[petsc-users] PETSC-3.5.0 with SuperLU and Hypre
Kai Song
ksong at lbl.gov
Fri Aug 29 10:59:47 CDT 2014
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
>
--
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
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