[petsc-users] PETSC-3.5.0 with SuperLU and Hypre
Matthew Knepley
knepley at gmail.com
Fri Aug 29 11:12:23 CDT 2014
On Fri, Aug 29, 2014 at 10:59 AM, Kai Song <ksong at lbl.gov> wrote:
> Hi Matt,
>
> Thanks for the quick response. Both logs are included in the attachment.
> Let me know if more log files are needed.
>
Jed, why does this not enter src/mat/impls/aij/seq/superlu?
Thanks,
Matt
> 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
>>
>
>
>
> --
> 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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