[petsc-users] [petsc-maint] PETSC-3.5.0 with SuperLU and Hypre

Fri Aug 29 11:11:38 CDT 2014

Looks like some sourcefiles didn't get compiled. I'm not sure why that
happened. [there is no entry for compile of hypre.o]

You can try the following to see if the problem persists.

make allclean
make

Also use --with-shared-libraries=0 for a prefix install. [I thought there
was a check for it..]

Satish

On Fri, 29 Aug 2014, Kai Song wrote:

> Hi Matt,
> 
> Thanks for the quick response. Both logs are included in the attachment.
> Let me know if more log files are needed.
> 
> Thanks!
> 
> Kai
> 
> 
> 
> On Fri, Aug 29, 2014 at 8:41 AM, Matthew Knepley <knepley at gmail.com> wrote:
> 
> > On Fri, Aug 29, 2014 at 10:37 AM, Kai Song <ksong at lbl.gov> wrote:
> >
> >> Dear PETSC community,
> >>
> >> I am trying to install petsc-3.5.0 with superlu and hypre support. The
> >> "configure", "make" and "make install" went fine, but "make test" won't
> >> work. It complains about superlu and hypre libraries undefined.
> >>
> >
> > Always send make.log and configure.log so that we can see what happened.
> >
> >    Matt
> >
> >
> >> The environment I set up is:
> >>  1) valgrind/3.7.0      2) cmake/2.8.11.2      3) gcc/4.4.7           4)
> >> openmpi/1.6.5-gcc
> >>
> >> Here is the configure line:
> >> ./configure
> >> --prefix=/clusterfs/voltaire/home/software/modules/petsc/3.5.0
> >> --download-fblaslapack=1 --download-mumps=1 --download-parmetis=1
> >> --download-scalapack --download-metis=1 --download-superlu=1
> >> --download-superlu_dist=1 --download-hypre=1
> >> --with-mpi-dir=/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/
> >>
> >> My "make" and "make install" lines:
> >> make PETSC_DIR=/clusterfs/voltaire/home/software/source/petsc-3.5.0
> >> PETSC_ARCH=arch-linux2-c-debug all
> >> make PETSC_DIR=/clusterfs/voltaire/home/software/source/petsc-3.5.0
> >> PETSC_ARCH=arch-linux2-c-debug install
> >>
> >> The "make test" line:
> >> make PETSC_DIR=/clusterfs/voltaire/home/software/modules/petsc/3.5.0 test
> >>
> >> I got the following error regarding SuperLU and Hypre:
> >> ====================================
> >> Running test examples to verify correct installation
> >> Using PETSC_DIR=/clusterfs/voltaire/home/software/modules/petsc/3.5.0 and
> >> PETSC_ARCH=arch-linux2-c-debug
> >> *******************Error detected during compile or
> >> link!*******************
> >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >> /clusterfs/voltaire/home/software/source/petsc-3.5.0/src/snes/examples/tutorials
> >> ex19
> >>
> >> *********************************************************************************
> >> *********************W-a-r-n-i-n-g*************************
> >> Your PETSC_DIR may not match the directory you are in
> >> PETSC_DIR  /clusterfs/voltaire/home/software/modules/petsc/3.5.0 Current
> >> directory
> >> /clusterfs/voltaire/home/software/source/petsc-3.5.0/src/snes/examples/tutorials
> >> Ignore this if you are running make test
> >> ******************************************************
> >> /global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/bin/mpicc
> >> -o ex19.o -c -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
> >> -Wno-unknown-pragmas -g3 -O0
> >> -I/clusterfs/voltaire/home/software/modules/petsc/3.5.0/include
> >> -I/clusterfs/voltaire/home/software/modules/petsc/3.5.0/include
> >> -I/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/include
> >> `pwd`/ex19.c
> >> /global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/bin/mpicc
> >> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3
> >> -O0  -o ex19  ex19.o
> >> -Wl,-rpath,/clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib
> >> -L/clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib  -lpetsc
> >> -Wl,-rpath,/clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib
> >> -lHYPRE
> >> -Wl,-rpath,/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/lib
> >> -L/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/lib
> >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7
> >> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -lmpi_cxx -lstdc++ -lcmumps
> >> -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack
> >> -lsuperlu_dist_3.3 -lsuperlu_4.3 -lflapack -lfblas -lparmetis -lmetis -lX11
> >> -lssl -lcrypto -lpthread -lmpi_f90 -lmpi_f77 -lgfortran -lm -lmpi_cxx
> >> -lstdc++ -lmpi_cxx -lstdc++ -ldl -lmpi -lnuma -lrt -lnsl -lutil -lgcc_s
> >> -lpthread -ldl
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `PCCreate_HYPRE'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `MatGetFactor_mpiaij_superlu_dist'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `MatGetFactor_seqaij_superlu_dist'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `MatGetFactor_seqaij_superlu'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `PCCreate_PFMG'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `MatCreate_HYPREStruct'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `PCCreate_SysPFMG'
> >> collect2: ld returned 1 exit status
> >> gmake[3]: [ex19] Error 1 (ignored)
> >> /bin/rm -f ex19.o
> >> *******************Error detected during compile or
> >> link!*******************
> >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >> /clusterfs/voltaire/home/software/source/petsc-3.5.0/src/snes/examples/tutorials
> >> ex5f
> >> *********************************************************
> >> /global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/bin/mpif90
> >> -c  -fPIC -Wall -Wno-unused-variable -ffree-line-length-0 -g -O0
> >> -I/clusterfs/voltaire/home/software/modules/petsc/3.5.0/include
> >> -I/clusterfs/voltaire/home/software/modules/petsc/3.5.0/include
> >> -I/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/include
> >> -o ex5f.o ex5f.F
> >> /global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/bin/mpif90
> >> -fPIC -Wall -Wno-unused-variable -ffree-line-length-0 -g -O0   -o ex5f
> >> ex5f.o -Wl,-rpath,/clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib
> >> -L/clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib  -lpetsc
> >> -Wl,-rpath,/clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib
> >> -lHYPRE
> >> -Wl,-rpath,/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/lib
> >> -L/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/lib
> >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7
> >> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -lmpi_cxx -lstdc++ -lcmumps
> >> -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack
> >> -lsuperlu_dist_3.3 -lsuperlu_4.3 -lflapack -lfblas -lparmetis -lmetis -lX11
> >> -lssl -lcrypto -lpthread -lmpi_f90 -lmpi_f77 -lgfortran -lm -lmpi_cxx
> >> -lstdc++ -lmpi_cxx -lstdc++ -ldl -lmpi -lnuma -lrt -lnsl -lutil -lgcc_s
> >> -lpthread -ldl
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `PCCreate_HYPRE'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `MatGetFactor_mpiaij_superlu_dist'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `MatGetFactor_seqaij_superlu_dist'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `MatGetFactor_seqaij_superlu'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `PCCreate_PFMG'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `MatCreate_HYPREStruct'
> >> /clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib/libpetsc.so:
> >> undefined reference to `PCCreate_SysPFMG'
> >> collect2: ld returned 1 exit status
> >> gmake[3]: [ex5f] Error 1 (ignored)
> >> /bin/rm -f ex5f.o
> >> Completed test examples
> >> =========================================
> >>
> >> I am not sure why hypre and superlu libraries are not linked properly. I
> >> do see the libraries in the $PETSC_DIR/lib/. Please let me know if you need
> >> any other information.
> >>
> >> Thanks in advance!
> >>
> >> Kai
> >>
> >>
> >> --
> >> Kai Song
> >> <ksong at lbl.gov> 1.510.495.2180
> >> 1 Cyclotron Rd. Berkeley, CA94720, MS-50B 3209
> >> High Performance Computing Services (HPCS)
> >> Lawrence Berkeley National Laboratory - http://scs.lbl.gov
> >>
> >
> >
> >
> > --
> > 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
> >
> 
> 
> 
> 