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

Fri Aug 29 10:41:39 CDT 2014

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
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