[petsc-dev] Error message while make test petsc-master

Fri Aug 28 21:25:30 CDT 2015

  Jeff,

   But note there is already a -lm after the -limf (in fact several in the absolutely disgraceful link line :-).

  Barry

/home/hector/installed/openmpi-intel/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3  -o ex19  ex19.o -L/home/hector/dwnld_prog/petsc-master/linux-intel-debug/lib  -lpetsc -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -Wl,-rpath,/home/hector/installed/petsc3.6-intel-debug/lib -L/home/hector/installed/petsc3.6-intel-debug/lib -lHYPRE -L/home/hector/installed/openmpi-intel/lib -L/home/hector/installed/gcc-5.1/lib/gcc/x86_64-unknown-linux-gnu/5.1.0 -L/home/hector/installed/gcc-5.1/lib64 -L/share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64 -L/share/apps/intel2/composer_xe_2015.3.187/mkl/lib/intel64 -L/home/hector/installed/gcc-5.1/lib -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -Wl,-rpath,/home/hector/installed/openmpi-intel/lib -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmpi_cxx -lstdc++ -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -Wl,-rpath,/home/hector/installed/zoltan/lib -L/home/hector/installed/zoltan/lib -lzoltan -Wl,-rpath,/home/hector/installed/parmetis/lib -L/home/hector/installed/parmetis/lib -lparmetis -lmetis -lX11 -lptesmumps -lptscotch -lptscotcherr -lscotch -lscotcherr -lssl -lcrypto -lm -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -limf -lm -lifport -lifcoremt -lsvml -lm -lipgo -lirc -lirc_s -lm -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmpi_cxx -lstdc++ -lrt -lm -lz -L/home/hector/installed/openmpi-intel/lib -L/home/hector/installed/gcc-5.1/lib/gcc/x86_64-unknown-linux-gnu/5.1.0 -L/home/hector/installed/gcc-5.1/lib64 -L/share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64 -L/share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64 -L/share/apps/intel2/composer_xe_2015.3.187/mkl/lib/intel64 -L/home/hector/installed/gcc-5.1/lib -ldl -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_intel_lp64 -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_core -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_intel_thread -liomp5 -lpthread -Wl,-rpath,/home/hector/installed/openmpi-intel/lib -lmpi -lgcc_s -ldl -Wl,--start-group /home/hector/mkl_static/libmkl_intel_lp64.a /home/hector/mkl_static/libmkl_core.a /home/hector/mkl_static/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl -lpthread -lm

> On Aug 28, 2015, at 9:09 PM, Jeff Hammond <jeff.science at gmail.com> wrote:
> 
> https://wiki.hpcc.msu.edu/plugins/servlet/mobile#content/view/5603524 describes how to make it go away (easily).
> 
> Jeff 
> 
> On Friday, August 28, 2015, Barry Smith <bsmith at mcs.anl.gov> wrote:
> 
>   You can safely ignore it.
> 
>   Barry
> 
> > On Aug 28, 2015, at 6:52 PM, Hector E Barrios Molano <hectorb at utexas.edu> wrote:
> >
> > Hi PETSc Experts!
> >
> > I'm compiling petsc-master, configuration and compilation goes ok.
> >
> > While making the tests to verify the compilation I got an error message, however the report also says the tests were successful. Is the libimf.so warning causing the error message?
> >
> > Here is the output from the test:
> >
> > make PETSC_DIR=/home/hector/dwnld_prog/petsc-master PETSC_ARCH=linux-intel-debug test
> > Running test examples to verify correct installation
> > Using PETSC_DIR=/home/hector/dwnld_prog/petsc-master and PETSC_ARCH=linux-intel-debug
> > *******************Error detected during compile or link!*******************
> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > /home/hector/dwnld_prog/petsc-master/src/snes/examples/tutorials ex19
> > *********************************************************************************
> > /home/hector/installed/openmpi-intel/bin/mpicc -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3   -I/home/hector/dwnld_prog/petsc-master/include -I/home/hector/dwnld_prog/petsc-master/linux-intel-debug/include -I/home/hector/installed/petsc3.6-intel-debug/include -I/home/hector/installed/zoltan/include -I/home/hector/installed/parmetis/include -I/home/hector/installed/include -I/home/hector/installed/openmpi-intel/include    `pwd`/ex19.c
> > /home/hector/installed/openmpi-intel/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3  -o ex19  ex19.o -L/home/hector/dwnld_prog/petsc-master/linux-intel-debug/lib  -lpetsc -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -Wl,-rpath,/home/hector/installed/petsc3.6-intel-debug/lib -L/home/hector/installed/petsc3.6-intel-debug/lib -lHYPRE -L/home/hector/installed/openmpi-intel/lib -L/home/hector/installed/gcc-5.1/lib/gcc/x86_64-unknown-linux-gnu/5.1.0 -L/home/hector/installed/gcc-5.1/lib64 -L/share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64 -L/share/apps/intel2/composer_xe_2015.3.187/mkl/lib/intel64 -L/home/hector/installed/gcc-5.1/lib -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -Wl,-rpath,/home/hector/installed/openmpi-intel/lib -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmpi_cxx -lstdc++ -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -Wl,-rpath,/home/hector/installed/zoltan/lib -L/home/hector/installed/zoltan/lib -lzoltan -Wl,-rpath,/home/hector/installed/parmetis/lib -L/home/hector/installed/parmetis/lib -lparmetis -lmetis -lX11 -lptesmumps -lptscotch -lptscotcherr -lscotch -lscotcherr -lssl -lcrypto -lm -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -limf -lm -lifport -lifcoremt -lsvml -lm -lipgo -lirc -lirc_s -lm -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmpi_cxx -lstdc++ -lrt -lm -lz -L/home/hector/installed/openmpi-intel/lib -L/home/hector/installed/gcc-5.1/lib/gcc/x86_64-unknown-linux-gnu/5.1.0 -L/home/hector/installed/gcc-5.1/lib64 -L/share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64 -L/share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64 -L/share/apps/intel2/composer_xe_2015.3.187/mkl/lib/intel64 -L/home/hector/installed/gcc-5.1/lib -ldl -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_intel_lp64 -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_core -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_intel_thread -liomp5 -lpthread -Wl,-rpath,/home/hector/installed/openmpi-intel/lib -lmpi -lgcc_s -ldl -Wl,--start-group /home/hector/mkl_static/libmkl_intel_lp64.a /home/hector/mkl_static/libmkl_core.a /home/hector/mkl_static/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl -lpthread -lm
> > /share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
> > /bin/rm -f 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-master/src/snes/examples/tutorials ex5f
> > *********************************************************
> > /home/hector/installed/openmpi-intel/bin/mpif90 -c -openmp -openmp-link static -g    -I/home/hector/dwnld_prog/petsc-master/include -I/home/hector/dwnld_prog/petsc-master/linux-intel-debug/include -I/home/hector/installed/petsc3.6-intel-debug/include -I/home/hector/installed/zoltan/include -I/home/hector/installed/parmetis/include -I/home/hector/installed/include -I/home/hector/installed/openmpi-intel/include    -o ex5f.o ex5f.F
> > /home/hector/installed/openmpi-intel/bin/mpif90 -openmp -openmp-link static -openmp -openmp-link static -g   -o ex5f ex5f.o -L/home/hector/dwnld_prog/petsc-master/linux-intel-debug/lib  -lpetsc -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -Wl,-rpath,/home/hector/installed/petsc3.6-intel-debug/lib -L/home/hector/installed/petsc3.6-intel-debug/lib -lHYPRE -L/home/hector/installed/openmpi-intel/lib -L/home/hector/installed/gcc-5.1/lib/gcc/x86_64-unknown-linux-gnu/5.1.0 -L/home/hector/installed/gcc-5.1/lib64 -L/share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64 -L/share/apps/intel2/composer_xe_2015.3.187/mkl/lib/intel64 -L/home/hector/installed/gcc-5.1/lib -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -Wl,-rpath,/home/hector/installed/openmpi-intel/lib -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmpi_cxx -lstdc++ -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -Wl,-rpath,/home/hector/installed/zoltan/lib -L/home/hector/installed/zoltan/lib -lzoltan -Wl,-rpath,/home/hector/installed/parmetis/lib -L/home/hector/installed/parmetis/lib -lparmetis -lmetis -lX11 -lptesmumps -lptscotch -lptscotcherr -lscotch -lscotcherr -lssl -lcrypto -lm -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -limf -lm -lifport -lifcoremt -lsvml -lm -lipgo -lirc -lirc_s -lm -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmpi_cxx -lstdc++ -lrt -lm -lz -L/home/hector/installed/openmpi-intel/lib -L/home/hector/installed/gcc-5.1/lib/gcc/x86_64-unknown-linux-gnu/5.1.0 -L/home/hector/installed/gcc-5.1/lib64 -L/share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64 -L/share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64 -L/share/apps/intel2/composer_xe_2015.3.187/mkl/lib/intel64 -L/home/hector/installed/gcc-5.1/lib -ldl -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_intel_lp64 -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_core -Wl,-rpath,/home/hector/mkl_static -L/home/hector/mkl_static -lmkl_intel_thread -liomp5 -lpthread -Wl,-rpath,/home/hector/installed/openmpi-intel/lib -lmpi -lgcc_s -ldl -Wl,--start-group /home/hector/mkl_static/libmkl_intel_lp64.a /home/hector/mkl_static/libmkl_core.a /home/hector/mkl_static/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl -lpthread -lm
> > /share/apps/intel2/composer_xe_2015.3.187/compiler/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
> > /bin/rm -f ex5f.o
> > Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process
> > Completed test examples
> > =========================================
> >
> >
> >
> > Here is the configuration command I used:
> >
> > ./configure --prefix=/home/hector/installed/petsc3.6-intel-debug --PETSC_DIR=/home/hector/dwnld_prog/petsc-master --PETSC_ARCH=linux-intel-debug --with-mpi-dir=/home/hector/installed/openmpi-intel/ --with-parmetis-dir=/home/hector/installed/parmetis/ --with-metis-dir=/home/hector/installed/parmetis/ --with-zoltan-dir=/home/hector/installed/zoltan/ --download-ptscotch --download-hypre --with-blas-lapack-lib=[/home/hector/mkl_static/libmkl_intel_lp64.a,/home/hector/mkl_static/libmkl_core.a,/home/hector/mkl_static/libmkl_intel_thread.a] --with-scalapack-include=/share/apps/intel2/mkl/include --with-scalapack-lib=[/home/hector/mkl_static/libmkl_scalapack_lp64.a,/home/hector/mkl_static/libmkl_blacs_openmpi_lp64.a] --with-valgrind=1 --with-valgrind-dir=/home/hector/installed --with-shared-libraries=0 --with-fortran-interfaces=1 --FC_LINKER_FLAGS="-openmp -openmp-link static" --FFLAGS="-openmp -openmp-link static" --LIBS="-Wl,--start-group /home/hector/mkl_static/libmkl_intel_lp64.a /home/hector/mkl_static/libmkl_core.a /home/hector/mkl_static/libmkl_intel_thread.a -Wl,--end-group -liomp5 -ldl -lpthread -lm"
> >
> > Thanks for your help!
> >
> > Hector
> 
> 
> 
> -- 
> Jeff Hammond
> jeff.science at gmail.com
> http://jeffhammond.github.io/