Looks like some sourcefiles didn't get compiled. I'm not sure why that happened. [there is no entry for compile of hypre.o]
You can try the following to see if the problem persists. make allclean make Also use --with-shared-libraries=0 for a prefix install. [I thought there was a check for it..] Satish On Fri, 29 Aug 2014, Kai Song wrote: > 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 <[email protected]> wrote: > > > 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 > > > > > >
