6/19/07, Barry Smith wrote: > > > Note that with 8 processors and a rtol of 1.e-5 the TRUE residual norm > is only 1.e-2 at the end while with one process it is 1.e-5. The > preconditioner is not working well with 8 processes, thought the > preconditioned residual norm is small the true residual norm is > not. > > What KSP are you using? If gmres try using -ksp_type fgmres > if cg try adding -ksp_norm_type unpreconditioned > > Is the matrix symmetric? Do you expect/want it to be symmetric? > > Barry > > > On Mon, 18 Jun 2007, Ben Tay wrote: > > > Oh btw, here's the output when KSPSetTolerances = 1.0e-5. > > > > > > 1: > > > > 0 KSP preconditioned resid norm 5.509130713952e+01 true resid norm > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 6.561453237357e+00 true resid norm > > 8.697577384386e+00 ||Ae||/||Ax|| 2.549285554017e-01 > > 2 KSP preconditioned resid norm 1.208347069756e+00 true resid norm > > 7.425376743449e+00 ||Ae||/||Ax|| 2.176399798315e-01 > > 3 KSP preconditioned resid norm 3.386218089799e-01 true resid norm > > 7.347207820518e+00 ||Ae||/||Ax|| 2.153488256722e-01 > > 4 KSP preconditioned resid norm 3.296482144730e-01 true resid norm > > 7.745880291985e+00 ||Ae||/||Ax|| 2.270340332579e-01 > > 5 KSP preconditioned resid norm 3.145738742595e-01 true resid norm > > 7.547707467510e+00 ||Ae||/||Ax|| 2.212255293918e-01 > > 6 KSP preconditioned resid norm 1.643048266097e-01 true resid norm > > 4.306709238860e+00 ||Ae||/||Ax|| 1.262309165273e-01 > > 7 KSP preconditioned resid norm 6.078974689223e-02 true resid norm > > 4.482652283996e+00 ||Ae||/||Ax|| 1.313878590122e-01 > > 8 KSP preconditioned resid norm 6.054372794034e-02 true resid norm > > 4.355614139989e+00 ||Ae||/||Ax|| 1.276643335865e-01 > > 9 KSP preconditioned resid norm 5.867972436189e-02 true resid norm > > 4.233715997285e+00 ||Ae||/||Ax|| 1.240914631132e-01 > > 10 KSP preconditioned resid norm 2.168073622951e-02 true resid norm > > 2.086394899960e+00 ||Ae||/||Ax|| 6.115284915993e-02 > > 11 KSP preconditioned resid norm 1.139327427516e-02 true resid norm > > 2.155289979633e+00 ||Ae||/||Ax|| 6.317218424133e-02 > > 12 KSP preconditioned resid norm 1.088027785149e-02 true resid norm > > 1.991898557592e+00 ||Ae||/||Ax|| 5.838313352696e-02 > > 13 KSP preconditioned resid norm 1.072820075665e-02 true resid norm > > 1.942479796672e+00 ||Ae||/||Ax|| 5.693465508586e-02 > > 14 KSP preconditioned resid norm 3.781319329677e-03 true resid norm > > 9.806622346091e-01 ||Ae||/||Ax|| 2.874349899487e-02 > > 15 KSP preconditioned resid norm 2.314101409645e-03 true resid norm > > 7.976384924484e-01 ||Ae||/||Ax|| 2.337901919420e-02 > > 16 KSP preconditioned resid norm 2.293131061139e-03 true resid norm > > 7.897410852774e-01 ||Ae||/||Ax|| 2.314754386348e-02 > > 17 KSP preconditioned resid norm 2.117223511336e-03 true resid norm > > 6.782416967980e-01 ||Ae||/||Ax|| 1.987946393996e-02 > > 18 KSP preconditioned resid norm 7.524359734379e-05 true resid norm > > 9.092345849564e-04 ||Ae||/||Ax|| 2.664993354130e-05 > > > > 2: > > > > 0 32 > > 32 64 > > 0 KSP preconditioned resid norm 4.902369798248e+01 true resid norm > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 8.253504641663e+00 true resid norm > > 1.259698849910e+01 ||Ae||/||Ax|| 3.692214439222e-01 > > 2 KSP preconditioned resid norm 3.797891005886e+00 true resid norm > > 1.195333867118e+01 ||Ae||/||Ax|| 3.503558778495e-01 > > 3 KSP preconditioned resid norm 2.578365901732e+00 true resid norm > > 1.159420670971e+01 ||Ae||/||Ax|| 3.398296142602e-01 > > 4 KSP preconditioned resid norm 1.568196901288e+00 true resid norm > > 9.963750299049e+00 ||Ae||/||Ax|| 2.920404565390e-01 > > 5 KSP preconditioned resid norm 1.317764005274e+00 true resid norm > > 9.066502566015e+00 ||Ae||/||Ax|| 2.657418611589e-01 > > 6 KSP preconditioned resid norm 6.023727405584e-01 true resid norm > > 8.058099054033e+00 ||Ae||/||Ax|| 2.361852571517e-01 > > 7 KSP preconditioned resid norm 4.957651340342e-02 true resid norm > > 7.520037445249e+00 ||Ae||/||Ax|| 2.204145128879e-01 > > 8 KSP preconditioned resid norm 2.449473557300e-02 true resid norm > > 7.475057378184e+00 ||Ae||/||Ax|| 2.190961338713e-01 > > 9 KSP preconditioned resid norm 2.361338376271e-02 true resid norm > > 7.217194046579e+00 ||Ae||/||Ax|| 2.115380836566e-01 > > 10 KSP preconditioned resid norm 2.307344735925e-02 true resid norm > > 7.205616297960e+00 ||Ae||/||Ax|| 2.111987364338e-01 > > 11 KSP preconditioned resid norm 1.934171008299e-02 true resid norm > > 5.261866236257e+00 ||Ae||/||Ax|| 1.542268495057e-01 > > 12 KSP preconditioned resid norm 5.190847895073e-03 true resid norm > > 4.466349759791e+00 ||Ae||/||Ax|| 1.309100272251e-01 > > 13 KSP preconditioned resid norm 4.871871781446e-03 true resid norm > > 4.194634080458e+00 ||Ae||/||Ax|| 1.229459606177e-01 > > 14 KSP preconditioned resid norm 4.823921505423e-03 true resid norm > > 4.173223968428e+00 ||Ae||/||Ax|| 1.223184239268e-01 > > 15 KSP preconditioned resid norm 4.701199647155e-03 true resid norm > > 3.957555688130e+00 ||Ae||/||Ax|| 1.159971230964e-01 > > 16 KSP preconditioned resid norm 1.035300954721e-03 true resid norm > > 2.196668371922e+00 ||Ae||/||Ax|| 6.438499710918e-02 > > 17 KSP preconditioned resid norm 8.832653700092e-04 true resid norm > > 1.916576324421e+00 ||Ae||/||Ax|| 5.617541668313e-02 > > 18 KSP preconditioned resid norm 8.703924311133e-04 true resid norm > > 1.916104922195e+00 ||Ae||/||Ax|| 5.616159974502e-02 > > 19 KSP preconditioned resid norm 8.698960956884e-04 true resid norm > > 1.913670720373e+00 ||Ae||/||Ax|| 5.609025257250e-02 > > 20 KSP preconditioned resid norm 3.690946760360e-04 true resid norm > > 7.994885772359e-01 ||Ae||/||Ax|| 2.343324572435e-02 > > > > 4: > > > > 0 16 > > 32 48 > > 48 64 > > 0 KSP preconditioned resid norm 4.414786383499e+01 true resid norm > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 7.579678467669e+00 true resid norm > > 1.423835009315e+01 ||Ae||/||Ax|| 4.173302357811e-01 > > 2 KSP preconditioned resid norm 2.972753009220e+00 true resid norm > > 1.290812750005e+01 ||Ae||/||Ax|| 3.783410197001e-01 > > 3 KSP preconditioned resid norm 1.347960602345e+00 true resid norm > > 1.173368275935e+01 ||Ae||/||Ax|| 3.439176983641e-01 > > 4 KSP preconditioned resid norm 1.111052862809e+00 true resid norm > > 1.106221549565e+01 ||Ae||/||Ax|| 3.242367950541e-01 > > 5 KSP preconditioned resid norm 9.872224937494e-01 true resid norm > > 1.005157038653e+01 ||Ae||/||Ax|| 2.946144891744e-01 > > 6 KSP preconditioned resid norm 7.251219493841e-01 true resid norm > > 9.007852893929e+00 ||Ae||/||Ax|| 2.640228219921e-01 > > 7 KSP preconditioned resid norm 5.925185640664e-01 true resid norm > > 8.104036732737e+00 ||Ae||/||Ax|| 2.375317040476e-01 > > 8 KSP preconditioned resid norm 3.381465672631e-01 true resid norm > > 7.256440004925e+00 ||Ae||/||Ax|| 2.126883942574e-01 > > 9 KSP preconditioned resid norm 1.647154013552e-01 true resid norm > > 7.263797232535e+00 ||Ae||/||Ax|| 2.129040367661e-01 > > 10 KSP preconditioned resid norm 7.697425793821e-02 true resid norm > > 7.155391777961e+00 ||Ae||/||Ax|| 2.097266409567e-01 > > 11 KSP preconditioned resid norm 3.477770299629e-02 true resid norm > > 7.127853631055e+00 ||Ae||/||Ax|| 2.089194897583e-01 > > 12 KSP preconditioned resid norm 2.573627666614e-02 true resid norm > > 7.088156599392e+00 ||Ae||/||Ax|| 2.077559580657e-01 > > 13 KSP preconditioned resid norm 2.221352319865e-02 true resid norm > > 7.093825972365e+00 ||Ae||/||Ax|| 2.079221290577e-01 > > 14 KSP preconditioned resid norm 2.093106984691e-02 true resid norm > > 7.062268285770e+00 ||Ae||/||Ax|| 2.069971639669e-01 > > 15 KSP preconditioned resid norm 2.034509930217e-02 true resid norm > > 7.031405865561e+00 ||Ae||/||Ax|| 2.060925773386e-01 > > 16 KSP preconditioned resid norm 2.029393080560e-02 true resid norm > > 7.008984378537e+00 ||Ae||/||Ax|| 2.054353969487e-01 > > 17 KSP preconditioned resid norm 1.587358534265e-02 true resid norm > > 4.635842103718e+00 ||Ae||/||Ax|| 1.358778977572e-01 > > 18 KSP preconditioned resid norm 1.055491860699e-02 true resid norm > > 3.773993858722e+00 ||Ae||/||Ax|| 1.106168718000e-01 > > 19 KSP preconditioned resid norm 5.655638925006e-03 true resid norm > > 4.203919883144e+00 ||Ae||/||Ax|| 1.232181302299e-01 > > 20 KSP preconditioned resid norm 4.767909232406e-03 true resid norm > > 4.121869307404e+00 ||Ae||/||Ax|| 1.208132036833e-01 > > 21 KSP preconditioned resid norm 4.648572929978e-03 true resid norm > > 4.076834878296e+00 ||Ae||/||Ax|| 1.194932312992e-01 > > 22 KSP preconditioned resid norm 4.638216815872e-03 true resid norm > > 4.058874907114e+00 ||Ae||/||Ax|| 1.189668192529e-01 > > 23 KSP preconditioned resid norm 1.851801714075e-03 true resid norm > > 2.017702443794e+00 ||Ae||/||Ax|| 5.913945303323e-02 > > 24 KSP preconditioned resid norm 9.594251508173e-04 true resid norm > > 2.065135975225e+00 ||Ae||/||Ax|| 6.052974381317e-02 > > 25 KSP preconditioned resid norm 8.609050236229e-04 true resid norm > > 1.901663497990e+00 ||Ae||/||Ax|| 5.573831734719e-02 > > 26 KSP preconditioned resid norm 8.607029066323e-04 true resid norm > > 1.901221069645e+00 ||Ae||/||Ax|| 5.572534964205e-02 > > 27 KSP preconditioned resid norm 6.010429111401e-04 true resid norm > > 1.025962923033e+00 ||Ae||/||Ax|| 3.007127551793e-02 > > 28 KSP preconditioned resid norm 2.036565987243e-04 true resid norm > > 8.385451121270e-01 ||Ae||/||Ax|| 2.457800426788e-02 > > > > 8: > > > > 8 16 > > 24 32 > > 56 64 > > 16 24 > > 48 56 > > 0 8 > > 32 40 > > 40 48 > > 0 KSP preconditioned resid norm 4.299803638671e+01 true resid norm > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > 1 KSP preconditioned resid norm 9.603727351867e+00 true resid norm > > 1.922897810349e+01 ||Ae||/||Ax|| 5.636070129797e-01 > > 2 KSP preconditioned resid norm 2.931835632556e+00 true resid norm > > 1.355792423218e+01 ||Ae||/||Ax|| 3.973867533457e-01 > > 3 KSP preconditioned resid norm 1.314351599619e+00 true resid norm > > 9.882281425137e+00 ||Ae||/||Ax|| 2.896525798443e-01 > > 4 KSP preconditioned resid norm 8.218956530484e-01 true resid norm > > 9.318760482806e+00 ||Ae||/||Ax|| 2.731356150140e-01 > > 5 KSP preconditioned resid norm 6.895693486764e-01 true resid norm > > 9.360126907217e+00 ||Ae||/||Ax|| 2.743480770998e-01 > > 6 KSP preconditioned resid norm 6.138748402770e-01 true resid norm > > 9.020243051395e+00 ||Ae||/||Ax|| 2.643859811575e-01 > > 7 KSP preconditioned resid norm 5.265342569996e-01 true resid norm > > 8.781477094899e+00 ||Ae||/||Ax|| 2.573876806333e-01 > > 8 KSP preconditioned resid norm 4.403325671754e-01 true resid norm > > 8.314776073768e+00 ||Ae||/||Ax|| 2.437085362160e-01 > > 9 KSP preconditioned resid norm 2.353592633657e-01 true resid norm > > 7.347976506279e+00 ||Ae||/||Ax|| 2.153713560783e-01 > > 10 KSP preconditioned resid norm 8.943808926292e-02 true resid norm > > 6.972332890712e+00 ||Ae||/||Ax|| 2.043611310432e-01 > > 11 KSP preconditioned resid norm 5.930469791557e-02 true resid norm > > 6.957386646797e+00 ||Ae||/||Ax|| 2.039230522310e-01 > > 12 KSP preconditioned resid norm 5.283812047599e-02 true resid norm > > 6.981023245883e+00 ||Ae||/||Ax|| 2.046158479134e-01 > > 13 KSP preconditioned resid norm 3.665176395384e-02 true resid norm > > 6.992078556546e+00 ||Ae||/||Ax|| 2.049398823258e-01 > > 14 KSP preconditioned resid norm 2.516790937741e-02 true resid norm > > 6.949891196404e+00 ||Ae||/||Ax|| 2.037033583718e-01 > > 15 KSP preconditioned resid norm 2.192690814272e-02 true resid norm > > 6.927621207906e+00 ||Ae||/||Ax|| 2.030506184483e-01 > > 16 KSP preconditioned resid norm 2.058802964863e-02 true resid norm > > 6.919125260713e+00 ||Ae||/||Ax|| 2.028015997332e-01 > > 17 KSP preconditioned resid norm 1.984533974458e-02 true resid norm > > 6.853733693988e+00 ||Ae||/||Ax|| 2.008849536484e-01 > > 18 KSP preconditioned resid norm 1.958243371255e-02 true resid norm > > 6.766030769290e+00 ||Ae||/||Ax|| 1.983143550887e-01 > > 19 KSP preconditioned resid norm 1.874262002187e-02 true resid norm > > 6.323230908702e+00 ||Ae||/||Ax|| 1.853357607281e-01 > > 20 KSP preconditioned resid norm 1.754461572091e-02 true resid norm > > 5.538708901675e+00 ||Ae||/||Ax|| 1.623411895857e-01 > > 21 KSP preconditioned resid norm 1.184321475064e-02 true resid norm > > 3.839931686898e+00 ||Ae||/||Ax|| 1.125495289688e-01 > > 22 KSP preconditioned resid norm 1.070434172478e-02 true resid norm > > 3.754159266432e+00 ||Ae||/||Ax|| 1.100355140568e-01 > > 23 KSP preconditioned resid norm 8.011880009497e-03 true resid norm > > 3.937870836170e+00 ||Ae||/||Ax|| 1.154201542864e-01 > > 24 KSP preconditioned resid norm 5.573761552253e-03 true resid norm > > 4.205066407359e+00 ||Ae||/||Ax|| 1.232517351924e-01 > > 25 KSP preconditioned resid norm 4.810675543540e-03 true resid norm > > 4.069723693466e+00 ||Ae||/||Ax|| 1.192848003769e-01 > > 26 KSP preconditioned resid norm 4.647944860704e-03 true resid norm > > 4.044329745280e+00 ||Ae||/||Ax|| 1.185404962746e-01 > > 27 KSP preconditioned resid norm 4.606926939804e-03 true resid norm > > 4.039416044569e+00 ||Ae||/||Ax|| 1.183964742593e-01 > > 28 KSP preconditioned resid norm 4.606174352197e-03 true resid norm > > 4.038658488893e+00 ||Ae||/||Ax|| 1.183742700792e-01 > > 29 KSP preconditioned resid norm 4.604980580071e-03 true resid norm > > 4.034721549326e+00 ||Ae||/||Ax|| 1.182588772207e-01 > > 30 KSP preconditioned resid norm 4.551931835395e-03 true resid norm > > 3.942692013899e+00 ||Ae||/||Ax|| 1.155614644259e-01 > > 31 KSP preconditioned resid norm 4.534435621643e-03 true resid norm > > 3.940744976447e+00 ||Ae||/||Ax|| 1.155043961846e-01 > > 32 KSP preconditioned resid norm 4.533889403959e-03 true resid norm > > 3.940661031251e+00 ||Ae||/||Ax|| 1.155019357261e-01 > > 33 KSP preconditioned resid norm 4.533315616020e-03 true resid norm > > 3.940962366962e+00 ||Ae||/||Ax|| 1.155107679646e-01 > > 34 KSP preconditioned resid norm 4.533098107272e-03 true resid norm > > 3.940998854473e+00 ||Ae||/||Ax|| 1.155118374243e-01 > > 35 KSP preconditioned resid norm 4.531113895054e-03 true resid norm > > 3.939900266217e+00 ||Ae||/||Ax|| 1.154796374789e-01 > > 36 KSP preconditioned resid norm 4.530789523555e-03 true resid norm > > 3.939483356865e+00 ||Ae||/||Ax|| 1.154674177430e-01 > > 37 KSP preconditioned resid norm 4.530789514003e-03 true resid norm > > 3.939490762772e+00 ||Ae||/||Ax|| 1.154676348123e-01 > > 38 KSP preconditioned resid norm 4.530624961751e-03 true resid norm > > 3.937889462104e+00 ||Ae||/||Ax|| 1.154207002179e-01 > > 39 KSP preconditioned resid norm 4.517785703071e-03 true resid norm > > 3.927441577896e+00 ||Ae||/||Ax|| 1.151144696539e-01 > > 40 KSP preconditioned resid norm 4.508890400648e-03 true resid norm > > 3.919421029911e+00 ||Ae||/||Ax|| 1.148793850297e-01 > > 41 KSP preconditioned resid norm 4.508823049754e-03 true resid norm > > 3.920408845458e+00 ||Ae||/||Ax|| 1.149083381943e-01 > > 42 KSP preconditioned resid norm 4.504581641358e-03 true resid norm > > 3.910936323861e+00 ||Ae||/||Ax|| 1.146306957958e-01 > > 43 KSP preconditioned resid norm 4.496299729031e-03 true resid norm > > 3.892573202489e+00 ||Ae||/||Ax|| 1.140924672987e-01 > > 44 KSP preconditioned resid norm 4.327165698785e-03 true resid norm > > 3.499303379330e+00 ||Ae||/||Ax|| 1.025656129265e-01 > > 45 KSP preconditioned resid norm 3.860049921599e-03 true resid norm > > 2.642394407576e+00 ||Ae||/||Ax|| 7.744935852298e-02 > > 46 KSP preconditioned resid norm 3.813681936798e-03 true resid norm > > 2.561643926848e+00 ||Ae||/||Ax|| 7.508253814415e-02 > > 47 KSP preconditioned resid norm 3.811608329841e-03 true resid norm > > 2.553393452252e+00 ||Ae||/||Ax|| 7.484071430319e-02 > > 48 KSP preconditioned resid norm 3.805700908518e-03 true resid norm > > 2.559614961583e+00 ||Ae||/||Ax|| 7.502306857451e-02 > > 49 KSP preconditioned resid norm 3.783124026053e-03 true resid norm > > 2.523808739092e+00 ||Ae||/||Ax|| 7.397357764494e-02 > > 50 KSP preconditioned resid norm 3.777662131381e-03 true resid norm > > 2.516105834856e+00 ||Ae||/||Ax|| 7.374780325255e-02 > > 51 KSP preconditioned resid norm 3.710923429451e-03 true resid norm > > 2.426657981798e+00 ||Ae||/||Ax|| 7.112606032852e-02 > > 52 KSP preconditioned resid norm 3.604808013597e-03 true resid norm > > 2.303594181107e+00 ||Ae||/||Ax|| 6.751902407624e-02 > > 53 KSP preconditioned resid norm 3.513880489788e-03 true resid norm > > 2.188212014004e+00 ||Ae||/||Ax|| 6.413713876742e-02 > > 54 KSP preconditioned resid norm 3.320184202285e-03 true resid norm > > 1.978987642137e+00 ||Ae||/||Ax|| 5.800471079148e-02 > > 55 KSP preconditioned resid norm 2.195662794099e-03 true resid norm > > 1.448538675887e+00 ||Ae||/||Ax|| 4.245709532291e-02 > > 56 KSP preconditioned resid norm 9.077826763324e-04 true resid norm > > 1.628573968470e+00 ||Ae||/||Ax|| 4.773398278607e-02 > > 57 KSP preconditioned resid norm 7.602131391716e-04 true resid norm > > 1.659109675600e+00 ||Ae||/||Ax|| 4.862899335772e-02 > > 58 KSP preconditioned resid norm 7.450227847936e-04 true resid norm > > 1.651479746174e+00 ||Ae||/||Ax|| 4.840535787852e-02 > > 59 KSP preconditioned resid norm 7.410161195392e-04 true resid norm > > 1.649502155114e+00 ||Ae||/||Ax|| 4.834739410196e-02 > > 60 KSP preconditioned resid norm 7.399447579004e-04 true resid norm > > 1.648188611058e+00 ||Ae||/||Ax|| 4.830889373871e-02 > > 61 KSP preconditioned resid norm 7.399146825366e-04 true resid norm > > 1.648156339888e+00 ||Ae||/||Ax|| 4.830794786121e-02 > > 62 KSP preconditioned resid norm 7.399119217730e-04 true resid norm > > 1.648143662498e+00 ||Ae||/||Ax|| 4.830757628317e-02 > > 63 KSP preconditioned resid norm 7.399115190929e-04 true resid norm > > 1.648149747433e+00 ||Ae||/||Ax|| 4.830775463441e-02 > > 64 KSP preconditioned resid norm 7.398927702838e-04 true resid norm > > 1.648083443482e+00 ||Ae||/||Ax|| 4.830581124607e-02 > > 65 KSP preconditioned resid norm 7.398398384099e-04 true resid norm > > 1.647873653551e+00 ||Ae||/||Ax|| 4.829966224141e-02 > > 66 KSP preconditioned resid norm 7.398251502315e-04 true resid norm > > 1.647783674785e+00 ||Ae||/||Ax|| 4.829702493725e-02 > > 67 KSP preconditioned resid norm 7.398217631044e-04 true resid norm > > 1.647733028046e+00 ||Ae||/||Ax|| 4.829554046641e-02 > > 68 KSP preconditioned resid norm 7.398045634717e-04 true resid norm > > 1.647630453201e+00 ||Ae||/||Ax|| 4.829253396748e-02 > > 69 KSP preconditioned resid norm 7.397586859381e-04 true resid norm > > 1.647387302132e+00 ||Ae||/||Ax|| 4.828540713804e-02 > > 70 KSP preconditioned resid norm 7.396782241138e-04 true resid norm > > 1.646889429724e+00 ||Ae||/||Ax|| 4.827081435109e-02 > > 71 KSP preconditioned resid norm 7.395189566969e-04 true resid norm > > 1.646041167917e+00 ||Ae||/||Ax|| 4.824595154763e-02 > > 72 KSP preconditioned resid norm 7.391300711199e-04 true resid norm > > 1.643970513576e+00 ||Ae||/||Ax|| 4.818526005889e-02 > > 73 KSP preconditioned resid norm 7.367639912300e-04 true resid norm > > 1.631221838831e+00 ||Ae||/||Ax|| 4.781159264642e-02 > > 74 KSP preconditioned resid norm 7.075386327019e-04 true resid norm > > 1.473482203196e+00 ||Ae||/||Ax|| 4.318819745660e-02 > > 75 KSP preconditioned resid norm 6.769663644505e-04 true resid norm > > 1.324870886213e+00 ||Ae||/||Ax|| 3.883235597562e-02 > > 76 KSP preconditioned resid norm 6.510062346881e-04 true resid norm > > 1.209103850108e+00 ||Ae||/||Ax|| 3.543919004296e-02 > > 77 KSP preconditioned resid norm 6.416005299115e-04 true resid norm > > 1.174343461999e+00 ||Ae||/||Ax|| 3.442035282725e-02 > > 78 KSP preconditioned resid norm 6.269785791288e-04 true resid norm > > 1.115598946804e+00 ||Ae||/||Ax|| 3.269853378102e-02 > > 79 KSP preconditioned resid norm 6.143599514076e-04 true resid norm > > 1.060258719301e+00 ||Ae||/||Ax|| 3.107649540993e-02 > > 80 KSP preconditioned resid norm 6.118239459355e-04 true resid norm > > 1.049506356947e+00 ||Ae||/||Ax|| 3.076134050174e-02 > > 81 KSP preconditioned resid norm 6.112876406857e-04 true resid norm > > 1.046662765401e+00 ||Ae||/||Ax|| 3.067799399581e-02 > > 82 KSP preconditioned resid norm 6.092506607543e-04 true resid norm > > 1.042978389425e+00 ||Ae||/||Ax|| 3.057000385056e-02 > > 83 KSP preconditioned resid norm 6.081618319409e-04 true resid norm > > 1.040456343908e+00 ||Ae||/||Ax|| 3.049608195349e-02 > > 84 KSP preconditioned resid norm 6.071647595071e-04 true resid norm > > 1.037276486552e+00 ||Ae||/||Ax|| 3.040287939761e-02 > > 85 KSP preconditioned resid norm 5.795095806265e-04 true resid norm > > 9.478301874350e-01 ||Ae||/||Ax|| 2.778118202003e-02 > > 86 KSP preconditioned resid norm 4.787555615154e-04 true resid norm > > 6.865840307207e-01 ||Ae||/||Ax|| 2.012398020485e-02 > > 87 KSP preconditioned resid norm 4.213257765496e-04 true resid norm > > 5.905989111727e-01 ||Ae||/||Ax|| 1.731062807413e-02 > > > > It seems that the no. of lines is much lesser compared to the eariler > case > > when KSPSetTolerances = 1.0e-8 > > > > Thanks again > > > > > > > > On 6/17/07, Barry Smith wrote: > > > > > > > > > Ben, > > > > > > > > > On Sat, 16 Jun 2007, Ben Tay wrote: > > > > > > > Hi, > > > > > > > > I am trying to use PETSc to solve my poisson eqn. In the past, when > I'm > > > not > > > > using MPI, I set KSPSetTolerances to 1.0e-5. This seems to be good > > > enuff. > > > > > > > > Now, I'm trying to use PETSc with MPI to solve the eqn. I am using a > > > very > > > > small no. of pts, only 16x4. On 1 processor, the ans is the same as > the > > > one > > > > without MPI. However, on 2 processors, I found that I've to increase > the > > > > KSPSetTolerances to 1.0e-6, else those grid pts on the edge will be > > > > different. On 4 processors, KSPSetTolerances has to be decreased to > > > 1.0e-7. > > > > On 8 processors, when KSPSetTolerances is 1.0e-8, the difference of > the > > > last > > > > pt between 1 and 8 processors is about 3%. > > > > > > > > > > Are you using the same number of grid points when changing the > number of > > > processors? > > > > > > Run the cases with -ksp_monitor_true_residual and send us ALL the > > > output. > > > > > > Barry > > > > > > > > > > > > > May I know why this is so? Also, does this happens only on very > small > > > grids? > > > > Does it happen on large grids as well? I usually solve grids with > approx > > > > 20000 to 55000 pts. > > > > > > > > Thank you. > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zonexo at gmail.com Tue Jun 19 06:28:30 2007 From: zonexo at gmail.com (Ben Tay) Date: Tue, 19 Jun 2007 19:28:30 +0800 Subject: KSPSetTolerances and processors size In-Reply-To: <804ab5d40706182014r224c6b21p95f0f2a8dc40fcf5@mail.gmail.com> References: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> <804ab5d40706171944s21ccd6able03542b0895e9b08@mail.gmail.com> <804ab5d40706182014r224c6b21p95f0f2a8dc40fcf5@mail.gmail.com> Message-ID: <804ab5d40706190428y61809a85p85e26f23e006b3a6@mail.gmail.com> Btw, it's non-symmetric. On 6/19/07, Ben Tay wrote: > > Hi, > > I've just tested with -ksp_type fgmres with rtol of 1.e-5 with 8 > proceesors. It 's much better, although the last value still has some > difference at .638e-2 and .635e-2. The original one was done with the > default precon and solver. > > Btw, if I use hypre as the precond then the value with 1 or 8 processors > is the same. > > So am I right to say that the problem is due to the precon? What is the > best way to ensure that my results are correct? > > I found that if I use the default precond and solver and did not use > > call > KSPSetTolerances(ksp,tol,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_INTEGER,ierr) > > to set the tolerence to 1.e-8 when using 8 processors, I 'll get incorrect > results. How can I avoid this? > > Thanks > > > > On 6/19/07, Barry Smith wrote: > > > > > > Note that with 8 processors and a rtol of 1.e-5 the TRUE residual norm > > is only 1.e-2 at the end while with one process it is 1.e-5. The > > preconditioner is not working well with 8 processes, thought the > > preconditioned residual norm is small the true residual norm is > > not. > > > > What KSP are you using? If gmres try using -ksp_type fgmres > > if cg try adding -ksp_norm_type unpreconditioned > > > > Is the matrix symmetric? Do you expect/want it to be symmetric? > > > > Barry > > > > > > On Mon, 18 Jun 2007, Ben Tay wrote: > > > > > Oh btw, here's the output when KSPSetTolerances = 1.0e-5. > > > > > > > > > 1: > > > > > > 0 KSP preconditioned resid norm 5.509130713952e+01 true resid norm > > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 6.561453237357e+00 true resid norm > > > 8.697577384386e+00 ||Ae||/||Ax|| 2.549285554017e-01 > > > 2 KSP preconditioned resid norm 1.208347069756e+00 true resid norm > > > 7.425376743449e+00 ||Ae||/||Ax|| 2.176399798315e-01 > > > 3 KSP preconditioned resid norm 3.386218089799e-01 true resid norm > > > 7.347207820518e+00 ||Ae||/||Ax|| 2.153488256722e-01 > > > 4 KSP preconditioned resid norm 3.296482144730e-01 true resid norm > > > 7.745880291985e+00 ||Ae||/||Ax|| 2.270340332579e-01 > > > 5 KSP preconditioned resid norm 3.145738742595e-01 true resid norm > > > 7.547707467510e+00 ||Ae||/||Ax|| 2.212255293918e-01 > > > 6 KSP preconditioned resid norm 1.643048266097e-01 true resid norm > > > 4.306709238860e+00 ||Ae||/||Ax|| 1.262309165273e-01 > > > 7 KSP preconditioned resid norm 6.078974689223e-02 true resid norm > > > 4.482652283996e+00 ||Ae||/||Ax|| 1.313878590122e-01 > > > 8 KSP preconditioned resid norm 6.054372794034e-02 true resid norm > > > 4.355614139989e+00 ||Ae||/||Ax|| 1.276643335865e-01 > > > 9 KSP preconditioned resid norm 5.867972436189e-02 true resid norm > > > 4.233715997285e+00 ||Ae||/||Ax|| 1.240914631132e-01 > > > 10 KSP preconditioned resid norm 2.168073622951e-02 true resid norm > > > 2.086394899960e+00 ||Ae||/||Ax|| 6.115284915993e-02 > > > 11 KSP preconditioned resid norm 1.139327427516e-02 true resid norm > > > 2.155289979633e+00 ||Ae||/||Ax|| 6.317218424133e-02 > > > 12 KSP preconditioned resid norm 1.088027785149e-02 true resid norm > > > 1.991898557592e+00 ||Ae||/||Ax|| 5.838313352696e-02 > > > 13 KSP preconditioned resid norm 1.072820075665e-02 true resid norm > > > 1.942479796672e+00 ||Ae||/||Ax|| 5.693465508586e-02 > > > 14 KSP preconditioned resid norm 3.781319329677e-03 true resid norm > > > 9.806622346091e-01 ||Ae||/||Ax|| 2.874349899487e-02 > > > 15 KSP preconditioned resid norm 2.314101409645e-03 true resid norm > > > 7.976384924484e-01 ||Ae||/||Ax|| 2.337901919420e-02 > > > 16 KSP preconditioned resid norm 2.293131061139e-03 true resid norm > > > 7.897410852774e-01 ||Ae||/||Ax|| 2.314754386348e-02 > > > 17 KSP preconditioned resid norm 2.117223511336e-03 true resid norm > > > 6.782416967980e-01 ||Ae||/||Ax|| 1.987946393996e-02 > > > 18 KSP preconditioned resid norm 7.524359734379e-05 true resid norm > > > 9.092345849564e-04 ||Ae||/||Ax|| 2.664993354130e-05 > > > > > > 2: > > > > > > 0 32 > > > 32 64 > > > 0 KSP preconditioned resid norm 4.902369798248e+01 true resid norm > > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 8.253504641663e+00 true resid norm > > > 1.259698849910e+01 ||Ae||/||Ax|| 3.692214439222e-01 > > > 2 KSP preconditioned resid norm 3.797891005886e+00 true resid norm > > > 1.195333867118e+01 ||Ae||/||Ax|| 3.503558778495e-01 > > > 3 KSP preconditioned resid norm 2.578365901732e+00 true resid norm > > > 1.159420670971e+01 ||Ae||/||Ax|| 3.398296142602e-01 > > > 4 KSP preconditioned resid norm 1.568196901288e+00 true resid norm > > > 9.963750299049e+00 ||Ae||/||Ax|| 2.920404565390e-01 > > > 5 KSP preconditioned resid norm 1.317764005274e+00 true resid norm > > > 9.066502566015e+00 ||Ae||/||Ax|| 2.657418611589e-01 > > > 6 KSP preconditioned resid norm 6.023727405584e-01 true resid norm > > > 8.058099054033e+00 ||Ae||/||Ax|| 2.361852571517e-01 > > > 7 KSP preconditioned resid norm 4.957651340342e-02 true resid norm > > > 7.520037445249e+00 ||Ae||/||Ax|| 2.204145128879e-01 > > > 8 KSP preconditioned resid norm 2.449473557300e-02 true resid norm > > > 7.475057378184e+00 ||Ae||/||Ax|| 2.190961338713e-01 > > > 9 KSP preconditioned resid norm 2.361338376271e-02 true resid norm > > > 7.217194046579e+00 ||Ae||/||Ax|| 2.115380836566e-01 > > > 10 KSP preconditioned resid norm 2.307344735925e-02 true resid norm > > > 7.205616297960e+00 ||Ae||/||Ax|| 2.111987364338e-01 > > > 11 KSP preconditioned resid norm 1.934171008299e-02 true resid norm > > > 5.261866236257e+00 ||Ae||/||Ax|| 1.542268495057e-01 > > > 12 KSP preconditioned resid norm 5.190847895073e-03 true resid norm > > > 4.466349759791e+00 ||Ae||/||Ax|| 1.309100272251e-01 > > > 13 KSP preconditioned resid norm 4.871871781446e-03 true resid norm > > > 4.194634080458e+00 ||Ae||/||Ax|| 1.229459606177e-01 > > > 14 KSP preconditioned resid norm 4.823921505423e-03 true resid norm > > > 4.173223968428e+00 ||Ae||/||Ax|| 1.223184239268e-01 > > > 15 KSP preconditioned resid norm 4.701199647155e-03 true resid norm > > > 3.957555688130e+00 ||Ae||/||Ax|| 1.159971230964e-01 > > > 16 KSP preconditioned resid norm 1.035300954721e-03 true resid norm > > > 2.196668371922e+00 ||Ae||/||Ax|| 6.438499710918e-02 > > > 17 KSP preconditioned resid norm 8.832653700092e-04 true resid norm > > > 1.916576324421e+00 ||Ae||/||Ax|| 5.617541668313e-02 > > > 18 KSP preconditioned resid norm 8.703924311133e-04 true resid norm > > > 1.916104922195e+00 ||Ae||/||Ax|| 5.616159974502e-02 > > > 19 KSP preconditioned resid norm 8.698960956884e-04 true resid norm > > > 1.913670720373e+00 ||Ae||/||Ax|| 5.609025257250e-02 > > > 20 KSP preconditioned resid norm 3.690946760360e-04 true resid norm > > > 7.994885772359e-01 ||Ae||/||Ax|| 2.343324572435e-02 > > > > > > 4: > > > > > > 0 16 > > > 32 48 > > > 48 64 > > > 0 KSP preconditioned resid norm 4.414786383499e+01 true resid norm > > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 7.579678467669e+00 true resid norm > > > 1.423835009315e+01 ||Ae||/||Ax|| 4.173302357811e-01 > > > 2 KSP preconditioned resid norm 2.972753009220e+00 true resid norm > > > 1.290812750005e+01 ||Ae||/||Ax|| 3.783410197001e-01 > > > 3 KSP preconditioned resid norm 1.347960602345e+00 true resid norm > > > 1.173368275935e+01 ||Ae||/||Ax|| 3.439176983641e-01 > > > 4 KSP preconditioned resid norm 1.111052862809e+00 true resid norm > > > 1.106221549565e+01 ||Ae||/||Ax|| 3.242367950541e-01 > > > 5 KSP preconditioned resid norm 9.872224937494e-01 true resid norm > > > 1.005157038653e+01 ||Ae||/||Ax|| 2.946144891744e-01 > > > 6 KSP preconditioned resid norm 7.251219493841e-01 true resid norm > > > 9.007852893929e+00 ||Ae||/||Ax|| 2.640228219921e-01 > > > 7 KSP preconditioned resid norm 5.925185640664e-01 true resid norm > > > 8.104036732737e+00 ||Ae||/||Ax|| 2.375317040476e-01 > > > 8 KSP preconditioned resid norm 3.381465672631e-01 true resid norm > > > 7.256440004925e+00 ||Ae||/||Ax|| 2.126883942574e-01 > > > 9 KSP preconditioned resid norm 1.647154013552e-01 true resid norm > > > 7.263797232535e+00 ||Ae||/||Ax|| 2.129040367661e-01 > > > 10 KSP preconditioned resid norm 7.697425793821e-02 true resid norm > > > 7.155391777961e+00 ||Ae||/||Ax|| 2.097266409567e-01 > > > 11 KSP preconditioned resid norm 3.477770299629e-02 true resid norm > > > 7.127853631055e+00 ||Ae||/||Ax|| 2.089194897583e-01 > > > 12 KSP preconditioned resid norm 2.573627666614e-02 true resid norm > > > 7.088156599392e+00 ||Ae||/||Ax|| 2.077559580657e-01 > > > 13 KSP preconditioned resid norm 2.221352319865e-02 true resid norm > > > 7.093825972365e+00 ||Ae||/||Ax|| 2.079221290577e-01 > > > 14 KSP preconditioned resid norm 2.093106984691e-02 true resid norm > > > 7.062268285770e+00 ||Ae||/||Ax|| 2.069971639669e-01 > > > 15 KSP preconditioned resid norm 2.034509930217e-02 true resid norm > > > 7.031405865561e+00 ||Ae||/||Ax|| 2.060925773386e-01 > > > 16 KSP preconditioned resid norm 2.029393080560e-02 true resid norm > > > 7.008984378537e+00 ||Ae||/||Ax|| 2.054353969487e-01 > > > 17 KSP preconditioned resid norm 1.587358534265e-02 true resid norm > > > 4.635842103718e+00 ||Ae||/||Ax|| 1.358778977572e-01 > > > 18 KSP preconditioned resid norm 1.055491860699e-02 true resid norm > > > 3.773993858722e+00 ||Ae||/||Ax|| 1.106168718000e-01 > > > 19 KSP preconditioned resid norm 5.655638925006e-03 true resid norm > > > 4.203919883144e+00 ||Ae||/||Ax|| 1.232181302299e-01 > > > 20 KSP preconditioned resid norm 4.767909232406e-03 true resid norm > > > 4.121869307404e+00 ||Ae||/||Ax|| 1.208132036833e-01 > > > 21 KSP preconditioned resid norm 4.648572929978e-03 true resid norm > > > 4.076834878296e+00 ||Ae||/||Ax|| 1.194932312992e-01 > > > 22 KSP preconditioned resid norm 4.638216815872e-03 true resid norm > > > 4.058874907114e+00 ||Ae||/||Ax|| 1.189668192529e-01 > > > 23 KSP preconditioned resid norm 1.851801714075e-03 true resid norm > > > 2.017702443794e+00 ||Ae||/||Ax|| 5.913945303323e-02 > > > 24 KSP preconditioned resid norm 9.594251508173e-04 true resid norm > > > 2.065135975225e+00 ||Ae||/||Ax|| 6.052974381317e-02 > > > 25 KSP preconditioned resid norm 8.609050236229e-04 true resid norm > > > 1.901663497990e+00 ||Ae||/||Ax|| 5.573831734719e-02 > > > 26 KSP preconditioned resid norm 8.607029066323e-04 true resid norm > > > 1.901221069645e+00 ||Ae||/||Ax|| 5.572534964205e-02 > > > 27 KSP preconditioned resid norm 6.010429111401e-04 true resid norm > > > 1.025962923033e+00 ||Ae||/||Ax|| 3.007127551793e-02 > > > 28 KSP preconditioned resid norm 2.036565987243e-04 true resid norm > > > 8.385451121270e-01 ||Ae||/||Ax|| 2.457800426788e-02 > > > > > > 8: > > > > > > 8 16 > > > 24 32 > > > 56 64 > > > 16 24 > > > 48 56 > > > 0 8 > > > 32 40 > > > 40 48 > > > 0 KSP preconditioned resid norm 4.299803638671e+01 true resid norm > > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 9.603727351867e+00 true resid norm > > > 1.922897810349e+01 ||Ae||/||Ax|| 5.636070129797e-01 > > > 2 KSP preconditioned resid norm 2.931835632556e+00 true resid norm > > > 1.355792423218e+01 ||Ae||/||Ax|| 3.973867533457e-01 > > > 3 KSP preconditioned resid norm 1.314351599619e+00 true resid norm > > > 9.882281425137e+00 ||Ae||/||Ax|| 2.896525798443e-01 > > > 4 KSP preconditioned resid norm 8.218956530484e-01 true resid norm > > > 9.318760482806e+00 ||Ae||/||Ax|| 2.731356150140e-01 > > > 5 KSP preconditioned resid norm 6.895693486764e-01 true resid norm > > > 9.360126907217e+00 ||Ae||/||Ax|| 2.743480770998e-01 > > > 6 KSP preconditioned resid norm 6.138748402770e-01 true resid norm > > > 9.020243051395e+00 ||Ae||/||Ax|| 2.643859811575e-01 > > > 7 KSP preconditioned resid norm 5.265342569996e-01 true resid norm > > > 8.781477094899e+00 ||Ae||/||Ax|| 2.573876806333e-01 > > > 8 KSP preconditioned resid norm 4.403325671754e-01 true resid norm > > > 8.314776073768e+00 ||Ae||/||Ax|| 2.437085362160e-01 > > > 9 KSP preconditioned resid norm 2.353592633657e-01 true resid norm > > > 7.347976506279e+00 ||Ae||/||Ax|| 2.153713560783e-01 > > > 10 KSP preconditioned resid norm 8.943808926292e-02 true resid norm > > > 6.972332890712e+00 ||Ae||/||Ax|| 2.043611310432e-01 > > > 11 KSP preconditioned resid norm 5.930469791557e-02 true resid norm > > > 6.957386646797e+00 ||Ae||/||Ax|| 2.039230522310e-01 > > > 12 KSP preconditioned resid norm 5.283812047599e-02 true resid norm > > > 6.981023245883e+00 ||Ae||/||Ax|| 2.046158479134e-01 > > > 13 KSP preconditioned resid norm 3.665176395384e-02 true resid norm > > > 6.992078556546e+00 ||Ae||/||Ax|| 2.049398823258e-01 > > > 14 KSP preconditioned resid norm 2.516790937741e-02 true resid norm > > > 6.949891196404e+00 ||Ae||/||Ax|| 2.037033583718e-01 > > > 15 KSP preconditioned resid norm 2.192690814272e-02 true resid norm > > > 6.927621207906e+00 ||Ae||/||Ax|| 2.030506184483e-01 > > > 16 KSP preconditioned resid norm 2.058802964863e-02 true resid norm > > > 6.919125260713e+00 ||Ae||/||Ax|| 2.028015997332e-01 > > > 17 KSP preconditioned resid norm 1.984533974458e-02 true resid norm > > > 6.853733693988e+00 ||Ae||/||Ax|| 2.008849536484e-01 > > > 18 KSP preconditioned resid norm 1.958243371255e-02 true resid norm > > > 6.766030769290e+00 ||Ae||/||Ax|| 1.983143550887e-01 > > > 19 KSP preconditioned resid norm 1.874262002187e-02 true resid norm > > > 6.323230908702e+00 ||Ae||/||Ax|| 1.853357607281e-01 > > > 20 KSP preconditioned resid norm 1.754461572091e-02 true resid norm > > > 5.538708901675e+00 ||Ae||/||Ax|| 1.623411895857e-01 > > > 21 KSP preconditioned resid norm 1.184321475064e-02 true resid norm > > > 3.839931686898e+00 ||Ae||/||Ax|| 1.125495289688e-01 > > > 22 KSP preconditioned resid norm 1.070434172478e-02 true resid norm > > > 3.754159266432e+00 ||Ae||/||Ax|| 1.100355140568e-01 > > > 23 KSP preconditioned resid norm 8.011880009497e-03 true resid norm > > > 3.937870836170e+00 ||Ae||/||Ax|| 1.154201542864e-01 > > > 24 KSP preconditioned resid norm 5.573761552253e-03 true resid norm > > > 4.205066407359e+00 ||Ae||/||Ax|| 1.232517351924e-01 > > > 25 KSP preconditioned resid norm 4.810675543540e-03 true resid norm > > > 4.069723693466e+00 ||Ae||/||Ax|| 1.192848003769e-01 > > > 26 KSP preconditioned resid norm 4.647944860704e-03 true resid norm > > > 4.044329745280e+00 ||Ae||/||Ax|| 1.185404962746e-01 > > > 27 KSP preconditioned resid norm 4.606926939804e-03 true resid norm > > > 4.039416044569e+00 ||Ae||/||Ax|| 1.183964742593e-01 > > > 28 KSP preconditioned resid norm 4.606174352197e-03 true resid norm > > > 4.038658488893e+00 ||Ae||/||Ax|| 1.183742700792e-01 > > > 29 KSP preconditioned resid norm 4.604980580071e-03 true resid norm > > > 4.034721549326e+00 ||Ae||/||Ax|| 1.182588772207e-01 > > > 30 KSP preconditioned resid norm 4.551931835395e-03 true resid norm > > > 3.942692013899e+00 ||Ae||/||Ax|| 1.155614644259e-01 > > > 31 KSP preconditioned resid norm 4.534435621643e-03 true resid norm > > > 3.940744976447e+00 ||Ae||/||Ax|| 1.155043961846e-01 > > > 32 KSP preconditioned resid norm 4.533889403959e-03 true resid norm > > > 3.940661031251e+00 ||Ae||/||Ax|| 1.155019357261e-01 > > > 33 KSP preconditioned resid norm 4.533315616020e-03 true resid norm > > > 3.940962366962e+00 ||Ae||/||Ax|| 1.155107679646e-01 > > > 34 KSP preconditioned resid norm 4.533098107272e-03 true resid norm > > > 3.940998854473e+00 ||Ae||/||Ax|| 1.155118374243e-01 > > > 35 KSP preconditioned resid norm 4.531113895054e-03 true resid norm > > > 3.939900266217e+00 ||Ae||/||Ax|| 1.154796374789e-01 > > > 36 KSP preconditioned resid norm 4.530789523555e-03 true resid norm > > > 3.939483356865e+00 ||Ae||/||Ax|| 1.154674177430e-01 > > > 37 KSP preconditioned resid norm 4.530789514003e-03 true resid norm > > > 3.939490762772e+00 ||Ae||/||Ax|| 1.154676348123e-01 > > > 38 KSP preconditioned resid norm 4.530624961751e-03 true resid norm > > > 3.937889462104e+00 ||Ae||/||Ax|| 1.154207002179e-01 > > > 39 KSP preconditioned resid norm 4.517785703071e-03 true resid norm > > > 3.927441577896e+00 ||Ae||/||Ax|| 1.151144696539e-01 > > > 40 KSP preconditioned resid norm 4.508890400648e-03 true resid norm > > > 3.919421029911e+00 ||Ae||/||Ax|| 1.148793850297e-01 > > > 41 KSP preconditioned resid norm 4.508823049754e-03 true resid norm > > > 3.920408845458e+00 ||Ae||/||Ax|| 1.149083381943e-01 > > > 42 KSP preconditioned resid norm 4.504581641358e-03 true resid norm > > > 3.910936323861e+00 ||Ae||/||Ax|| 1.146306957958e-01 > > > 43 KSP preconditioned resid norm 4.496299729031e-03 true resid norm > > > 3.892573202489e+00 ||Ae||/||Ax|| 1.140924672987e-01 > > > 44 KSP preconditioned resid norm 4.327165698785e-03 true resid norm > > > 3.499303379330e+00 ||Ae||/||Ax|| 1.025656129265e-01 > > > 45 KSP preconditioned resid norm 3.860049921599e-03 true resid norm > > > 2.642394407576e+00 ||Ae||/||Ax|| 7.744935852298e-02 > > > 46 KSP preconditioned resid norm 3.813681936798e-03 true resid norm > > > 2.561643926848e+00 ||Ae||/||Ax|| 7.508253814415e-02 > > > 47 KSP preconditioned resid norm 3.811608329841e-03 true resid norm > > > 2.553393452252e+00 ||Ae||/||Ax|| 7.484071430319e-02 > > > 48 KSP preconditioned resid norm 3.805700908518e-03 true resid norm > > > 2.559614961583e+00 ||Ae||/||Ax|| 7.502306857451e-02 > > > 49 KSP preconditioned resid norm 3.783124026053e-03 true resid norm > > > 2.523808739092e+00 ||Ae||/||Ax|| 7.397357764494e-02 > > > 50 KSP preconditioned resid norm 3.777662131381e-03 true resid norm > > > 2.516105834856e+00 ||Ae||/||Ax|| 7.374780325255e-02 > > > 51 KSP preconditioned resid norm 3.710923429451e-03 true resid norm > > > 2.426657981798e+00 ||Ae||/||Ax|| 7.112606032852e-02 > > > 52 KSP preconditioned resid norm 3.604808013597e-03 true resid norm > > > 2.303594181107e+00 ||Ae||/||Ax|| 6.751902407624e-02 > > > 53 KSP preconditioned resid norm 3.513880489788e-03 true resid norm > > > 2.188212014004e+00 ||Ae||/||Ax|| 6.413713876742e-02 > > > 54 KSP preconditioned resid norm 3.320184202285e-03 true resid norm > > > 1.978987642137e+00 ||Ae||/||Ax|| 5.800471079148e-02 > > > 55 KSP preconditioned resid norm 2.195662794099e-03 true resid norm > > > 1.448538675887e+00 ||Ae||/||Ax|| 4.245709532291e-02 > > > 56 KSP preconditioned resid norm 9.077826763324e-04 true resid norm > > > 1.628573968470e+00 ||Ae||/||Ax|| 4.773398278607e-02 > > > 57 KSP preconditioned resid norm 7.602131391716e-04 true resid norm > > > 1.659109675600e+00 ||Ae||/||Ax|| 4.862899335772e-02 > > > 58 KSP preconditioned resid norm 7.450227847936e-04 true resid norm > > > 1.651479746174e+00 ||Ae||/||Ax|| 4.840535787852e-02 > > > 59 KSP preconditioned resid norm 7.410161195392e-04 true resid norm > > > 1.649502155114e+00 ||Ae||/||Ax|| 4.834739410196e-02 > > > 60 KSP preconditioned resid norm 7.399447579004e-04 true resid norm > > > 1.648188611058e+00 ||Ae||/||Ax|| 4.830889373871e-02 > > > 61 KSP preconditioned resid norm 7.399146825366e-04 true resid norm > > > 1.648156339888e+00 ||Ae||/||Ax|| 4.830794786121e-02 > > > 62 KSP preconditioned resid norm 7.399119217730e-04 true resid norm > > > 1.648143662498e+00 ||Ae||/||Ax|| 4.830757628317e-02 > > > 63 KSP preconditioned resid norm 7.399115190929e-04 true resid norm > > > 1.648149747433e+00 ||Ae||/||Ax|| 4.830775463441e-02 > > > 64 KSP preconditioned resid norm 7.398927702838e-04 true resid norm > > > 1.648083443482e+00 ||Ae||/||Ax|| 4.830581124607e-02 > > > 65 KSP preconditioned resid norm 7.398398384099e-04 true resid norm > > > 1.647873653551e+00 ||Ae||/||Ax|| 4.829966224141e-02 > > > 66 KSP preconditioned resid norm 7.398251502315e-04 true resid norm > > > 1.647783674785e+00 ||Ae||/||Ax|| 4.829702493725e-02 > > > 67 KSP preconditioned resid norm 7.398217631044e-04 true resid norm > > > 1.647733028046e+00 ||Ae||/||Ax|| 4.829554046641e-02 > > > 68 KSP preconditioned resid norm 7.398045634717e-04 true resid norm > > > 1.647630453201e+00 ||Ae||/||Ax|| 4.829253396748e-02 > > > 69 KSP preconditioned resid norm 7.397586859381e-04 true resid norm > > > 1.647387302132e+00 ||Ae||/||Ax|| 4.828540713804e-02 > > > 70 KSP preconditioned resid norm 7.396782241138e-04 true resid norm > > > 1.646889429724e+00 ||Ae||/||Ax|| 4.827081435109e-02 > > > 71 KSP preconditioned resid norm 7.395189566969e-04 true resid norm > > > 1.646041167917e+00 ||Ae||/||Ax|| 4.824595154763e-02 > > > 72 KSP preconditioned resid norm 7.391300711199e-04 true resid norm > > > 1.643970513576e+00 ||Ae||/||Ax|| 4.818526005889e-02 > > > 73 KSP preconditioned resid norm 7.367639912300e-04 true resid norm > > > 1.631221838831e+00 ||Ae||/||Ax|| 4.781159264642e-02 > > > 74 KSP preconditioned resid norm 7.075386327019e-04 true resid norm > > > 1.473482203196e+00 ||Ae||/||Ax|| 4.318819745660e-02 > > > 75 KSP preconditioned resid norm 6.769663644505e-04 true resid norm > > > 1.324870886213e+00 ||Ae||/||Ax|| 3.883235597562e-02 > > > 76 KSP preconditioned resid norm 6.510062346881e-04 true resid norm > > > 1.209103850108e+00 ||Ae||/||Ax|| 3.543919004296e-02 > > > 77 KSP preconditioned resid norm 6.416005299115e-04 true resid norm > > > 1.174343461999e+00 ||Ae||/||Ax|| 3.442035282725e-02 > > > 78 KSP preconditioned resid norm 6.269785791288e-04 true resid norm > > > 1.115598946804e+00 ||Ae||/||Ax|| 3.269853378102e-02 > > > 79 KSP preconditioned resid norm 6.143599514076e-04 true resid norm > > > 1.060258719301e+00 ||Ae||/||Ax|| 3.107649540993e-02 > > > 80 KSP preconditioned resid norm 6.118239459355e-04 true resid norm > > > 1.049506356947e+00 ||Ae||/||Ax|| 3.076134050174e-02 > > > 81 KSP preconditioned resid norm 6.112876406857e-04 true resid norm > > > 1.046662765401e+00 ||Ae||/||Ax|| 3.067799399581e-02 > > > 82 KSP preconditioned resid norm 6.092506607543e-04 true resid norm > > > 1.042978389425e+00 ||Ae||/||Ax|| 3.057000385056e-02 > > > 83 KSP preconditioned resid norm 6.081618319409e-04 true resid norm > > > 1.040456343908e+00 ||Ae||/||Ax|| 3.049608195349e-02 > > > 84 KSP preconditioned resid norm 6.071647595071e-04 true resid norm > > > 1.037276486552e+00 ||Ae||/||Ax|| 3.040287939761e-02 > > > 85 KSP preconditioned resid norm 5.795095806265e-04 true resid norm > > > 9.478301874350e-01 ||Ae||/||Ax|| 2.778118202003e-02 > > > 86 KSP preconditioned resid norm 4.787555615154e-04 true resid norm > > > 6.865840307207e-01 ||Ae||/||Ax|| 2.012398020485e-02 > > > 87 KSP preconditioned resid norm 4.213257765496e-04 true resid norm > > > 5.905989111727e-01 ||Ae||/||Ax|| 1.731062807413e-02 > > > > > > It seems that the no. of lines is much lesser compared to the eariler > > case > > > when KSPSetTolerances = 1.0e-8 > > > > > > Thanks again > > > > > > > > > > > > On 6/17/07, Barry Smith wrote: > > > > > > > > > > > > Ben, > > > > > > > > > > > > On Sat, 16 Jun 2007, Ben Tay wrote: > > > > > > > > > Hi, > > > > > > > > > > I am trying to use PETSc to solve my poisson eqn. In the past, > > when I'm > > > > not > > > > > using MPI, I set KSPSetTolerances to 1.0e-5 . This seems to be > > good > > > > enuff. > > > > > > > > > > Now, I'm trying to use PETSc with MPI to solve the eqn. I am using > > a > > > > very > > > > > small no. of pts, only 16x4. On 1 processor, the ans is the same > > as the > > > > one > > > > > without MPI. However, on 2 processors, I found that I've to > > increase the > > > > > KSPSetTolerances to 1.0e-6, else those grid pts on the edge will > > be > > > > > different. On 4 processors, KSPSetTolerances has to be decreased > > to > > > > 1.0e-7. > > > > > On 8 processors, when KSPSetTolerances is 1.0e-8, the difference > > of the > > > > last > > > > > pt between 1 and 8 processors is about 3%. > > > > > > > > > > > > > Are you using the same number of grid points when changing the > > number of > > > > processors? > > > > > > > > Run the cases with -ksp_monitor_true_residual and send us ALL the > > > > output. > > > > > > > > Barry > > > > > > > > > > > > > > > > > May I know why this is so? Also, does this happens only on very > > small > > > > grids? > > > > > Does it happen on large grids as well? I usually solve grids with > > approx > > > > > 20000 to 55000 pts. > > > > > > > > > > Thank you. > > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Tue Jun 19 12:36:52 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Tue, 19 Jun 2007 12:36:52 -0500 (CDT) Subject: KSPSetTolerances and processors size In-Reply-To: <804ab5d40706182014r224c6b21p95f0f2a8dc40fcf5@mail.gmail.com> References: <804ab5d40706152217t8944debrdd92223bd1f001b0@mail.gmail.com> <804ab5d40706171944s21ccd6able03542b0895e9b08@mail.gmail.com> <804ab5d40706182014r224c6b21p95f0f2a8dc40fcf5@mail.gmail.com> Message-ID: On Tue, 19 Jun 2007, Ben Tay wrote: > Hi, > > I've just tested with -ksp_type fgmres with rtol of 1.e-5 with 8 proceesors. > It 's much better, although the last value still has some difference at > .638e-2 and .635e-2. The original one was done with the default precon and > solver. > > Btw, if I use hypre as the precond then the value with 1 or 8 processors is > the same. > > So am I right to say that the problem is due to the precon? What is the best > way to ensure that my results are correct? > > I found that if I use the default precond and solver and did not use > > call > KSPSetTolerances(ksp,tol,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_INTEGER,ierr) > > to set the tolerence to 1.e-8 when using 8 processors, I 'll get incorrect > results. How can I avoid this? Unfortunately with iterative solvers there are NO guarantees. At the end of the solve you can compute the TRUE residual via b - A*x, but this still does not measure the error and is to late to change the solve anyways. It sounds like hypre (with boomerAMG?) is the way for you to go. Barry > > Thanks > > > > On 6/19/07, Barry Smith wrote: > > > > > > Note that with 8 processors and a rtol of 1.e-5 the TRUE residual norm > > is only 1.e-2 at the end while with one process it is 1.e-5. The > > preconditioner is not working well with 8 processes, thought the > > preconditioned residual norm is small the true residual norm is > > not. > > > > What KSP are you using? If gmres try using -ksp_type fgmres > > if cg try adding -ksp_norm_type unpreconditioned > > > > Is the matrix symmetric? Do you expect/want it to be symmetric? > > > > Barry > > > > > > On Mon, 18 Jun 2007, Ben Tay wrote: > > > > > Oh btw, here's the output when KSPSetTolerances = 1.0e-5. > > > > > > > > > 1: > > > > > > 0 KSP preconditioned resid norm 5.509130713952e+01 true resid norm > > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 6.561453237357e+00 true resid norm > > > 8.697577384386e+00 ||Ae||/||Ax|| 2.549285554017e-01 > > > 2 KSP preconditioned resid norm 1.208347069756e+00 true resid norm > > > 7.425376743449e+00 ||Ae||/||Ax|| 2.176399798315e-01 > > > 3 KSP preconditioned resid norm 3.386218089799e-01 true resid norm > > > 7.347207820518e+00 ||Ae||/||Ax|| 2.153488256722e-01 > > > 4 KSP preconditioned resid norm 3.296482144730e-01 true resid norm > > > 7.745880291985e+00 ||Ae||/||Ax|| 2.270340332579e-01 > > > 5 KSP preconditioned resid norm 3.145738742595e-01 true resid norm > > > 7.547707467510e+00 ||Ae||/||Ax|| 2.212255293918e-01 > > > 6 KSP preconditioned resid norm 1.643048266097e-01 true resid norm > > > 4.306709238860e+00 ||Ae||/||Ax|| 1.262309165273e-01 > > > 7 KSP preconditioned resid norm 6.078974689223e-02 true resid norm > > > 4.482652283996e+00 ||Ae||/||Ax|| 1.313878590122e-01 > > > 8 KSP preconditioned resid norm 6.054372794034e-02 true resid norm > > > 4.355614139989e+00 ||Ae||/||Ax|| 1.276643335865e-01 > > > 9 KSP preconditioned resid norm 5.867972436189e-02 true resid norm > > > 4.233715997285e+00 ||Ae||/||Ax|| 1.240914631132e-01 > > > 10 KSP preconditioned resid norm 2.168073622951e-02 true resid norm > > > 2.086394899960e+00 ||Ae||/||Ax|| 6.115284915993e-02 > > > 11 KSP preconditioned resid norm 1.139327427516e-02 true resid norm > > > 2.155289979633e+00 ||Ae||/||Ax|| 6.317218424133e-02 > > > 12 KSP preconditioned resid norm 1.088027785149e-02 true resid norm > > > 1.991898557592e+00 ||Ae||/||Ax|| 5.838313352696e-02 > > > 13 KSP preconditioned resid norm 1.072820075665e-02 true resid norm > > > 1.942479796672e+00 ||Ae||/||Ax|| 5.693465508586e-02 > > > 14 KSP preconditioned resid norm 3.781319329677e-03 true resid norm > > > 9.806622346091e-01 ||Ae||/||Ax|| 2.874349899487e-02 > > > 15 KSP preconditioned resid norm 2.314101409645e-03 true resid norm > > > 7.976384924484e-01 ||Ae||/||Ax|| 2.337901919420e-02 > > > 16 KSP preconditioned resid norm 2.293131061139e-03 true resid norm > > > 7.897410852774e-01 ||Ae||/||Ax|| 2.314754386348e-02 > > > 17 KSP preconditioned resid norm 2.117223511336e-03 true resid norm > > > 6.782416967980e-01 ||Ae||/||Ax|| 1.987946393996e-02 > > > 18 KSP preconditioned resid norm 7.524359734379e-05 true resid norm > > > 9.092345849564e-04 ||Ae||/||Ax|| 2.664993354130e-05 > > > > > > 2: > > > > > > 0 32 > > > 32 64 > > > 0 KSP preconditioned resid norm 4.902369798248e+01 true resid norm > > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 8.253504641663e+00 true resid norm > > > 1.259698849910e+01 ||Ae||/||Ax|| 3.692214439222e-01 > > > 2 KSP preconditioned resid norm 3.797891005886e+00 true resid norm > > > 1.195333867118e+01 ||Ae||/||Ax|| 3.503558778495e-01 > > > 3 KSP preconditioned resid norm 2.578365901732e+00 true resid norm > > > 1.159420670971e+01 ||Ae||/||Ax|| 3.398296142602e-01 > > > 4 KSP preconditioned resid norm 1.568196901288e+00 true resid norm > > > 9.963750299049e+00 ||Ae||/||Ax|| 2.920404565390e-01 > > > 5 KSP preconditioned resid norm 1.317764005274e+00 true resid norm > > > 9.066502566015e+00 ||Ae||/||Ax|| 2.657418611589e-01 > > > 6 KSP preconditioned resid norm 6.023727405584e-01 true resid norm > > > 8.058099054033e+00 ||Ae||/||Ax|| 2.361852571517e-01 > > > 7 KSP preconditioned resid norm 4.957651340342e-02 true resid norm > > > 7.520037445249e+00 ||Ae||/||Ax|| 2.204145128879e-01 > > > 8 KSP preconditioned resid norm 2.449473557300e-02 true resid norm > > > 7.475057378184e+00 ||Ae||/||Ax|| 2.190961338713e-01 > > > 9 KSP preconditioned resid norm 2.361338376271e-02 true resid norm > > > 7.217194046579e+00 ||Ae||/||Ax|| 2.115380836566e-01 > > > 10 KSP preconditioned resid norm 2.307344735925e-02 true resid norm > > > 7.205616297960e+00 ||Ae||/||Ax|| 2.111987364338e-01 > > > 11 KSP preconditioned resid norm 1.934171008299e-02 true resid norm > > > 5.261866236257e+00 ||Ae||/||Ax|| 1.542268495057e-01 > > > 12 KSP preconditioned resid norm 5.190847895073e-03 true resid norm > > > 4.466349759791e+00 ||Ae||/||Ax|| 1.309100272251e-01 > > > 13 KSP preconditioned resid norm 4.871871781446e-03 true resid norm > > > 4.194634080458e+00 ||Ae||/||Ax|| 1.229459606177e-01 > > > 14 KSP preconditioned resid norm 4.823921505423e-03 true resid norm > > > 4.173223968428e+00 ||Ae||/||Ax|| 1.223184239268e-01 > > > 15 KSP preconditioned resid norm 4.701199647155e-03 true resid norm > > > 3.957555688130e+00 ||Ae||/||Ax|| 1.159971230964e-01 > > > 16 KSP preconditioned resid norm 1.035300954721e-03 true resid norm > > > 2.196668371922e+00 ||Ae||/||Ax|| 6.438499710918e-02 > > > 17 KSP preconditioned resid norm 8.832653700092e-04 true resid norm > > > 1.916576324421e+00 ||Ae||/||Ax|| 5.617541668313e-02 > > > 18 KSP preconditioned resid norm 8.703924311133e-04 true resid norm > > > 1.916104922195e+00 ||Ae||/||Ax|| 5.616159974502e-02 > > > 19 KSP preconditioned resid norm 8.698960956884e-04 true resid norm > > > 1.913670720373e+00 ||Ae||/||Ax|| 5.609025257250e-02 > > > 20 KSP preconditioned resid norm 3.690946760360e-04 true resid norm > > > 7.994885772359e-01 ||Ae||/||Ax|| 2.343324572435e-02 > > > > > > 4: > > > > > > 0 16 > > > 32 48 > > > 48 64 > > > 0 KSP preconditioned resid norm 4.414786383499e+01 true resid norm > > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 7.579678467669e+00 true resid norm > > > 1.423835009315e+01 ||Ae||/||Ax|| 4.173302357811e-01 > > > 2 KSP preconditioned resid norm 2.972753009220e+00 true resid norm > > > 1.290812750005e+01 ||Ae||/||Ax|| 3.783410197001e-01 > > > 3 KSP preconditioned resid norm 1.347960602345e+00 true resid norm > > > 1.173368275935e+01 ||Ae||/||Ax|| 3.439176983641e-01 > > > 4 KSP preconditioned resid norm 1.111052862809e+00 true resid norm > > > 1.106221549565e+01 ||Ae||/||Ax|| 3.242367950541e-01 > > > 5 KSP preconditioned resid norm 9.872224937494e-01 true resid norm > > > 1.005157038653e+01 ||Ae||/||Ax|| 2.946144891744e-01 > > > 6 KSP preconditioned resid norm 7.251219493841e-01 true resid norm > > > 9.007852893929e+00 ||Ae||/||Ax|| 2.640228219921e-01 > > > 7 KSP preconditioned resid norm 5.925185640664e-01 true resid norm > > > 8.104036732737e+00 ||Ae||/||Ax|| 2.375317040476e-01 > > > 8 KSP preconditioned resid norm 3.381465672631e-01 true resid norm > > > 7.256440004925e+00 ||Ae||/||Ax|| 2.126883942574e-01 > > > 9 KSP preconditioned resid norm 1.647154013552e-01 true resid norm > > > 7.263797232535e+00 ||Ae||/||Ax|| 2.129040367661e-01 > > > 10 KSP preconditioned resid norm 7.697425793821e-02 true resid norm > > > 7.155391777961e+00 ||Ae||/||Ax|| 2.097266409567e-01 > > > 11 KSP preconditioned resid norm 3.477770299629e-02 true resid norm > > > 7.127853631055e+00 ||Ae||/||Ax|| 2.089194897583e-01 > > > 12 KSP preconditioned resid norm 2.573627666614e-02 true resid norm > > > 7.088156599392e+00 ||Ae||/||Ax|| 2.077559580657e-01 > > > 13 KSP preconditioned resid norm 2.221352319865e-02 true resid norm > > > 7.093825972365e+00 ||Ae||/||Ax|| 2.079221290577e-01 > > > 14 KSP preconditioned resid norm 2.093106984691e-02 true resid norm > > > 7.062268285770e+00 ||Ae||/||Ax|| 2.069971639669e-01 > > > 15 KSP preconditioned resid norm 2.034509930217e-02 true resid norm > > > 7.031405865561e+00 ||Ae||/||Ax|| 2.060925773386e-01 > > > 16 KSP preconditioned resid norm 2.029393080560e-02 true resid norm > > > 7.008984378537e+00 ||Ae||/||Ax|| 2.054353969487e-01 > > > 17 KSP preconditioned resid norm 1.587358534265e-02 true resid norm > > > 4.635842103718e+00 ||Ae||/||Ax|| 1.358778977572e-01 > > > 18 KSP preconditioned resid norm 1.055491860699e-02 true resid norm > > > 3.773993858722e+00 ||Ae||/||Ax|| 1.106168718000e-01 > > > 19 KSP preconditioned resid norm 5.655638925006e-03 true resid norm > > > 4.203919883144e+00 ||Ae||/||Ax|| 1.232181302299e-01 > > > 20 KSP preconditioned resid norm 4.767909232406e-03 true resid norm > > > 4.121869307404e+00 ||Ae||/||Ax|| 1.208132036833e-01 > > > 21 KSP preconditioned resid norm 4.648572929978e-03 true resid norm > > > 4.076834878296e+00 ||Ae||/||Ax|| 1.194932312992e-01 > > > 22 KSP preconditioned resid norm 4.638216815872e-03 true resid norm > > > 4.058874907114e+00 ||Ae||/||Ax|| 1.189668192529e-01 > > > 23 KSP preconditioned resid norm 1.851801714075e-03 true resid norm > > > 2.017702443794e+00 ||Ae||/||Ax|| 5.913945303323e-02 > > > 24 KSP preconditioned resid norm 9.594251508173e-04 true resid norm > > > 2.065135975225e+00 ||Ae||/||Ax|| 6.052974381317e-02 > > > 25 KSP preconditioned resid norm 8.609050236229e-04 true resid norm > > > 1.901663497990e+00 ||Ae||/||Ax|| 5.573831734719e-02 > > > 26 KSP preconditioned resid norm 8.607029066323e-04 true resid norm > > > 1.901221069645e+00 ||Ae||/||Ax|| 5.572534964205e-02 > > > 27 KSP preconditioned resid norm 6.010429111401e-04 true resid norm > > > 1.025962923033e+00 ||Ae||/||Ax|| 3.007127551793e-02 > > > 28 KSP preconditioned resid norm 2.036565987243e-04 true resid norm > > > 8.385451121270e-01 ||Ae||/||Ax|| 2.457800426788e-02 > > > > > > 8: > > > > > > 8 16 > > > 24 32 > > > 56 64 > > > 16 24 > > > 48 56 > > > 0 8 > > > 32 40 > > > 40 48 > > > 0 KSP preconditioned resid norm 4.299803638671e+01 true resid norm > > > 3.411770553001e+01 ||Ae||/||Ax|| 1.000000000000e+00 > > > 1 KSP preconditioned resid norm 9.603727351867e+00 true resid norm > > > 1.922897810349e+01 ||Ae||/||Ax|| 5.636070129797e-01 > > > 2 KSP preconditioned resid norm 2.931835632556e+00 true resid norm > > > 1.355792423218e+01 ||Ae||/||Ax|| 3.973867533457e-01 > > > 3 KSP preconditioned resid norm 1.314351599619e+00 true resid norm > > > 9.882281425137e+00 ||Ae||/||Ax|| 2.896525798443e-01 > > > 4 KSP preconditioned resid norm 8.218956530484e-01 true resid norm > > > 9.318760482806e+00 ||Ae||/||Ax|| 2.731356150140e-01 > > > 5 KSP preconditioned resid norm 6.895693486764e-01 true resid norm > > > 9.360126907217e+00 ||Ae||/||Ax|| 2.743480770998e-01 > > > 6 KSP preconditioned resid norm 6.138748402770e-01 true resid norm > > > 9.020243051395e+00 ||Ae||/||Ax|| 2.643859811575e-01 > > > 7 KSP preconditioned resid norm 5.265342569996e-01 true resid norm > > > 8.781477094899e+00 ||Ae||/||Ax|| 2.573876806333e-01 > > > 8 KSP preconditioned resid norm 4.403325671754e-01 true resid norm > > > 8.314776073768e+00 ||Ae||/||Ax|| 2.437085362160e-01 > > > 9 KSP preconditioned resid norm 2.353592633657e-01 true resid norm > > > 7.347976506279e+00 ||Ae||/||Ax|| 2.153713560783e-01 > > > 10 KSP preconditioned resid norm 8.943808926292e-02 true resid norm > > > 6.972332890712e+00 ||Ae||/||Ax|| 2.043611310432e-01 > > > 11 KSP preconditioned resid norm 5.930469791557e-02 true resid norm > > > 6.957386646797e+00 ||Ae||/||Ax|| 2.039230522310e-01 > > > 12 KSP preconditioned resid norm 5.283812047599e-02 true resid norm > > > 6.981023245883e+00 ||Ae||/||Ax|| 2.046158479134e-01 > > > 13 KSP preconditioned resid norm 3.665176395384e-02 true resid norm > > > 6.992078556546e+00 ||Ae||/||Ax|| 2.049398823258e-01 > > > 14 KSP preconditioned resid norm 2.516790937741e-02 true resid norm > > > 6.949891196404e+00 ||Ae||/||Ax|| 2.037033583718e-01 > > > 15 KSP preconditioned resid norm 2.192690814272e-02 true resid norm > > > 6.927621207906e+00 ||Ae||/||Ax|| 2.030506184483e-01 > > > 16 KSP preconditioned resid norm 2.058802964863e-02 true resid norm > > > 6.919125260713e+00 ||Ae||/||Ax|| 2.028015997332e-01 > > > 17 KSP preconditioned resid norm 1.984533974458e-02 true resid norm > > > 6.853733693988e+00 ||Ae||/||Ax|| 2.008849536484e-01 > > > 18 KSP preconditioned resid norm 1.958243371255e-02 true resid norm > > > 6.766030769290e+00 ||Ae||/||Ax|| 1.983143550887e-01 > > > 19 KSP preconditioned resid norm 1.874262002187e-02 true resid norm > > > 6.323230908702e+00 ||Ae||/||Ax|| 1.853357607281e-01 > > > 20 KSP preconditioned resid norm 1.754461572091e-02 true resid norm > > > 5.538708901675e+00 ||Ae||/||Ax|| 1.623411895857e-01 > > > 21 KSP preconditioned resid norm 1.184321475064e-02 true resid norm > > > 3.839931686898e+00 ||Ae||/||Ax|| 1.125495289688e-01 > > > 22 KSP preconditioned resid norm 1.070434172478e-02 true resid norm > > > 3.754159266432e+00 ||Ae||/||Ax|| 1.100355140568e-01 > > > 23 KSP preconditioned resid norm 8.011880009497e-03 true resid norm > > > 3.937870836170e+00 ||Ae||/||Ax|| 1.154201542864e-01 > > > 24 KSP preconditioned resid norm 5.573761552253e-03 true resid norm > > > 4.205066407359e+00 ||Ae||/||Ax|| 1.232517351924e-01 > > > 25 KSP preconditioned resid norm 4.810675543540e-03 true resid norm > > > 4.069723693466e+00 ||Ae||/||Ax|| 1.192848003769e-01 > > > 26 KSP preconditioned resid norm 4.647944860704e-03 true resid norm > > > 4.044329745280e+00 ||Ae||/||Ax|| 1.185404962746e-01 > > > 27 KSP preconditioned resid norm 4.606926939804e-03 true resid norm > > > 4.039416044569e+00 ||Ae||/||Ax|| 1.183964742593e-01 > > > 28 KSP preconditioned resid norm 4.606174352197e-03 true resid norm > > > 4.038658488893e+00 ||Ae||/||Ax|| 1.183742700792e-01 > > > 29 KSP preconditioned resid norm 4.604980580071e-03 true resid norm > > > 4.034721549326e+00 ||Ae||/||Ax|| 1.182588772207e-01 > > > 30 KSP preconditioned resid norm 4.551931835395e-03 true resid norm > > > 3.942692013899e+00 ||Ae||/||Ax|| 1.155614644259e-01 > > > 31 KSP preconditioned resid norm 4.534435621643e-03 true resid norm > > > 3.940744976447e+00 ||Ae||/||Ax|| 1.155043961846e-01 > > > 32 KSP preconditioned resid norm 4.533889403959e-03 true resid norm > > > 3.940661031251e+00 ||Ae||/||Ax|| 1.155019357261e-01 > > > 33 KSP preconditioned resid norm 4.533315616020e-03 true resid norm > > > 3.940962366962e+00 ||Ae||/||Ax|| 1.155107679646e-01 > > > 34 KSP preconditioned resid norm 4.533098107272e-03 true resid norm > > > 3.940998854473e+00 ||Ae||/||Ax|| 1.155118374243e-01 > > > 35 KSP preconditioned resid norm 4.531113895054e-03 true resid norm > > > 3.939900266217e+00 ||Ae||/||Ax|| 1.154796374789e-01 > > > 36 KSP preconditioned resid norm 4.530789523555e-03 true resid norm > > > 3.939483356865e+00 ||Ae||/||Ax|| 1.154674177430e-01 > > > 37 KSP preconditioned resid norm 4.530789514003e-03 true resid norm > > > 3.939490762772e+00 ||Ae||/||Ax|| 1.154676348123e-01 > > > 38 KSP preconditioned resid norm 4.530624961751e-03 true resid norm > > > 3.937889462104e+00 ||Ae||/||Ax|| 1.154207002179e-01 > > > 39 KSP preconditioned resid norm 4.517785703071e-03 true resid norm > > > 3.927441577896e+00 ||Ae||/||Ax|| 1.151144696539e-01 > > > 40 KSP preconditioned resid norm 4.508890400648e-03 true resid norm > > > 3.919421029911e+00 ||Ae||/||Ax|| 1.148793850297e-01 > > > 41 KSP preconditioned resid norm 4.508823049754e-03 true resid norm > > > 3.920408845458e+00 ||Ae||/||Ax|| 1.149083381943e-01 > > > 42 KSP preconditioned resid norm 4.504581641358e-03 true resid norm > > > 3.910936323861e+00 ||Ae||/||Ax|| 1.146306957958e-01 > > > 43 KSP preconditioned resid norm 4.496299729031e-03 true resid norm > > > 3.892573202489e+00 ||Ae||/||Ax|| 1.140924672987e-01 > > > 44 KSP preconditioned resid norm 4.327165698785e-03 true resid norm > > > 3.499303379330e+00 ||Ae||/||Ax|| 1.025656129265e-01 > > > 45 KSP preconditioned resid norm 3.860049921599e-03 true resid norm > > > 2.642394407576e+00 ||Ae||/||Ax|| 7.744935852298e-02 > > > 46 KSP preconditioned resid norm 3.813681936798e-03 true resid norm > > > 2.561643926848e+00 ||Ae||/||Ax|| 7.508253814415e-02 > > > 47 KSP preconditioned resid norm 3.811608329841e-03 true resid norm > > > 2.553393452252e+00 ||Ae||/||Ax|| 7.484071430319e-02 > > > 48 KSP preconditioned resid norm 3.805700908518e-03 true resid norm > > > 2.559614961583e+00 ||Ae||/||Ax|| 7.502306857451e-02 > > > 49 KSP preconditioned resid norm 3.783124026053e-03 true resid norm > > > 2.523808739092e+00 ||Ae||/||Ax|| 7.397357764494e-02 > > > 50 KSP preconditioned resid norm 3.777662131381e-03 true resid norm > > > 2.516105834856e+00 ||Ae||/||Ax|| 7.374780325255e-02 > > > 51 KSP preconditioned resid norm 3.710923429451e-03 true resid norm > > > 2.426657981798e+00 ||Ae||/||Ax|| 7.112606032852e-02 > > > 52 KSP preconditioned resid norm 3.604808013597e-03 true resid norm > > > 2.303594181107e+00 ||Ae||/||Ax|| 6.751902407624e-02 > > > 53 KSP preconditioned resid norm 3.513880489788e-03 true resid norm > > > 2.188212014004e+00 ||Ae||/||Ax|| 6.413713876742e-02 > > > 54 KSP preconditioned resid norm 3.320184202285e-03 true resid norm > > > 1.978987642137e+00 ||Ae||/||Ax|| 5.800471079148e-02 > > > 55 KSP preconditioned resid norm 2.195662794099e-03 true resid norm > > > 1.448538675887e+00 ||Ae||/||Ax|| 4.245709532291e-02 > > > 56 KSP preconditioned resid norm 9.077826763324e-04 true resid norm > > > 1.628573968470e+00 ||Ae||/||Ax|| 4.773398278607e-02 > > > 57 KSP preconditioned resid norm 7.602131391716e-04 true resid norm > > > 1.659109675600e+00 ||Ae||/||Ax|| 4.862899335772e-02 > > > 58 KSP preconditioned resid norm 7.450227847936e-04 true resid norm > > > 1.651479746174e+00 ||Ae||/||Ax|| 4.840535787852e-02 > > > 59 KSP preconditioned resid norm 7.410161195392e-04 true resid norm > > > 1.649502155114e+00 ||Ae||/||Ax|| 4.834739410196e-02 > > > 60 KSP preconditioned resid norm 7.399447579004e-04 true resid norm > > > 1.648188611058e+00 ||Ae||/||Ax|| 4.830889373871e-02 > > > 61 KSP preconditioned resid norm 7.399146825366e-04 true resid norm > > > 1.648156339888e+00 ||Ae||/||Ax|| 4.830794786121e-02 > > > 62 KSP preconditioned resid norm 7.399119217730e-04 true resid norm > > > 1.648143662498e+00 ||Ae||/||Ax|| 4.830757628317e-02 > > > 63 KSP preconditioned resid norm 7.399115190929e-04 true resid norm > > > 1.648149747433e+00 ||Ae||/||Ax|| 4.830775463441e-02 > > > 64 KSP preconditioned resid norm 7.398927702838e-04 true resid norm > > > 1.648083443482e+00 ||Ae||/||Ax|| 4.830581124607e-02 > > > 65 KSP preconditioned resid norm 7.398398384099e-04 true resid norm > > > 1.647873653551e+00 ||Ae||/||Ax|| 4.829966224141e-02 > > > 66 KSP preconditioned resid norm 7.398251502315e-04 true resid norm > > > 1.647783674785e+00 ||Ae||/||Ax|| 4.829702493725e-02 > > > 67 KSP preconditioned resid norm 7.398217631044e-04 true resid norm > > > 1.647733028046e+00 ||Ae||/||Ax|| 4.829554046641e-02 > > > 68 KSP preconditioned resid norm 7.398045634717e-04 true resid norm > > > 1.647630453201e+00 ||Ae||/||Ax|| 4.829253396748e-02 > > > 69 KSP preconditioned resid norm 7.397586859381e-04 true resid norm > > > 1.647387302132e+00 ||Ae||/||Ax|| 4.828540713804e-02 > > > 70 KSP preconditioned resid norm 7.396782241138e-04 true resid norm > > > 1.646889429724e+00 ||Ae||/||Ax|| 4.827081435109e-02 > > > 71 KSP preconditioned resid norm 7.395189566969e-04 true resid norm > > > 1.646041167917e+00 ||Ae||/||Ax|| 4.824595154763e-02 > > > 72 KSP preconditioned resid norm 7.391300711199e-04 true resid norm > > > 1.643970513576e+00 ||Ae||/||Ax|| 4.818526005889e-02 > > > 73 KSP preconditioned resid norm 7.367639912300e-04 true resid norm > > > 1.631221838831e+00 ||Ae||/||Ax|| 4.781159264642e-02 > > > 74 KSP preconditioned resid norm 7.075386327019e-04 true resid norm > > > 1.473482203196e+00 ||Ae||/||Ax|| 4.318819745660e-02 > > > 75 KSP preconditioned resid norm 6.769663644505e-04 true resid norm > > > 1.324870886213e+00 ||Ae||/||Ax|| 3.883235597562e-02 > > > 76 KSP preconditioned resid norm 6.510062346881e-04 true resid norm > > > 1.209103850108e+00 ||Ae||/||Ax|| 3.543919004296e-02 > > > 77 KSP preconditioned resid norm 6.416005299115e-04 true resid norm > > > 1.174343461999e+00 ||Ae||/||Ax|| 3.442035282725e-02 > > > 78 KSP preconditioned resid norm 6.269785791288e-04 true resid norm > > > 1.115598946804e+00 ||Ae||/||Ax|| 3.269853378102e-02 > > > 79 KSP preconditioned resid norm 6.143599514076e-04 true resid norm > > > 1.060258719301e+00 ||Ae||/||Ax|| 3.107649540993e-02 > > > 80 KSP preconditioned resid norm 6.118239459355e-04 true resid norm > > > 1.049506356947e+00 ||Ae||/||Ax|| 3.076134050174e-02 > > > 81 KSP preconditioned resid norm 6.112876406857e-04 true resid norm > > > 1.046662765401e+00 ||Ae||/||Ax|| 3.067799399581e-02 > > > 82 KSP preconditioned resid norm 6.092506607543e-04 true resid norm > > > 1.042978389425e+00 ||Ae||/||Ax|| 3.057000385056e-02 > > > 83 KSP preconditioned resid norm 6.081618319409e-04 true resid norm > > > 1.040456343908e+00 ||Ae||/||Ax|| 3.049608195349e-02 > > > 84 KSP preconditioned resid norm 6.071647595071e-04 true resid norm > > > 1.037276486552e+00 ||Ae||/||Ax|| 3.040287939761e-02 > > > 85 KSP preconditioned resid norm 5.795095806265e-04 true resid norm > > > 9.478301874350e-01 ||Ae||/||Ax|| 2.778118202003e-02 > > > 86 KSP preconditioned resid norm 4.787555615154e-04 true resid norm > > > 6.865840307207e-01 ||Ae||/||Ax|| 2.012398020485e-02 > > > 87 KSP preconditioned resid norm 4.213257765496e-04 true resid norm > > > 5.905989111727e-01 ||Ae||/||Ax|| 1.731062807413e-02 > > > > > > It seems that the no. of lines is much lesser compared to the eariler > > case > > > when KSPSetTolerances = 1.0e-8 > > > > > > Thanks again > > > > > > > > > > > > On 6/17/07, Barry Smith wrote: > > > > > > > > > > > > Ben, > > > > > > > > > > > > On Sat, 16 Jun 2007, Ben Tay wrote: > > > > > > > > > Hi, > > > > > > > > > > I am trying to use PETSc to solve my poisson eqn. In the past, when > > I'm > > > > not > > > > > using MPI, I set KSPSetTolerances to 1.0e-5. This seems to be good > > > > enuff. > > > > > > > > > > Now, I'm trying to use PETSc with MPI to solve the eqn. I am using a > > > > very > > > > > small no. of pts, only 16x4. On 1 processor, the ans is the same as > > the > > > > one > > > > > without MPI. However, on 2 processors, I found that I've to increase > > the > > > > > KSPSetTolerances to 1.0e-6, else those grid pts on the edge will be > > > > > different. On 4 processors, KSPSetTolerances has to be decreased to > > > > 1.0e-7. > > > > > On 8 processors, when KSPSetTolerances is 1.0e-8, the difference of > > the > > > > last > > > > > pt between 1 and 8 processors is about 3%. > > > > > > > > > > > > > Are you using the same number of grid points when changing the > > number of > > > > processors? > > > > > > > > Run the cases with -ksp_monitor_true_residual and send us ALL the > > > > output. > > > > > > > > Barry > > > > > > > > > > > > > > > > > May I know why this is so? Also, does this happens only on very > > small > > > > grids? > > > > > Does it happen on large grids as well? I usually solve grids with > > approx > > > > > 20000 to 55000 pts. > > > > > > > > > > Thank you. > > > > > > > > > > > > > > > > > > > > > From zonexo at gmail.com Wed Jun 20 03:10:42 2007 From: zonexo at gmail.com (Ben Tay) Date: Wed, 20 Jun 2007 16:10:42 +0800 Subject: View just 1 row in a matrix Message-ID: <804ab5d40706200110q33b60016tf63f362c27af1b1d@mail.gmail.com> Hi, I have a rather big matrix. May I know if it's possible to just view a particular row of the matrix? I don't think Matview can do it. Is there anyway to do it? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From zonexo at gmail.com Wed Jun 20 03:40:40 2007 From: zonexo at gmail.com (Ben Tay) Date: Wed, 20 Jun 2007 16:40:40 +0800 Subject: How to zero all values on a particular row? In-Reply-To: References: <804ab5d40706100713jec08cd8q3a4df577866f414@mail.gmail.com> <804ab5d40706101747l7059b624i88cfe0bdb3893d14@mail.gmail.com> Message-ID: <804ab5d40706200140s65df9c57q75f2f13faba1fafe@mail.gmail.com> Hi, I tried to do it in 2 ways: A: 1.Do initial sweep: do j=1,size_y do i=1,size_x matsetvalue .... end do end do" 2.matssemblybegin/end 3 do a loop using matzerorows to zeros the particular rows 4. do loop and use matsetvalues to insert values into those rows which I had zeroed previously 5 matssemblybegin/end 6 solve B: 1. Same as A 2 use matsetvalues to put zeros into those location where I earlier insert in the 1st full i,j sweep 3. insert correct value using matsetvalues 4. finally matassemblybegin/end - just once. 5. solve l realised that B is about 3 times faster than A. May I know why this is so? In A, I only call matssemblybegin/end once more. Is it so serious to the performance? Thanks On 6/11/07, Barry Smith wrote: > > > On Mon, 11 Jun 2007, Ben Tay wrote: > > > Thanks Barry, > > > > I managed to get it working. I realise that I had to call > > matssemblybegin/end each time after I zero a particular row. I also > tried > > MatSetOption(mat,MAT_KEEP_ZEROED_ROWS) as what you 've suggested. > > > > So do I have to callMatSetOption(mat,MAT_KEEP_ZEROED_ROWS) everytime > just > > before I need to zero it or just once ie after the 1st > matassemblybegin/end? > > Call it once when the matrix is created is fine. > > > > Calling matassemblybegin/end each time before matzerorows gives me the > > impression that it is very inefficient. Is that so? > > Yes, if you do this a bunch of imes > > > > > In that case, I wonder if it is better for me to : > > > > 1 use matsetvalues to put zeros into those location where I earlier > insert > > in the 1st full i,j sweep > > 2. insert correct value using matsetvalues > > 3. finally matassemblybegin/end - just once. > > You can do this > > > > > Lastly, is MatZeroRowsIS exactly the same as matzerorows, except that it > is > > meant for just 1 row instead of consecutive no. of rows? > > They are the same but one takes an array of integers while the other > takes an IS. Neither require "consecutive no. of rows" you can zero > whatever rows you want together. > > Barry > > > > > Thanks again > > > > > > On 6/11/07, Barry Smith wrote: > > > > > > > > > > > > On Sun, 10 Jun 2007, Ben Tay wrote: > > > > > > > Hi, > > > > > > > > I need to insert values into a matrix and then solve this poisson > eqn as > > > > part of my cfd code. For efficiency sake, I simply use > > > > > > > > "do j=1,size_y > > > > > > > > do i=1,size_x > > > > > > > > matsetvalue .... > > > > > > > > end do > > > > > > > > end do" > > > > > > > > to insert values into all the cells > > > > > > > > Then for specific cells, I need to enter some other values. In other > > > words, > > > > for specific rows of the matrix, I need to zero the whole row and > insert > > > new > > > > values. How can I do that? > > > > > > > > I tried to use MatZeroRows but it says it's not for unassembled > matrix. > > > But > > > > I need to zero the particular row, insert values, and then finally > > > assembly > > > > it. Is there a command to do this? > > > > > > matassemblybegin/end > > > matzerorows > > > matsetvalues, matsetvalues, matsetvalue > > > matssemblybegin/end > > > > > > For improved efficiency you will want to call > > > MatSetOption(mat,MAT_KEEP_ZEROED_ROWS); before the matzerorows() > > > > > > > > > > > Thanks > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Wed Jun 20 08:41:29 2007 From: knepley at gmail.com (Matthew Knepley) Date: Wed, 20 Jun 2007 08:41:29 -0500 Subject: View just 1 row in a matrix In-Reply-To: <804ab5d40706200110q33b60016tf63f362c27af1b1d@mail.gmail.com> References: <804ab5d40706200110q33b60016tf63f362c27af1b1d@mail.gmail.com> Message-ID: MatGetRow() and Printf() Matt On 6/20/07, Ben Tay wrote: > Hi, > > I have a rather big matrix. May I know if it's possible to just view a > particular row of the matrix? I don't think Matview can do it. Is there > anyway to do it? > > Thanks -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From bsmith at mcs.anl.gov Wed Jun 20 10:38:42 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Wed, 20 Jun 2007 10:38:42 -0500 (CDT) Subject: How to zero all values on a particular row? In-Reply-To: <804ab5d40706200140s65df9c57q75f2f13faba1fafe@mail.gmail.com> References: <804ab5d40706100713jec08cd8q3a4df577866f414@mail.gmail.com> <804ab5d40706101747l7059b624i88cfe0bdb3893d14@mail.gmail.com> <804ab5d40706200140s65df9c57q75f2f13faba1fafe@mail.gmail.com> Message-ID: Ben, You'll want to use MatZeroRows() (even if it is just one row) Also take a look at MatSetOption() and the option MAT_KEEP_ZEROED_ROWS. Barry On Wed, 20 Jun 2007, Ben Tay wrote: > Hi, > > I tried to do it in 2 ways: > > A: > > 1.Do initial sweep: > > do j=1,size_y > > do i=1,size_x > > matsetvalue .... > > end do > > end do" > > 2.matssemblybegin/end > > 3 do a loop using matzerorows to zeros the particular rows > > 4. do loop and use matsetvalues to insert values into those rows which I had > zeroed previously > > 5 matssemblybegin/end > > 6 solve > > > > B: > > 1. Same as A > > 2 use matsetvalues to put zeros into those location where I earlier insert > in the 1st full i,j sweep > 3. insert correct value using matsetvalues > > 4. finally matassemblybegin/end - just once. > > 5. solve > > l realised that B is about 3 times faster than A. May I know why this is > so? In A, I only call matssemblybegin/end once more. Is it so serious to the > performance? > > > > Thanks > > On 6/11/07, Barry Smith wrote: > > > > > > > On Mon, 11 Jun 2007, Ben Tay wrote: > > > > > Thanks Barry, > > > > > > I managed to get it working. I realise that I had to call > > > matssemblybegin/end each time after I zero a particular row. I also > > tried > > > MatSetOption(mat,MAT_KEEP_ZEROED_ROWS) as what you 've suggested. > > > > > > So do I have to callMatSetOption(mat,MAT_KEEP_ZEROED_ROWS) everytime > > just > > > before I need to zero it or just once ie after the 1st > > matassemblybegin/end? > > > > Call it once when the matrix is created is fine. > > > > > > Calling matassemblybegin/end each time before matzerorows gives me the > > > impression that it is very inefficient. Is that so? > > > > Yes, if you do this a bunch of imes > > > > > > > > In that case, I wonder if it is better for me to : > > > > > > 1 use matsetvalues to put zeros into those location where I earlier > > insert > > > in the 1st full i,j sweep > > > 2. insert correct value using matsetvalues > > > 3. finally matassemblybegin/end - just once. > > > > You can do this > > > > > > > > Lastly, is MatZeroRowsIS exactly the same as matzerorows, except that it > > is > > > meant for just 1 row instead of consecutive no. of rows? > > > > They are the same but one takes an array of integers while the other > > takes an IS. Neither require "consecutive no. of rows" you can zero > > whatever rows you want together. > > > > Barry > > > > > > > > Thanks again > > > > > > > > > On 6/11/07, Barry Smith wrote: > > > > > > > > > > > > > > > > On Sun, 10 Jun 2007, Ben Tay wrote: > > > > > > > > > Hi, > > > > > > > > > > I need to insert values into a matrix and then solve this poisson > > eqn as > > > > > part of my cfd code. For efficiency sake, I simply use > > > > > > > > > > "do j=1,size_y > > > > > > > > > > do i=1,size_x > > > > > > > > > > matsetvalue .... > > > > > > > > > > end do > > > > > > > > > > end do" > > > > > > > > > > to insert values into all the cells > > > > > > > > > > Then for specific cells, I need to enter some other values. In other > > > > words, > > > > > for specific rows of the matrix, I need to zero the whole row and > > insert > > > > new > > > > > values. How can I do that? > > > > > > > > > > I tried to use MatZeroRows but it says it's not for unassembled > > matrix. > > > > But > > > > > I need to zero the particular row, insert values, and then finally > > > > assembly > > > > > it. Is there a command to do this? > > > > > > > > matassemblybegin/end > > > > matzerorows > > > > matsetvalues, matsetvalues, matsetvalue > > > > matssemblybegin/end > > > > > > > > For improved efficiency you will want to call > > > > MatSetOption(mat,MAT_KEEP_ZEROED_ROWS); before the matzerorows() > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > > > > > > From billy at dem.uminho.pt Fri Jun 22 04:40:38 2007 From: billy at dem.uminho.pt (billy at dem.uminho.pt) Date: Fri, 22 Jun 2007 10:40:38 +0100 Subject: Parallel conjugate gradient? Message-ID: <1182505238.467b99163629c@serv-g1.ccom.uminho.pt> Hi, Is there any parallel conjugate gradient solver implemented in PETSC? Thanks, Billy. From bsmith at mcs.anl.gov Fri Jun 22 08:11:56 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 22 Jun 2007 08:11:56 -0500 (CDT) Subject: Parallel conjugate gradient? In-Reply-To: <1182505238.467b99163629c@serv-g1.ccom.uminho.pt> References: <1182505238.467b99163629c@serv-g1.ccom.uminho.pt> Message-ID: http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/KSP/KSPCG.html On Fri, 22 Jun 2007, billy at dem.uminho.pt wrote: > > Hi, > > Is there any parallel conjugate gradient solver implemented in PETSC? > > Thanks, > > Billy. > > From billy at dem.uminho.pt Fri Jun 22 08:29:30 2007 From: billy at dem.uminho.pt (billy at dem.uminho.pt) Date: Fri, 22 Jun 2007 14:29:30 +0100 Subject: Parallel conjugate gradient? In-Reply-To: References: <1182505238.467b99163629c@serv-g1.ccom.uminho.pt> Message-ID: <1182518970.467bceba51cf4@serv-g1.ccom.uminho.pt> Hi, Thanks. I had the idea this KSPCG only worked in serial mode. Billy. Quoting Barry Smith : > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/KSP/KSPCG.html > > > On Fri, 22 Jun 2007, billy at dem.uminho.pt wrote: > > > > > Hi, > > > > Is there any parallel conjugate gradient solver implemented in PETSC? > > > > Thanks, > > > > Billy. > > > > > > From timothy.stitt at ichec.ie Wed Jun 27 06:08:44 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Wed, 27 Jun 2007 12:08:44 +0100 Subject: Compiler Optimization Override Message-ID: <200706271208.44921.timothy.stitt@ichec.ie> Hi PETSc Users/Developers, Could someone explain how I can override the default optimization level that comes with my PETSc build (currently -O). I want to set a more aggressive optimization level (e.g. -O3) for my compiler (PathScale). Ideally I would prefer a solution which doesn't involve rebuilding PETSc each time I want to switch the optimization level. I tried to add the switch to the petscrules file but it always defaulted to the first (lower?) optimization switch that appeared in the application compile command line which seems to be built into PETSc. Any help gratefully received. Regards, Tim. -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From aja2111 at columbia.edu Wed Jun 27 08:19:08 2007 From: aja2111 at columbia.edu (Aron Ahmadia) Date: Wed, 27 Jun 2007 09:19:08 -0400 Subject: Compiler Optimization Override In-Reply-To: <200706271208.44921.timothy.stitt@ichec.ie> References: <200706271208.44921.timothy.stitt@ichec.ie> Message-ID: <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> Dear Tim, I was just in Ireland a few weeks ago, had a great time climbing Carantouhil and the Pilgrim's Path :D Have you tried declaring a new $PETSC_ARCH and then overriding the optimization flags in ./conf/configure? PETSc likes to use the $PETSC_ARCH flag to maintain all local builds under the same directory structure instead of the -prefix flags common to autoconf-style builds. Ideally you'd do something like this... declare -x PETSC_ARCH=petsc_linux_o3 cd $PETSC_DIR ./config/configure.py --COPTFLAGS=-O3 make If you want to build a debugging version as well, then type: declare -x PETSC_ARCH=petsc_debug ./config/configure.py --with-debugging=1 you'll then be able to use PETSc makefiles to build your code as long as you declare your PETSC_ARCH and PETSC_DIR variables ahead of time. Let me know if this works! ~Aron On 6/27/07, Tim Stitt wrote: > Hi PETSc Users/Developers, > > Could someone explain how I can override the default optimization level that > comes with my PETSc build (currently -O). I want to set a more aggressive > optimization level (e.g. -O3) for my compiler (PathScale). > > Ideally I would prefer a solution which doesn't involve rebuilding PETSc each > time I want to switch the optimization level. I tried to add the switch to > the petscrules file but it always defaulted to the first (lower?) > optimization switch that appeared in the application compile command line > which seems to be built into PETSc. > > Any help gratefully received. > > Regards, > > Tim. > > -- > Dr. Timothy Stitt > HPC Application Consultant - ICHEC (www.ichec.ie) > > Dublin Institute for Advanced Studies > 5 Merrion Square - Dublin 2 - Ireland > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > From aja2111 at columbia.edu Wed Jun 27 08:20:33 2007 From: aja2111 at columbia.edu (Aron Ahmadia) Date: Wed, 27 Jun 2007 09:20:33 -0400 Subject: Compiler Optimization Override In-Reply-To: <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> References: <200706271208.44921.timothy.stitt@ichec.ie> <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> Message-ID: <37604ab40706270620o991a5d1s4989ff5da7a48b1b@mail.gmail.com> And as a correction to my last email, PETSC_ARCH is a 'global' environment variable, it along with PETSC_DIR help you coordinate multiple PETSc installations and builds. ~A On 6/27/07, Aron Ahmadia wrote: > Dear Tim, > > I was just in Ireland a few weeks ago, had a great time climbing > Carantouhil and the Pilgrim's Path :D > > Have you tried declaring a new $PETSC_ARCH and then overriding the > optimization flags in ./conf/configure? PETSc likes to use the > $PETSC_ARCH flag to maintain all local builds under the same directory > structure instead of the -prefix flags common to autoconf-style > builds. > > Ideally you'd do something like this... > > declare -x PETSC_ARCH=petsc_linux_o3 > cd $PETSC_DIR > ./config/configure.py --COPTFLAGS=-O3 > make > > If you want to build a debugging version as well, then type: > declare -x PETSC_ARCH=petsc_debug > ./config/configure.py --with-debugging=1 > > you'll then be able to use PETSc makefiles to build your code as long > as you declare your PETSC_ARCH and PETSC_DIR variables ahead of time. > > Let me know if this works! > ~Aron > > On 6/27/07, Tim Stitt wrote: > > Hi PETSc Users/Developers, > > > > Could someone explain how I can override the default optimization level that > > comes with my PETSc build (currently -O). I want to set a more aggressive > > optimization level (e.g. -O3) for my compiler (PathScale). > > > > Ideally I would prefer a solution which doesn't involve rebuilding PETSc each > > time I want to switch the optimization level. I tried to add the switch to > > the petscrules file but it always defaulted to the first (lower?) > > optimization switch that appeared in the application compile command line > > which seems to be built into PETSc. > > > > Any help gratefully received. > > > > Regards, > > > > Tim. > > > > -- > > Dr. Timothy Stitt > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > Dublin Institute for Advanced Studies > > 5 Merrion Square - Dublin 2 - Ireland > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) > > > > > From balay at mcs.anl.gov Wed Jun 27 08:21:46 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Wed, 27 Jun 2007 08:21:46 -0500 (CDT) Subject: Compiler Optimization Override In-Reply-To: <200706271208.44921.timothy.stitt@ichec.ie> References: <200706271208.44921.timothy.stitt@ichec.ie> Message-ID: On Wed, 27 Jun 2007, Tim Stitt wrote: > Hi PETSc Users/Developers, > > Could someone explain how I can override the default optimization level that > comes with my PETSc build (currently -O). I want to set a more aggressive > optimization level (e.g. -O3) for my compiler (PathScale). Rebuild a different variant of the libraires [with a different PETSC_ARCH] using COPTFLAGS=-O3 FOPTFLAGS=-O3 > Ideally I would prefer a solution which doesn't involve rebuilding PETSc each > time I want to switch the optimization level. You just build both versions once, and switch between them by switching PETSC_ARCH make PETSC_ARCH=opt mybinary make PETSC_ARCH=opt-3 mybinary > I tried to add the switch to the petscrules file but it always > defaulted to the first (lower?) optimization switch that appeared > in the application compile command line which seems to be built into > PETSc. If you are chaning config files manually, then you'll have to change all occurances of -O in petscconf file [not petscrules]. Also - if you've used --download-mpich, then mpicc etc wrappers would need this modification aswell. So its best to build different variants of PETSc libraries with different PETSC_ARCH values. Satish From timothy.stitt at ichec.ie Wed Jun 27 08:32:40 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Wed, 27 Jun 2007 14:32:40 +0100 Subject: Compiler Optimization Override In-Reply-To: References: <200706271208.44921.timothy.stitt@ichec.ie> Message-ID: <200706271432.40369.timothy.stitt@ichec.ie> Perfect...thanks for the info. On Wednesday 27 June 2007 14:21, Satish Balay wrote: > On Wed, 27 Jun 2007, Tim Stitt wrote: > > Hi PETSc Users/Developers, > > > > Could someone explain how I can override the default optimization level > > that comes with my PETSc build (currently -O). I want to set a more > > aggressive optimization level (e.g. -O3) for my compiler (PathScale). > > Rebuild a different variant of the libraires [with a different > PETSC_ARCH] using COPTFLAGS=-O3 FOPTFLAGS=-O3 > > > Ideally I would prefer a solution which doesn't involve rebuilding PETSc > > each time I want to switch the optimization level. > > You just build both versions once, and switch between them by switching > PETSC_ARCH > > make PETSC_ARCH=opt mybinary > make PETSC_ARCH=opt-3 mybinary > > > I tried to add the switch to the petscrules file but it always > > defaulted to the first (lower?) optimization switch that appeared > > in the application compile command line which seems to be built into > > PETSc. > > If you are chaning config files manually, then you'll have to change > all occurances of -O in petscconf file [not petscrules]. Also - if > you've used --download-mpich, then mpicc etc wrappers would need > this modification aswell. > > So its best to build different variants of PETSc libraries with > different PETSC_ARCH values. > > Satish -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From balay at mcs.anl.gov Wed Jun 27 08:45:26 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Wed, 27 Jun 2007 08:45:26 -0500 (CDT) Subject: Compiler Optimization Override In-Reply-To: <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> References: <200706271208.44921.timothy.stitt@ichec.ie> <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> Message-ID: On Wed, 27 Jun 2007, Aron Ahmadia wrote: > declare -x PETSC_ARCH=petsc_linux_o3 > cd $PETSC_DIR > ./config/configure.py --COPTFLAGS=-O3 > make Or you could just do: ./config/configure.py PETSC_ARCH=petsc_linux_o3 COPTFLAGS=-O3 make Satish From timothy.stitt at ichec.ie Wed Jun 27 08:46:15 2007 From: timothy.stitt at ichec.ie (Tim Stitt) Date: Wed, 27 Jun 2007 14:46:15 +0100 Subject: Compiler Optimization Override In-Reply-To: <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> References: <200706271208.44921.timothy.stitt@ichec.ie> <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> Message-ID: <200706271446.15946.timothy.stitt@ichec.ie> Hi Aron, Thanks for the information...everything is clear now. Hope you will be back to Ireland soon. Sure the weather can be miserable but nothing beats a good hike in the rain followed by a good pint of Guinness. Actually Guinness is pretty good with everything including PETSc coding :-) Regards. On Wednesday 27 June 2007 14:19, Aron Ahmadia wrote: > Dear Tim, > > I was just in Ireland a few weeks ago, had a great time climbing > Carantouhil and the Pilgrim's Path :D > > Have you tried declaring a new $PETSC_ARCH and then overriding the > optimization flags in ./conf/configure? PETSc likes to use the > $PETSC_ARCH flag to maintain all local builds under the same directory > structure instead of the -prefix flags common to autoconf-style > builds. > > Ideally you'd do something like this... > > declare -x PETSC_ARCH=petsc_linux_o3 > cd $PETSC_DIR > ./config/configure.py --COPTFLAGS=-O3 > make > > If you want to build a debugging version as well, then type: > declare -x PETSC_ARCH=petsc_debug > ./config/configure.py --with-debugging=1 > > you'll then be able to use PETSc makefiles to build your code as long > as you declare your PETSC_ARCH and PETSC_DIR variables ahead of time. > > Let me know if this works! > ~Aron > > On 6/27/07, Tim Stitt wrote: > > Hi PETSc Users/Developers, > > > > Could someone explain how I can override the default optimization level > > that comes with my PETSc build (currently -O). I want to set a more > > aggressive optimization level (e.g. -O3) for my compiler (PathScale). > > > > Ideally I would prefer a solution which doesn't involve rebuilding PETSc > > each time I want to switch the optimization level. I tried to add the > > switch to the petscrules file but it always defaulted to the first > > (lower?) optimization switch that appeared in the application compile > > command line which seems to be built into PETSc. > > > > Any help gratefully received. > > > > Regards, > > > > Tim. > > > > -- > > Dr. Timothy Stitt > > HPC Application Consultant - ICHEC (www.ichec.ie) > > > > Dublin Institute for Advanced Studies > > 5 Merrion Square - Dublin 2 - Ireland > > > > +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) -- Dr. Timothy Stitt HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile) From fuentes at ices.utexas.edu Wed Jun 27 12:12:56 2007 From: fuentes at ices.utexas.edu (David Fuentes) Date: Wed, 27 Jun 2007 12:12:56 -0500 (CDT) Subject: MPI_Send and PetscScalar In-Reply-To: <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> References: <200706271208.44921.timothy.stitt@ichec.ie> <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> Message-ID: Hello, I need to send a single PetscScalar Value from one processor to another. I want to use MPI_Send. Is MPIU_SCALAR the correct MPI_Datatype to MPI_Send a PetscScalar value between processors? thank you, David Fuentes From knepley at gmail.com Wed Jun 27 13:12:07 2007 From: knepley at gmail.com (Matthew Knepley) Date: Wed, 27 Jun 2007 13:12:07 -0500 Subject: MPI_Send and PetscScalar In-Reply-To: References: <200706271208.44921.timothy.stitt@ichec.ie> <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> Message-ID: Yes. Thanks, Matt On 6/27/07, David Fuentes wrote: > > Hello, > > I need to send a single PetscScalar Value from one processor to another. > > I want to use MPI_Send. > > Is MPIU_SCALAR the correct MPI_Datatype to MPI_Send a PetscScalar value > between processors? > > > thank you, > David Fuentes > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From bsmith at mcs.anl.gov Wed Jun 27 13:59:36 2007 From: bsmith at mcs.anl.gov (Barry Smith) Date: Wed, 27 Jun 2007 13:59:36 -0500 (CDT) Subject: MPI_Send and PetscScalar In-Reply-To: References: <200706271208.44921.timothy.stitt@ichec.ie> <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> Message-ID: Yes. Note that with real number PETSc PetscScalar is exactly an double and MPIU_SCALAR is exactly MPI_DOUBLE. Barry On Wed, 27 Jun 2007, David Fuentes wrote: > > Hello, > > I need to send a single PetscScalar Value from one processor to another. > > I want to use MPI_Send. > > Is MPIU_SCALAR the correct MPI_Datatype to MPI_Send a PetscScalar value > between processors? > > > thank you, > David Fuentes > > From r.gori at cineca.it Thu Jun 28 12:09:55 2007 From: r.gori at cineca.it (Roberto Gori) Date: Thu, 28 Jun 2007 19:09:55 +0200 (MEST) Subject: problems with ACML and single precision Message-ID: <002201c7b9a7$15fce240$c241a8c0@int.cineca.it> Hi, i'm trying to install PETSc 2.3.3-p3 on a Linux amd64 cluster. There's no problems w?th double precison but when I add the single precision option to my configure command I get the following error: ================================================================================= Configuring PETSc to compile on your system ================================================================================= TESTING: checkMissing from config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:446) ********************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------- Need to use --download-c-blas-lapack when using --with-precision=longdouble/single ********************************************************************************* This is my configure: config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 --with-blas-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a --with-lapack-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a --with-precision=single Maybe ACML is not supported for single precision? Thanks Roberto -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Jun 28 13:50:12 2007 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 28 Jun 2007 13:50:12 -0500 Subject: problems with ACML and single precision In-Reply-To: <002201c7b9a7$15fce240$c241a8c0@int.cineca.it> References: <002201c7b9a7$15fce240$c241a8c0@int.cineca.it> Message-ID: Yes, you need to let us compile for single precision. Use the option in the error message. Thanks, Matt On 6/28/07, Roberto Gori wrote: > > > Hi, > > i'm trying to install PETSc 2.3.3-p3 on a Linux amd64 cluster. > > There's no problems w?th double precison but when I add the single precision > option to my configure command I get the following error: > > ================================================================================= > Configuring PETSc to compile on your system > > ================================================================================= > TESTING: checkMissing from > config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:446) > > > ********************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > --------------------------------------------------------------------------------------- > Need to use --download-c-blas-lapack when using > --with-precision=longdouble/single > ********************************************************************************* > > > This is my configure: > config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 > --with-blas-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a > --with-lapack-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a > --with-precision=single > > > Maybe ACML is not supported for single precision? > > Thanks > > Roberto -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From randy at geosystem.us Thu Jun 28 13:50:52 2007 From: randy at geosystem.us (Randall Mackie) Date: Thu, 28 Jun 2007 11:50:52 -0700 Subject: compiling PETSC with mvapich Message-ID: <4684030C.8030204@geosystem.us> I am trying to build PETSC with mvapich, and in the configure step, I am getting the message ********************************************************************************* UNABLE to EXECUTE BINARIES for config/configure.py --------------------------------------------------------------------------------------- Cannot run executables created with C. It is likely that you will need to configure using --with-batch which allows configuration without interactive sessions. So if I add the --with-batch, and then --with-mpi-shared=1, then I get the following messages: ================================================================================= Since your compute nodes require use of a batch system or mpiexec you must: 1) Submit ./conftest to 1 processor of your batch system or system you are cross-compiling for; this will generate the file reconfigure.py 2) Run ./reconfigure.py (to complete the configure process). ================================================================================= However, using mvapich requires at least 2 processors, so I appear to be stuck. Any advice? Thanks, Randy -- Randall Mackie GSY-USA, Inc. PMB# 643 2261 Market St., San Francisco, CA 94114-1600 Tel (415) 469-8649 Fax (415) 469-5044 California Registered Geophysicist License No. GP 1034 From knepley at gmail.com Thu Jun 28 14:06:23 2007 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 28 Jun 2007 14:06:23 -0500 Subject: compiling PETSC with mvapich In-Reply-To: <4684030C.8030204@geosystem.us> References: <4684030C.8030204@geosystem.us> Message-ID: On 6/28/07, Randall Mackie wrote: > I am trying to build PETSC with mvapich, and in the configure step, I am getting the message > > ********************************************************************************* > UNABLE to EXECUTE BINARIES for config/configure.py > --------------------------------------------------------------------------------------- > Cannot run executables created with C. It is likely that you will need to configure using --with-batch which allows > configuration without interactive sessions. > > > > So if I add the --with-batch, and then --with-mpi-shared=1, then I get the following messages: > > ================================================================================= > Since your compute nodes require use of a batch system or mpiexec you must: > 1) Submit ./conftest to 1 processor of your batch system or system you are > cross-compiling for; this will generate the file reconfigure.py > 2) Run ./reconfigure.py (to complete the configure process). > ================================================================================= > > > However, using mvapich requires at least 2 processors, so I appear to be stuck. Wow, that sounds like a really broken way to operate. However, running on two processors might be alright, depending on whether the file system is shared. Each process will open 'reconfigure.py'. If they do not overwrite each other, you are fine. Are you sure things cnanot be run on 1 proc? Thanks, Matt > Any advice? > > Thanks, Randy > > > -- > Randall Mackie > GSY-USA, Inc. > PMB# 643 > 2261 Market St., > San Francisco, CA 94114-1600 > Tel (415) 469-8649 > Fax (415) 469-5044 > > California Registered Geophysicist > License No. GP 1034 > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From randy at geosystem.us Thu Jun 28 14:19:19 2007 From: randy at geosystem.us (Randall Mackie) Date: Thu, 28 Jun 2007 12:19:19 -0700 Subject: compiling PETSC with mvapich In-Reply-To: References: <4684030C.8030204@geosystem.us> Message-ID: <468409B7.1040101@geosystem.us> I was able to run it on one processor, using the mpirun_rsh command as follows: /usr/local/ofed/mpi/intel/mvapich-0.9.7-mlx2.2.0/bin/mpirun_rsh -np 1 hpcluster.local ./conftest I am now running ./reconfigure.py as instructed. What I don't understand is why the configure tool is unable to execute binaries created with C. Has anyone else used mvapich? (this is for use on infiniband). Randy Matthew Knepley wrote: > On 6/28/07, Randall Mackie wrote: >> I am trying to build PETSC with mvapich, and in the configure step, I >> am getting the message >> >> ********************************************************************************* >> >> UNABLE to EXECUTE BINARIES for config/configure.py >> --------------------------------------------------------------------------------------- >> >> Cannot run executables created with C. It is likely that you will need >> to configure using --with-batch which allows >> configuration without interactive sessions. >> >> >> >> So if I add the --with-batch, and then --with-mpi-shared=1, then I get >> the following messages: >> >> ================================================================================= >> >> Since your compute nodes require use of a batch system or mpiexec >> you must: >> 1) Submit ./conftest to 1 processor of your batch system or system >> you are >> cross-compiling for; this will generate the file reconfigure.py >> 2) Run ./reconfigure.py (to complete the configure process). >> ================================================================================= >> >> >> >> However, using mvapich requires at least 2 processors, so I appear to >> be stuck. > > Wow, that sounds like a really broken way to operate. However, running > on two > processors might be alright, depending on whether the file system is > shared. Each > process will open 'reconfigure.py'. If they do not overwrite each > other, you are fine. > Are you sure things cnanot be run on 1 proc? > > Thanks, > > Matt > >> Any advice? >> >> Thanks, Randy >> >> >> -- >> Randall Mackie >> GSY-USA, Inc. >> PMB# 643 >> 2261 Market St., >> San Francisco, CA 94114-1600 >> Tel (415) 469-8649 >> Fax (415) 469-5044 >> >> California Registered Geophysicist >> License No. GP 1034 >> >> > > -- Randall Mackie GSY-USA, Inc. PMB# 643 2261 Market St., San Francisco, CA 94114-1600 Tel (415) 469-8649 Fax (415) 469-5044 California Registered Geophysicist License No. GP 1034 From knepley at gmail.com Thu Jun 28 14:20:47 2007 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 28 Jun 2007 14:20:47 -0500 Subject: compiling PETSC with mvapich In-Reply-To: <468409B7.1040101@geosystem.us> References: <4684030C.8030204@geosystem.us> <468409B7.1040101@geosystem.us> Message-ID: On 6/28/07, Randall Mackie wrote: > I was able to run it on one processor, using the mpirun_rsh command as follows: > > /usr/local/ofed/mpi/intel/mvapich-0.9.7-mlx2.2.0/bin/mpirun_rsh -np 1 hpcluster.local ./conftest > > I am now running ./reconfigure.py as instructed. > > What I don't understand is why the configure tool is unable to execute binaries created > with C. Send the original configure.log to petsc-maint and we can try and figure it out. MAtt > Has anyone else used mvapich? (this is for use on infiniband). > > Randy > > Matthew Knepley wrote: > > On 6/28/07, Randall Mackie wrote: > >> I am trying to build PETSC with mvapich, and in the configure step, I > >> am getting the message > >> > >> ********************************************************************************* > >> > >> UNABLE to EXECUTE BINARIES for config/configure.py > >> --------------------------------------------------------------------------------------- > >> > >> Cannot run executables created with C. It is likely that you will need > >> to configure using --with-batch which allows > >> configuration without interactive sessions. > >> > >> > >> > >> So if I add the --with-batch, and then --with-mpi-shared=1, then I get > >> the following messages: > >> > >> ================================================================================= > >> > >> Since your compute nodes require use of a batch system or mpiexec > >> you must: > >> 1) Submit ./conftest to 1 processor of your batch system or system > >> you are > >> cross-compiling for; this will generate the file reconfigure.py > >> 2) Run ./reconfigure.py (to complete the configure process). > >> ================================================================================= > >> > >> > >> > >> However, using mvapich requires at least 2 processors, so I appear to > >> be stuck. > > > > Wow, that sounds like a really broken way to operate. However, running > > on two > > processors might be alright, depending on whether the file system is > > shared. Each > > process will open 'reconfigure.py'. If they do not overwrite each > > other, you are fine. > > Are you sure things cnanot be run on 1 proc? > > > > Thanks, > > > > Matt > > > >> Any advice? > >> > >> Thanks, Randy > >> > >> > >> -- > >> Randall Mackie > >> GSY-USA, Inc. > >> PMB# 643 > >> 2261 Market St., > >> San Francisco, CA 94114-1600 > >> Tel (415) 469-8649 > >> Fax (415) 469-5044 > >> > >> California Registered Geophysicist > >> License No. GP 1034 > >> > >> > > > > > > -- > Randall Mackie > GSY-USA, Inc. > PMB# 643 > 2261 Market St., > San Francisco, CA 94114-1600 > Tel (415) 469-8649 > Fax (415) 469-5044 > > California Registered Geophysicist > License No. GP 1034 > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener From r.gori at cineca.it Fri Jun 29 04:06:18 2007 From: r.gori at cineca.it (Roberto Gori) Date: Fri, 29 Jun 2007 11:06:18 +0200 (MEST) Subject: problems with ACML and single precision References: <002201c7b9a7$15fce240$c241a8c0@int.cineca.it> Message-ID: <004c01c7ba2c$b103c490$c241a8c0@int.cineca.it> Thank you Matthew, I tried, now my configure looks like this: >config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 --with-precision=single --download-c-blas-lapack=yes and I get the following error: ================================================================================= Configuring PETSc to compile on your system ================================================================================= TESTING: configureLibrary from config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:384) ********************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------- Should request f-blas-lapack, not --download-c-blas-lapack=yes since you have a fortran compiler? ********************************************************************************* so i changed my configure: >config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 --with-precision=single --download-f-blas-lapack=yes ================================================================================= Configuring PETSc to compile on your system ================================================================================= ================================================================================= Compiling FBLASLAPACK; this may take several minutes ================================================================================= TESTING: checkMissing from config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:446) ********************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------- Need to use --download-c-blas-lapack when using --with-precision=longdouble/single ********************************************************************************* I'm in loop. Moreover to achieve better performance i would prefer to use acml instead of the BlasLapack sources. Everything works when i build petsc 2.3.1 with the Intel's compiler. I'm not able to do that with petsc 2.3.2. Roberto ----- Original Message ----- From: Matthew Knepley To: petsc-users at mcs.anl.gov Sent: Thursday, June 28, 2007 8:50 PM Subject: Re: problems with ACML and single precision Yes, you need to let us compile for single precision. Use the option in the error message. Thanks, Matt On 6/28/07, Roberto Gori wrote: > > > Hi, > > i'm trying to install PETSc 2.3.3-p3 on a Linux amd64 cluster. > > There's no problems w?th double precison but when I add the single precision > option to my configure command I get the following error: > > ================================================================================= > Configuring PETSc to compile on your system > > ================================================================================= > TESTING: checkMissing from > config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:446) > > > ********************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > --------------------------------------------------------------------------------------- > Need to use --download-c-blas-lapack when using > --with-precision=longdouble/single > ********************************************************************************* > > > This is my configure: > config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 > --with-blas-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a > --with-lapack-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a > --with-precision=single > > > Maybe ACML is not supported for single precision? > > Thanks > > Roberto -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -------------- next part -------------- An HTML attachment was scrubbed... URL: From li76pan at yahoo.com Fri Jun 29 06:20:19 2007 From: li76pan at yahoo.com (li pan) Date: Fri, 29 Jun 2007 04:20:19 -0700 (PDT) Subject: question about total allocated memory Message-ID: <352499.59947.qm@web36812.mail.mud.yahoo.com> Dear developers, I have a question about total allocated memory: I run my code under a PC with 2GB memory and got following error ----------------------------------------------------------------------- [0]PETSC ERROR: PetscMallocAlign() line 62 in src/sys/src/memory/mal.c [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 1234050304 Memory used by process 1099702272 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 766976840! Then I run it at another PC with 4GB memory. But got the same error. My question is, what the total memory needed. Is that 1234050304 + 766976840 ? kind regards pan ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/ From balay at mcs.anl.gov Fri Jun 29 08:28:52 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 29 Jun 2007 08:28:52 -0500 (CDT) Subject: problems with ACML and single precision In-Reply-To: <004c01c7ba2c$b103c490$c241a8c0@int.cineca.it> References: <002201c7b9a7$15fce240$c241a8c0@int.cineca.it> <004c01c7ba2c$b103c490$c241a8c0@int.cineca.it> Message-ID: yeah - singleprecision requires cblaslapack, and cblaslapack can't be used in conjunction with fortran. Are you planning to use single precision PETSc from fortran? If so, currently its not possible. [we'll have to figureout how to get this working]. However if you wish do this from c, then just use the additional configure option --with-fc=0 Satish On Fri, 29 Jun 2007, Roberto Gori wrote: > Thank you Matthew, > > I tried, > > now my configure looks like this: > > >config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 --with-precision=single --download-c-blas-lapack=yes > > and I get the following error: > > ================================================================================= > Configuring PETSc to compile on your system > ================================================================================= > TESTING: configureLibrary from config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:384) ********************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > --------------------------------------------------------------------------------------- > Should request f-blas-lapack, not --download-c-blas-lapack=yes since you have a fortran compiler? > ********************************************************************************* > > so i changed my configure: > > >config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 --with-precision=single --download-f-blas-lapack=yes > > ================================================================================= > Configuring PETSc to compile on your system > ================================================================================= > ================================================================================= > Compiling FBLASLAPACK; this may take several minutes ================================================================================= > TESTING: checkMissing from config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:446) ********************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > --------------------------------------------------------------------------------------- > Need to use --download-c-blas-lapack when using --with-precision=longdouble/single > ********************************************************************************* > > > I'm in loop. > > Moreover to achieve better performance i would prefer to use acml instead of the BlasLapack sources. > Everything works when i build petsc 2.3.1 with the Intel's compiler. I'm not able to do that with petsc 2.3.2. > > Roberto > ----- Original Message ----- > From: Matthew Knepley > To: petsc-users at mcs.anl.gov > Sent: Thursday, June 28, 2007 8:50 PM > Subject: Re: problems with ACML and single precision > > > Yes, you need to let us compile for single precision. Use the option in the > error message. > > Thanks, > > Matt > > On 6/28/07, Roberto Gori wrote: > > > > > > Hi, > > > > i'm trying to install PETSc 2.3.3-p3 on a Linux amd64 cluster. > > > > There's no problems w?th double precison but when I add the single precision > > option to my configure command I get the following error: > > > > ================================================================================= > > Configuring PETSc to compile on your system > > > > ================================================================================= > > TESTING: checkMissing from > > config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:446) > > > > > > ********************************************************************************* > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > details): > > --------------------------------------------------------------------------------------- > > Need to use --download-c-blas-lapack when using > > --with-precision=longdouble/single > > ********************************************************************************* > > > > > > This is my configure: > > config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 > > --with-blas-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a > > --with-lapack-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a > > --with-precision=single > > > > > > Maybe ACML is not supported for single precision? > > > > Thanks > > > > Roberto > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which > their experiments lead. > -- Norbert Wiener > > > From balay at mcs.anl.gov Fri Jun 29 08:39:59 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 29 Jun 2007 08:39:59 -0500 (CDT) Subject: question about total allocated memory In-Reply-To: <352499.59947.qm@web36812.mail.mud.yahoo.com> References: <352499.59947.qm@web36812.mail.mud.yahoo.com> Message-ID: On Fri, 29 Jun 2007, li pan wrote: > Dear developers, > I have a question about total allocated memory: > I run my code under a PC with 2GB memory and got > following error > ----------------------------------------------------------------------- > [0]PETSC ERROR: PetscMallocAlign() line 62 in > src/sys/src/memory/mal.c > [0]PETSC ERROR: Out of memory. This could be due to > allocating > [0]PETSC ERROR: too large an object or bleeding by not > properly > [0]PETSC ERROR: destroying unneeded objects. > [0]PETSC ERROR: Memory allocated 1234050304 Memory > used by process 1099702272 > [0]PETSC ERROR: Try running with -malloc_dump or > -malloc_log for info. > [0]PETSC ERROR: Memory requested 766976840! > > Then I run it at another PC with 4GB memory. But got > the same error. Are these 2 machines in 32bit mode? Most 32bit OSes don't let a single processes use more than 2GB of RAM [even if you have 4GB total] > My question is, what the total memory > needed. Is that 1234050304 + 766976840 ? This is an estimate of the memory PETSc is keeping track of. The app could be using more memory that the above number [for eg: if it uses malloc() not PetscMalloc() etc..]. However normally memory available = RAM + swap [but due to this 2GB limit on most 32bit OSes, the swap also doesn't help here] Satish From r.gori at cineca.it Fri Jun 29 08:59:02 2007 From: r.gori at cineca.it (Roberto Gori) Date: Fri, 29 Jun 2007 15:59:02 +0200 (MEST) Subject: problems with ACML and single precision References: <002201c7b9a7$15fce240$c241a8c0@int.cineca.it> <004c01c7ba2c$b103c490$c241a8c0@int.cineca.it> Message-ID: <010a01c7ba55$9667f3d0$c241a8c0@int.cineca.it> Hi Satish, i would use C. I mean ... for the single precision i would like to use the acml library with the intel C compiler as in petsc 2.3.1. Is this impossibile for the current version or in the next future? Roberto ----- Original Message ----- From: Satish Balay To: petsc-users at mcs.anl.gov Sent: Friday, June 29, 2007 3:28 PM Subject: Re: problems with ACML and single precision yeah - singleprecision requires cblaslapack, and cblaslapack can't be used in conjunction with fortran. Are you planning to use single precision PETSc from fortran? If so, currently its not possible. [we'll have to figureout how to get this working]. However if you wish do this from c, then just use the additional configure option --with-fc=0 Satish On Fri, 29 Jun 2007, Roberto Gori wrote: > Thank you Matthew, > > I tried, > > now my configure looks like this: > > >config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 --with-precision=single --download-c-blas-lapack=yes > > and I get the following error: > > ================================================================================= > Configuring PETSc to compile on your system > ================================================================================= > TESTING: configureLibrary from config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:384) ********************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > --------------------------------------------------------------------------------------- > Should request f-blas-lapack, not --download-c-blas-lapack=yes since you have a fortran compiler? > ********************************************************************************* > > so i changed my configure: > > >config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 --with-precision=single --download-f-blas-lapack=yes > > ================================================================================= > Configuring PETSc to compile on your system > ================================================================================= > ================================================================================= > Compiling FBLASLAPACK; this may take several minutes ================================================================================= > TESTING: checkMissing from config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:446) ********************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > --------------------------------------------------------------------------------------- > Need to use --download-c-blas-lapack when using --with-precision=longdouble/single > ********************************************************************************* > > > I'm in loop. > > Moreover to achieve better performance i would prefer to use acml instead of the BlasLapack sources. > Everything works when i build petsc 2.3.1 with the Intel's compiler. I'm not able to do that with petsc 2.3.2. > > Roberto > ----- Original Message ----- > From: Matthew Knepley > To: petsc-users at mcs.anl.gov > Sent: Thursday, June 28, 2007 8:50 PM > Subject: Re: problems with ACML and single precision > > > Yes, you need to let us compile for single precision. Use the option in the > error message. > > Thanks, > > Matt > > On 6/28/07, Roberto Gori wrote: > > > > > > Hi, > > > > i'm trying to install PETSc 2.3.3-p3 on a Linux amd64 cluster. > > > > There's no problems w?th double precison but when I add the single precision > > option to my configure command I get the following error: > > > > ================================================================================= > > Configuring PETSc to compile on your system > > > > ================================================================================= > > TESTING: checkMissing from > > config.packages.BlasLapack(python/BuildSystem/config/packages/BlasLapack.py:446) > > > > > > ********************************************************************************* > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > details): > > --------------------------------------------------------------------------------------- > > Need to use --download-c-blas-lapack when using > > --with-precision=longdouble/single > > ********************************************************************************* > > > > > > This is my configure: > > config/configure.py --with-mpirun=mpirun.lsf --with-shared=0 > > --with-blas-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a > > --with-lapack-lib=/cineca/prod/acml/3.6.0/ifort64/lib/libacml.a > > --with-precision=single > > > > > > Maybe ACML is not supported for single precision? > > > > Thanks > > > > Roberto > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which > their experiments lead. > -- Norbert Wiener > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From li76pan at yahoo.com Fri Jun 29 09:09:35 2007 From: li76pan at yahoo.com (li pan) Date: Fri, 29 Jun 2007 07:09:35 -0700 (PDT) Subject: question about total allocated memory Message-ID: <965906.13151.qm@web36807.mail.mud.yahoo.com> hi Satish, thanx for your quick answer. I'm testing my code at a PC with 32bits 2GB memory and a PC with 64 bits CPU 4GB memory. Both are runing linux system. I heard that windows system doesn't allow 32 bits CPU allocating more than 2GB. Is it also true under linux system? pan On Fri, 29 Jun 2007, li pan wrote: > Dear developers, > I have a question about total allocated memory: > I run my code under a PC with 2GB memory and got > following error > ----------------------------------------------------------------------- > [0]PETSC ERROR: PetscMallocAlign() line 62 in > src/sys/src/memory/mal.c > [0]PETSC ERROR: Out of memory. This could be due to > allocating > [0]PETSC ERROR: too large an object or bleeding by not > properly > [0]PETSC ERROR: destroying unneeded objects. > [0]PETSC ERROR: Memory allocated 1234050304 Memory > used by process 1099702272 > [0]PETSC ERROR: Try running with -malloc_dump or > -malloc_log for info. > [0]PETSC ERROR: Memory requested 766976840! > > Then I run it at another PC with 4GB memory. But got > the same error. Are these 2 machines in 32bit mode? Most 32bit OSes don't let a single processes use more than 2GB of RAM [even if you have 4GB total] > My question is, what the total memory > needed. Is that 1234050304 + 766976840 ? This is an estimate of the memory PETSc is keeping track of. The app could be using more memory that the above number [for eg: if it uses malloc() not PetscMalloc() etc..]. However normally memory available = RAM + swap [but due to this 2GB limit on most 32bit OSes, the swap also doesn't help here] Satish ____________________________________________________________________________________ Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front From balay at mcs.anl.gov Fri Jun 29 09:21:56 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 29 Jun 2007 09:21:56 -0500 (CDT) Subject: problems with ACML and single precision In-Reply-To: <010a01c7ba55$9667f3d0$c241a8c0@int.cineca.it> References: <002201c7b9a7$15fce240$c241a8c0@int.cineca.it> <004c01c7ba2c$b103c490$c241a8c0@int.cineca.it> <010a01c7ba55$9667f3d0$c241a8c0@int.cineca.it> Message-ID: On Fri, 29 Jun 2007, Roberto Gori wrote: > i would use C. I mean ... for the single precision i would like to > use the acml library with the intel C compiler as in petsc 2.3.1. > Is this impossibile for the current version or in the next future? Not sure why it was disabled. You can reverse this change with the attach patch, and see if it works for you. cd petsc-2.3.3-p3/python/BuildSystem patch -Np1 -R < ~/singleprecision.patch Satish -------------- next part -------------- tree 432027e85207 parent ea4189ae214c author bsmith at anlext2wls147.wl.anl-external.org 1177707677 18000 committer bsmith at anlext2wls147.wl.anl-external.org 1177707677 18000 revision 1985 if configuring with --with-batch should not require locating mpiexec diff --git a/config/packages/BlasLapack.py b/config/packages/BlasLapack.py --- a/config/packages/BlasLapack.py +++ b/config/packages/BlasLapack.py @@ -472,8 +472,8 @@ class Configure(config.package.Package): self.executeTest(self.checkESSL) self.executeTest(self.checkPESSL) self.executeTest(self.checkMissing) - if (self.defaultPrecision == 'longdouble' or self.defaultPrecision == 'int') and not self.f2cpkg: - raise RuntimeError('Need to use --download-c-blas-lapack when using --with-precision=longdouble/int') + if (self.defaultPrecision == 'longdouble' or self.defaultPrecision == 'single') and not self.f2cpkg: + raise RuntimeError('Need to use --download-c-blas-lapack when using --with-precision=longdouble/single') return if __name__ == '__main__': From balay at mcs.anl.gov Fri Jun 29 09:24:50 2007 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 29 Jun 2007 09:24:50 -0500 (CDT) Subject: question about total allocated memory In-Reply-To: <965906.13151.qm@web36807.mail.mud.yahoo.com> References: <965906.13151.qm@web36807.mail.mud.yahoo.com> Message-ID: On Fri, 29 Jun 2007, li pan wrote: > hi Satish, thanx for your quick answer. I'm testing my code at a PC > with 32bits 2GB memory and a PC with 64 bits CPU 4GB memory. Both > are runing linux system. [Eventhough the CPU is 64bit] is the OS/comilers 32bit on this second machine? You'll probably have to install a 64bit linux on this machine for what you want. > I heard that windows system doesn't allow 32 bits CPU allocating > more than 2GB. Is it also true under linux system? I belive its true for linux aswell. Satish From dalcinl at gmail.com Fri Jun 29 13:12:38 2007 From: dalcinl at gmail.com (Lisandro Dalcin) Date: Fri, 29 Jun 2007 15:12:38 -0300 Subject: question about total allocated memory In-Reply-To: References: <965906.13151.qm@web36807.mail.mud.yahoo.com> Message-ID: On 6/29/07, Satish Balay wrote: > > I heard that windows system doesn't allow 32 bits CPU allocating > > more than 2GB. Is it also true under linux system? > > I belive its true for linux aswell. Look at this link: http://linux-mm.org/HighMemory "Currently the 32 bit x86 architecture is the most popular type of computer. In this architecture, traditionally the Linux kernel has split the 4GB of virtual memory address space into 3GB for user programs and 1GB for the kernel." [snip] "The third issue is that, on a 32 bit system, no process will be able to effectively use more than 3GB of memory. This means that buying more than 4GB of memory is only useful if none of the processes on your system need all of the memory" -- Lisandro Dalc?n --------------- Centro Internacional de M?todos Computacionales en Ingenier?a (CIMEC) Instituto de Desarrollo Tecnol?gico para la Industria Qu?mica (INTEC) Consejo Nacional de Investigaciones Cient?ficas y T?cnicas (CONICET) PTLC - G?emes 3450, (3000) Santa Fe, Argentina Tel/Fax: +54-(0)342-451.1594 From fuentes at ices.utexas.edu Sat Jun 30 10:07:00 2007 From: fuentes at ices.utexas.edu (David Fuentes) Date: Sat, 30 Jun 2007 10:07:00 -0500 (CDT) Subject: Petsc Vec In-Reply-To: References: <200706271208.44921.timothy.stitt@ichec.ie> <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> Message-ID: Hello, I would like to write a Vec to a file and read it in at a later point in time. Are there any utilities in Petsc to do this? thank you, David Fuentes From aja2111 at columbia.edu Sat Jun 30 13:05:42 2007 From: aja2111 at columbia.edu (Aron Ahmadia) Date: Sat, 30 Jun 2007 14:05:42 -0400 Subject: Petsc Vec In-Reply-To: References: <200706271208.44921.timothy.stitt@ichec.ie> <37604ab40706270619h58d88a06o51496d0f95fd7321@mail.gmail.com> Message-ID: <37604ab40706301105t376ab8fatc988116da4fbf661@mail.gmail.com> Hi David, You're looking to use a PetscViewer. I see that there's not much in the user's manual on how to use them, but the basic idea is that you create a binary or ascii viewer (PetscViewerASCIIOpen, PetscViewerBinaryOpen), then call VecView to save it to disk. The inverse call is VecLoad. I direct you to the man pages from here on :) http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/ ~A On 6/30/07, David Fuentes wrote: > Hello, > > > I would like to write a Vec to a file and read it in at a later point in > time. Are there any utilities in Petsc to do this? > > > thank you, > David Fuentes > > From sumit_vaidya at persistent.co.in Wed Jun 13 07:21:35 2007 From: sumit_vaidya at persistent.co.in (Sumit Vaidya) Date: Wed, 13 Jun 2007 17:51:35 +0530 Subject: Windows version of PETSc Message-ID: <000001c7adb5$62c286f0$4598580a@persistent.co.in> Hi, These are the machines supported by PETSc. http://www.caspur.it/risorse/softappl/doc/petsc_docs/machines.html >From this, I came to know that PETSc is already available for Windows with 32-bit processor. Where can I get this software version of PETSc for windows? Waiting for your reply, Sumit DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. 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