Hello everyone I'm trying to compile nektar++-4.4.1 on a BG/Q cluster. So far my attempts are unsuccessful. I found this post quite helpful however still ended up with some errors: https://www.nektar.info/nektar-on-mira-cluster/ I've updated "$srcdir/cmake/ThirdPartyZlib.cmake" as it is written in that post. Then from $builddir I am running the following cmake:
cmake $srcdir \ -DNEKTAR_USE_MPI=ON \ -DTHIRDPARTY_BUILD_ZLIB=OFF \ -DNEKTAR_USE_SYSTEM_BLAS_LAPACK=ON \ -DCMAKE_INSTALL_PREFIX=$prf
zlib and lapack are already installed on this cluster therefore I want to use those versions. This is the cmake output:
-- The C compiler identification is GNU 4.8.1 -- The CXX compiler identification is GNU 4.8.1 -- Check for working C compiler: /....../gcc/4.8.1/mpi/bin/mpicc -- Check for working C compiler: /....../gcc/4.8.1/mpi/bin/mpicc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /....../gcc/4.8.1/mpi/bin/mpicxx -- Check for working CXX compiler: /....../gcc/4.8.1/mpi/bin/mpicxx -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Looking for a Fortran compiler -- Looking for a Fortran compiler - /....../gcc/4.8.1/mpi/bin/mpif90 -- The Fortran compiler identification is GNU -- Check for working Fortran compiler: /....../gcc/4.8.1/mpi/bin/mpif90 -- Check for working Fortran compiler: /....../gcc/4.8.1/mpi/bin/mpif90 -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /....../gcc/4.8.1/mpi/bin/mpif90 supports Fortran 90 -- Checking whether /....../gcc/4.8.1/mpi/bin/mpif90 supports Fortran 90 -- yes -- Build TinyXML:
/....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/libtinyxml.a
-- Build Loki: /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/include -- Build Metis:
/....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/libmetis.a *> -- Found Zlib: /usr/lib64/libz.so (version 1.2.3)*
-- Searching for Boost: -- -- Pre-installed Boost thread library not found -- -- Pre-installed Boost iostreams library not found -- -- Pre-installed Boost date_time library not found -- -- Pre-installed Boost filesystem library not found -- -- Pre-installed Boost system library not found -- -- Pre-installed Boost program_options library not found -- -- Pre-installed Boost regex library not found -- -- Pre-installed Boost timer library not found -- -- Pre-installed Boost chrono library not found -- Build boost libs: thread, iostreams, date_time, filesystem, system, program_options, regex, timer, chrono -- Looking for include file mpi.h -- Looking for include file mpi.h - found -- Looking for MPI_Send -- Looking for MPI_Send - found -- Found MPI: built in -- Build GSMPI: /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/libgsmpi.a -- Build XXT: /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/libxxt.a -- Build blas:
/....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/libblas.a
-- Build lapack:
/....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/lapack.a
CMake Warning (dev) at library/LibUtilities/CMakeLists.txt:422 (TARGET_LINK_LIBRARIES): Link library type specifier "debug" is followed by specifier "optimized" instead of a library name. The first specifier will be ignored. This warning is for project developers. Use -Wno-dev to suppress it.
CMake Error at library/LibUtilities/CMakeLists.txt:422 (TARGET_LINK_LIBRARIES): The "optimized" argument must be followed by a library.
-- Configuring incomplete, errors occurred! See also "/....../nektar/nektar++-4.4.1-build/CMakeFiles/CMakeOutput.log".
I've added the cmake.log as well. First thing I am confused is this line:
-- Build lapack:
/....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/lapack.a
I've specified:
-DNEKTAR_USE_SYSTEM_BLAS_LAPACK=ON \
but it looks like somehow cmake is configured to use the third-party version. I can see both libblas.a and liblapack.a (created a symlink lapack.a too) are in my environment. Do they have to be shared libs? Should I update my LD_LIBRARY_PATH as well? Another thing is at the end of the cmake output above:
CMake Error at library/LibUtilities/CMakeLists.txt:422 (TARGET_LINK_LIBRARIES): The "optimized" argument must be followed by a library.
I don't see any files in "nektar++-4.4.1-build/library/LibUtilities/CMakeFiles/". Therefore I have no idea why it says optimized argument must be followed by a library. When I search for optimized, this is all I get:
bgqdev-fen1-$ grep -rn "optimized" * CMakeCache.txt:105:// /Ot /Oy /Gs will produce slightly less optimized but smaller CMakeCache.txt:125:// /Ot /Oy /Gs will produce slightly less optimized but smaller CMakeCache.txt:163:// /Ot /Oy /Gs will produce slightly less optimized but smaller
So, I don't know how to proceed any further at the moment. One last thing. Scaling achieved on Mira cluster looks impressive: https://www.nektar.info/nektar-strong-scaling-performance-on-mira/ Was it obtained using gcc or xl compilers? Any help is highly appreciated. // Fatih Ertinaz
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Fatih Ertinaz