[petsc-dev] Errors when testing PETSc build on Windows

Wed Jun 17 15:01:01 CDT 2015

/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib

This is the wrong version of MKL. You should look for lp64 variant [not ilp64]

[you can just edit PETSC_DIR/PETSC_ARCH/lib/petsc/conf/petscvariables and make this
change manually - and retry compiling the example]

Satish

On Wed, 17 Jun 2015, Hector E Barrios Molano wrote:

> Hi PETSc Experts!
> 
> I'm trying to build PETSc on a Windows machine, I got errors during
> the test part. I downloaded petsc-dev from git.
> 
> 
> This are my configuration command:
> 
> $ ./configure --with-cc='win32fe cl' --with-fc='win32fe ifort'
> --prefix=/cygdrive/c/Installed/petsc/ --PETSC_ARCH=windows-intel
> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include
> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
> --with-metis-include=/cygdrive/c/Installed/parmetis/include
> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
> --with-mpi-include=[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]
> --with-mpi-lib=[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]
> --with-blas-lapack-lib=[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]
> --with-scalapack-include=/cygdrive/c/Installed/mkl/include
> --with-scalapack-lib=[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib]
> --with-sowing=0
> 
> 
> I was able con configure and compile:
> 
>  make PETSC_DIR=/cygdrive/c/Installed/petsc-dev/petsc
> PETSC_ARCH=windows-intel all
> 
> However, when testing I got these errors:
> 
> $ make PETSC_DIR=/cygdrive/c/Installed/petsc-dev/petsc
> PETSC_ARCH=windows-intel test
> Running test examples to verify correct installation
> Using PETSC_DIR=/cygdrive/c/Installed/petsc-dev/petsc and
> PETSC_ARCH=windows-intel
> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> lid velocity = 0.0016, prandtl # = 1, grashof # = 1
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
> OS X to find memory corruption errors
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> [0]PETSC ERROR:       INSTEAD the line number of the start of the function
> [0]PETSC ERROR:       is given.
> [0]PETSC ERROR: [0] VecNorm_Seq line 240
> C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\impls\seq\bvec2.c
> [0]PETSC ERROR: [0] VecNorm line 228
> C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\INTERF~1\rvector.c
> [0]PETSC ERROR: [0] SNESSolve_NEWTONLS line 150
> C:\INSTAL~1\PETSC-~1\petsc\src\snes\impls\ls\ls.c
> [0]PETSC ERROR: [0] SNESSolve line 3847
> C:\INSTAL~1\PETSC-~1\petsc\src\snes\INTERF~1\snes.c
> [0]PETSC ERROR: [0] main line 108
> C:\INSTAL~1\PETSC-~1\petsc\src\snes\examples\TUTORI~1\ex19.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: unknown  GIT Date: unknown
> [0]PETSC ERROR: ./ex19 on a windows-intel named HECTOR-PC by hector
> Wed Jun 17 14:21:38 2015
> [0]PETSC ERROR: Configure options --with-cc="win32fe cl"
> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/
> --PETSC_ARCH=windows-intel
> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include
> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
> --with-metis-include=/cygdrive/c/Installed/parmetis/include
> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]"
> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]"
> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]"
> --with-scalapack-include=/cygdrive/c/Installed/mkl/include
> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib]"
> --with-sowing=0
> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
> 
> job aborted:
> [ranks] message
> 
> [0] application aborted
> aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0
> 
> ---- error analysis -----
> 
> [0] on hector-PC
> ./ex19 aborted the job. abort code 59
> 
> ---- error analysis -----
> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2
> MPI processes
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> lid velocity = 0.0016, prandtl # = 1, grashof # = 1
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> Caught signal number 11 SEGV: Segmentation Violation, probably memory
> access out of range
> Caught signal number 11 SEGV: Segmentation Violation, probably memory
> access out of range
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> Try option -start_in_debugger or -on_error_attach_debugger
> Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> or try http://valgrind.org on GNU/linux and Apple Mac OS X to find
> memory corruption errors
> or try http://valgrind.org on GNU/linux and Apple Mac OS X to find
> memory corruption errors
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> likely location of problem given in stack below
> likely location of problem given in stack below
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> ---------------------  Stack Frames ------------------------------------
> ---------------------  Stack Frames ------------------------------------
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> Note: The EXACT line numbers in the stack are not available,
> Note: The EXACT line numbers in the stack are not available,
> [0]PETSC ERROR:
> [1]PETSC ERROR:
>       INSTEAD the line number of the start of the function
>       INSTEAD the line number of the start of the function
> [0]PETSC ERROR:
> [1]PETSC ERROR:
>       is given.
>       is given.
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> [0] VecNorm_MPI line 57 C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\impls\mpi\pvec2.c
> [1] VecNorm_MPI line 57 C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\impls\mpi\pvec2.c
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> [0] VecNorm line 228 C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\INTERF~1\rvector.c
> [1] VecNorm line 228 C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\INTERF~1\rvector.c
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> [0] SNESSolve_NEWTONLS line 150
> C:\INSTAL~1\PETSC-~1\petsc\src\snes\impls\ls\ls.c
> [1] SNESSolve_NEWTONLS line 150
> C:\INSTAL~1\PETSC-~1\petsc\src\snes\impls\ls\ls.c
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> [0] SNESSolve line 3847 C:\INSTAL~1\PETSC-~1\petsc\src\snes\INTERF~1\snes.c
> [1] SNESSolve line 3847 C:\INSTAL~1\PETSC-~1\petsc\src\snes\INTERF~1\snes.c
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> [0] main line 108 C:\INSTAL~1\PETSC-~1\petsc\src\snes\examples\TUTORI~1\ex19.c
> [1] main line 108 C:\INSTAL~1\PETSC-~1\petsc\src\snes\examples\TUTORI~1\ex19.c
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> --------------------- Error Message
> --------------------------------------------------------------
> --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> Signal received
> Signal received
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> Petsc Development GIT revision: unknown  GIT Date: unknown
> Petsc Development GIT revision: unknown  GIT Date: unknown
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> ./ex19 on a windows-intel named HECTOR-PC by hector Wed Jun 17 14:21:38 2015
> ./ex19 on a windows-intel named HECTOR-PC by hector Wed Jun 17 14:21:38 2015
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> Configure options --with-cc="win32fe cl" --with-fc="win32fe ifort"
> --prefix=/cygdrive/c/Installed/petsc/ --PETSC_ARCH=windows-intel
> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include
> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
> --with-metis-include=/cygdrive/c/Installed/parmetis/include
> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]"
> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]"
> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]"
> --with-scalapack-include=/cygdrive/c/Installed/mkl/include
> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib]"
> --with-sowing=0
> Configure options --with-cc="win32fe cl" --with-fc="win32fe ifort"
> --prefix=/cygdrive/c/Installed/petsc/ --PETSC_ARCH=windows-intel
> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include
> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
> --with-metis-include=/cygdrive/c/Installed/parmetis/include
> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]"
> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]"
> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]"
> --with-scalapack-include=/cygdrive/c/Installed/mkl/include
> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib]"
> --with-sowing=0
> [0]PETSC ERROR:
> [1]PETSC ERROR:
> #1 User provided function() line 0 in  unknown file
> #1 User provided function() line 0 in  unknown file
> 
> job aborted:
> [ranks] message
> 
> [0] application aborted
> aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0
> 
> [1] application aborted
> aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 1
> 
> ---- error analysis -----
> 
> [0-1] on hector-PC
> ./ex19 aborted the job. abort code 59
> 
> ---- error analysis -----
> *******************Error detected during compile or link!*******************
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> /cygdrive/c/Installed/petsc-dev/petsc/src/snes/examples/tutorials ex5f
> *********************************************************
> /cygdrive/c/Installed/petsc-dev/petsc/bin/win32fe/win32fe ifort -c
> -MT -Z7 -fpp  -I/cygdrive/c/Installed/petsc-dev/petsc/include
> -I/cygdrive/c/Installed/petsc-dev/petsc/windows-intel/include
> -I/cygdrive/c/Installed/parmetis/include
> -I/cygdrive/c/Installed/msmpi/Include
> -I/cygdrive/c/Installed/msmpi/Include/x64    -o ex5f.o ex5f.F
> /cygdrive/c/Installed/petsc-dev/petsc/bin/win32fe/win32fe ifort -MT
> -Z7 -fpp  -o ex5f ex5f.o
> -L/cygdrive/c/Installed/petsc-dev/petsc/windows-intel/lib  -lpetsc
> /cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib
> /cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib
> /cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib
> /cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib
> /cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib
> /cygdrive/c/Installed/parmetis/lib/parmetis.lib
> /cygdrive/c/Installed/parmetis/lib/metis.lib
> /cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib
> /cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib Gdi32.lib User32.lib
> Advapi32.lib Kernel32.lib Ws2_32.lib
> ex5f.obj : error LNK2019: unresolved external symbol SNESCREATE
> referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol
> DMCREATEGLOBALVECTOR referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol VECDUPLICATE
> referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol DMDAGETCORNERS
> referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol
> DMDAGETGHOSTCORNERS referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol SNESSETDM
> referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol
> SNESSETFROMOPTIONS referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol
> SNESGETITERATIONNUMBER referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol VECDESTROY
> referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol SNESDESTROY
> referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol DMDESTROY
> referenced in function MAIN__
> ex5f.obj : error LNK2019: unresolved external symbol MATSETVALUESLOCAL
> referenced in function FORMJACOBIANLOCAL
> ex5f.obj : error LNK2019: unresolved external symbol MATASSEMBLYBEGIN
> referenced in function FORMJACOBIANLOCAL
> ex5f.obj : error LNK2019: unresolved external symbol MATASSEMBLYEND
> referenced in function FORMJACOBIANLOCAL
> C:\INSTAL~1\PETSC-~1\petsc\src\snes\examples\TUTORI~1\ex5f.exe : fatal
> error LNK1120: 14 unresolved externals
> makefile:50: recipe for target 'ex5f' failed
> make[3]: [ex5f] Error 96 (ignored)
> /usr/bin/rm -f ex5f.o
> Completed test examples
> =========================================
> Now to evaluate the computer systems you plan use - do:
> make PETSC_DIR=/cygdrive/c/Installed/petsc-dev/petsc
> PETSC_ARCH=windows-intel streams NPMAX=<number of MPI processes you
> intend to use>
> 
> 
> Best Regards,
> 
> Hector
> 