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
