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 <[email protected]> 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 <[email protected]> wrote: > > You can safely ignore it. > > Barry > > > On Aug 28, 2015, at 6:52 PM, Hector E Barrios Molano <[email protected]> > > 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 > [email protected] > http://jeffhammond.github.io/
