On Fri, Aug 29, 2014 at 10:37 AM, Kai Song <[email protected]> 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 > <[email protected]> 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
