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

Fri Aug 29 10:37:12 CDT 2014

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.

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
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