[petsc-dev] Error while testing PETSc installation

[Smith, Barry F.]

    This is a harmless (and rather silly warning).

    Barry


> On Oct 17, 2018, at 2:16 PM, Hector E Barrios Molano <hectorb at utexas.edu> wrote:
> 
> Hi PETSc Experts!
> 
> I am compiling PETSc from git repository. Everything goes smooth. However, when I test the installation I get the following output:
> 
> make PETSC_DIR=/home/hector/installed/libraries_intel/petsc_git-debug PETSC_ARCH="" test
> Running test examples to verify correct installation
> Using PETSC_DIR=/home/hector/installed/libraries_intel/petsc_git-debug and PETSC_ARCH=
> *******************Error detected during compile or link!*******************
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> /home/hector/dwnld_prog/petsc/src/snes/examples/tutorials ex19
> *********************************************************************************
> mpicc -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3 -fopenmp   -I/home/hector/installed/libraries_intel/petsc_git-debug/include -I/home/hector/installed/libraries_intel/hypre/include -I/home/hector/installed/libraries_intel/zoltan/include -I/home/hector/installed/libraries_intel/parmetis/include -I/home/hector/installed/include    `pwd`/ex19.c
> mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3 -fopenmp  -o ex19 ex19.o  -L/home/hector/installed/libraries_intel/petsc_git-debug/lib -Wl,-rpath,/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64 -Wl,-rpath,/home/hector/installed/libraries_intel/hypre/lib -L/home/hector/installed/libraries_intel/hypre/lib -Wl,-rpath,/home/hector/installed/libraries_intel/zoltan/lib -L/home/hector/installed/libraries_intel/zoltan/lib -Wl,-rpath,/home/hector/installed/libraries_intel/parmetis/lib -L/home/hector/installed/libraries_intel/parmetis/lib -Wl,-rpath,/home/hector/installed/libraries_intel/petsc_git-debug/lib -L/home/hector/installed/libraries_intel/petsc_git-debug/lib -L/home/hector/installed/libraries_intel/openmpi/lib -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/ipp/lib/intel64 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64/gcc4.1 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/daal/lib/intel64_lin -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64_lin/gcc4.4 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64_lin -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -Wl,-rpath,/home/hector/installed/libraries_intel/openmpi/lib -Wl,--start-group -Wl,--end-group -lpetsc -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lHYPRE -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lzoltan -lparmetis -lmetis -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lX11 -lstdc++ -ldl -liomp5 -lpthread -lm -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -limf -lifport -lifcoremt -lsvml -lipgo -lirc -lgcc_s -lirc_s -lrt -lm -lpthread -lz -lstdc++ -ldl -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm
> /share/apps/intel3/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
> true ex19
> rm ex19.o
> C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process
> C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes
> *******************Error detected during compile or link!*******************
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> /home/hector/dwnld_prog/petsc/src/snes/examples/tutorials ex5f
> *********************************************************
> mpifort -c -qopenmp -qopenmp-link static -g  -fopenmp   -I/home/hector/installed/libraries_intel/petsc_git-debug/include -I/home/hector/installed/libraries_intel/hypre/include -I/home/hector/installed/libraries_intel/zoltan/include -I/home/hector/installed/libraries_intel/parmetis/include -I/home/hector/installed/include    -o ex5f.o ex5f.F90
> mpifort -qopenmp -qopenmp-link static -qopenmp -qopenmp-link static -g  -fopenmp  -o ex5f ex5f.o  -L/home/hector/installed/libraries_intel/petsc_git-debug/lib -Wl,-rpath,/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64 -Wl,-rpath,/home/hector/installed/libraries_intel/hypre/lib -L/home/hector/installed/libraries_intel/hypre/lib -Wl,-rpath,/home/hector/installed/libraries_intel/zoltan/lib -L/home/hector/installed/libraries_intel/zoltan/lib -Wl,-rpath,/home/hector/installed/libraries_intel/parmetis/lib -L/home/hector/installed/libraries_intel/parmetis/lib -Wl,-rpath,/home/hector/installed/libraries_intel/petsc_git-debug/lib -L/home/hector/installed/libraries_intel/petsc_git-debug/lib -L/home/hector/installed/libraries_intel/openmpi/lib -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/ipp/lib/intel64 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64/gcc4.1 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/daal/lib/intel64_lin -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64_lin/gcc4.4 -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64_lin -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -Wl,-rpath,/home/hector/installed/libraries_intel/openmpi/lib -Wl,--start-group -Wl,--end-group -lpetsc -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lHYPRE -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lzoltan -lparmetis -lmetis -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lX11 -lstdc++ -ldl -liomp5 -lpthread -lm -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -limf -lifport -lifcoremt -lsvml -lipgo -lirc -lgcc_s -lirc_s -lrt -lm -lpthread -lz -lstdc++ -ldl -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm
> /share/apps/intel3/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
> rm ex5f.o
> Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process
> Completed test examples
> 
> Here is the configure command I am using:
> 
> ./configure --prefix=$DEV_lib_dir/petsc_git-debug --PETSC_DIR=/home/hector/dwnld_prog/petsc --PETSC_ARCH=linux-intel-debug --CC=mpicc --FC=mpifort --CXX=mpicxx --with-openmp=1 --with-valgrind=1 --with-valgrind-dir=/home/hector/installed --with-parmetis-dir=$DEV_lib_dir/parmetis/ --with-metis-dir=$DEV_lib_dir/parmetis/ --with-zoltan-dir=$DEV_lib_dir/zoltan/ --with-hypre-dir=$DEV_lib_dir/hypre --download-ptscotch --with-blas-lapack-lib=\[${MKLROOT}/lib/intel64/libmkl_intel_lp64.a,${MKLROOT}/lib/intel64/libmkl_core.a,${MKLROOT}/lib/intel64/libmkl_intel_thread.a\] --with-scalapack-include=${MKLROOT}/include --with-scalapack-lib=\[${MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a,${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a\] --with-shared-libraries=0 --FC_LINKER_FLAGS="-qopenmp -qopenmp-link static" --FFLAGS="-qopenmp -qopenmp-link static" --LIBS="-Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl -lpthread -lm"
> 
> What could be the problem?
> 
> Thank you for your help!
> 
> Hector