Hi, recently, I have the same problem. When I complie the PETsc, it link the debug_mt/linmpi.so. So I think the reason is that Petsc is complied in Debugging, not Release. So I add the paras when configure the Petsc,--with-debugging=0 and give the opt-paras, COPTFLAG="-O2" CXXOPTFLAG="-O2" FOPTFLAG="-O2". Then the problm is solved.
On Monday, 30 July 2018 00:00:28 UTC+8, Eva Lilje wrote: > > Dear dealii Team, > > the Dealii Installation fails because it uses the wrong MPI Version of the > intel compiler. It uses debug_mt instead of release_mt. > > > =============================================================================== > > WARNING! Compiling PETSc with no debugging, this should only be done for > timing and production runs. All development should be done when configured > using --with-debugging=1 > =============================================================================== > > > > Looks good, uses the release_mt version of intel mpi 2018 / intel studio > 2018 > > Using PETSc configure options: > --prefix=/home/tuamende/deal.ii-candi/petsc-3.9.0 --with-debugging=0 > --with-shared-libraries=1 --with-mpi=1 --with-x=0 > --with-mpi-dir=/cluster/intel/intel2018/impi/2018.1.163/intel64/ > --with-64-bit-indices=0 PETSC_ARCH=linux-gnu-intel --with-debugging=0 > --download-hypre=1 > --with-blaslapack-dir=/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 > > --with-parmetis-dir=/home/tuamende/deal.ii-candi/parmetis-4.0.3 > --with-metis-dir=/home/tuamende/deal.ii-candi/parmetis-4.0.3 > --download-scalapack=1 --download-mumps=1 > > #define PETSC_MPICC_SHOW "icc > -I/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/include > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/release_mt > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib > > -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker > /cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/release_mt > > -Xlinker -rpath -Xlinker > /cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib > > -Xlinker -rpath -Xlinker /opt/intel/mpi-rt/2017.0.0/intel64/lib/release_mt > -Xlinker -rpath -Xlinker /opt/intel/mpi-rt/2017.0.0/intel64/lib -lmpifort > -lmpi -lmpigi -ldl -lrt -lpthread" > > > But then it decides to use only the debug version, even when the correct > intel envs are set: > > export I_MPI_LIBRARY_KIND=release_mt > > source > /cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/bin/mpivars.sh > > release_mt > > > Using libraries: > -Wl,-rpath,/home/tuamende/deal.ii-candi/tmp/build/slepc-3.9.2/installed-arch-linux2-c-opt/lib > > -L/home/tuamende/deal.ii-candi/tmp/build/slepc-3.9.2/installed-arch-linux2-c-opt/lib > > -lslepc -Wl,-rpath,/home/tuamende/deal.ii-candi/petsc-3.9.0/lib > -L/home/tuamende/deal.ii-candi/petsc-3.9.0/lib > -Wl,-rpath,/home/tuamende/deal.ii-candi/petsc-3.9.0/lib > -L/home/tuamende/deal.ii-candi/petsc-3.9.0/lib > -Wl,-rpath,/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 > > -Wl,-rpath,/home/tuamende/deal.ii-candi/parmetis-4.0.3/lib > -L/home/tuamende/deal.ii-candi/parmetis-4.0.3/lib > -Wl,-rpath,/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/debug_mt > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/debug_mt > > -Wl,-rpath,/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib > > -Wl,-rpath,/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/ipp/lib/intel64 > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/ipp/lib/intel64 > > -Wl,-rpath,/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/compiler/lib/intel64_lin > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/compiler/lib/intel64_lin > > -Wl,-rpath,/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin > > -Wl,-rpath,/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/tbb/lib/intel64/gcc4.7 > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/tbb/lib/intel64/gcc4.7 > > -Wl,-rpath,/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/daal/lib/intel64_lin > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/daal/lib/intel64_lin > > -Wl,-rpath,/cluster/comp/gcc/6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0 > -L/cluster/comp/gcc/6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0 > -Wl,-rpath,/cluster/comp/gcc/6.3.0/lib64 -L/cluster/comp/gcc/6.3.0/lib64 > -Wl,-rpath,/cluster/comp/gcc/6.3.0/lib -L/cluster/comp/gcc/6.3.0/lib > -Wl,-rpath,/opt/intel/mpi-rt/2017.0.0/intel64/lib/debug_mt > -Wl,-rpath,/opt/intel/mpi-rt/2017.0.0/intel64/lib -lpetsc -lcmumps -ldmumps > -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lHYPRE > -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lparmetis -lmetis > -lstdc++ -ldl -lmpifort -lmpi -lmpigi -lrt -lpthread -lifport > -lifcoremt_pic -limf -lsvml -lm -lipgo -lirc -lgcc_s -lirc_s -lstdc++ -ldl > > > Which fails the build: > > PETSC has to be compiled against the same MPI library as deal.II but the > link line of PETSC contains: > > /cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/debug_mt/libmpi.so > > > > which is not listed in MPI_LIBRARIES: > > MPI_LIBRARIES = > "/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/libmpicxx.so > > /cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/libmpifort.so > > /cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/release_mt/libmpi.so > > /cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/libmpigi.a > > /lib64/libdl.so /lib64/librt.so /lib64/libpthread.so" > > > > Here is the pkgconf: > > > ./PETSc.pc:Libs.private: -L/home/tuamende/deal.ii-candi/petsc-3.9.0/lib > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 > > -L/home/tuamende/deal.ii-candi/parmetis-4.0.3/lib > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/debug_mt > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/ipp/lib/intel64 > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/compiler/lib/intel64_lin > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/tbb/lib/intel64/gcc4.7 > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/daal/lib/intel64_lin > > -L/cluster/comp/gcc/6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0 > -L/cluster/comp/gcc/6.3.0/lib64 -L/cluster/comp/gcc/6.3.0/lib -lcmumps > -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lHYPRE > -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lparmetis -lmetis > -lstdc++ -ldl -lmpifort -lmpi -lmpigi -lrt -lpthread -lifport > -lifcoremt_pic -limf -lsvml -lm -lipgo -lirc -lgcc_s -lirc_s -lstdc++ -ldl > > > > My self build petsc on the same cluster knows both mpi versions > (release_mt and debug_mt): > > ./lib/pkgconfig/PETSc.pc:Libs.private: > -L/cluster/intel/intel2018/mkl/lib/intel64 > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/release_mt > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/ipp/lib/intel64 > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/compiler/lib/intel64_lin > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/tbb/lib/intel64/gcc4.7 > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/daal/lib/intel64_lin > > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/tbb/lib/intel64_lin/gcc4.4 > > -L/cluster/comp/gcc/6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0 > -L/cluster/comp/gcc/6.3.0/lib64 -L/cluster/comp/gcc/6.3.0/lib > -L/cluster/intel/intel2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/debug_mt > > -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lX11 -lifport > -lifcoremt_pic -lmpicxx -ldl -lmpifort -lmpi -lmpigi -lrt -lpthread -limf > -lsvml -lirng -lm -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lirc_s > -ldl > > > > Is there something I need to change? I am using Intel > compilers_and_libraries_2018.1.163 . > > Kind regards > > > PS: Please make this group open, some people avoid for privacy reasons to > have google accounts. My girlfriend copied this post for me. > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/d9e25d58-c050-4f70-8ffd-4f45f8dbf36e%40googlegroups.com.
