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Compilation instructions for gromacs 4.6.7 with plumed2 2.1-hrex (branch by Bussi) with intel-compilers, intel-mpi and intel-mkl
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| How to compile these two little monsters |
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| #!/usr/bin/env bash | |
| module purge | |
| module add intel-compilers/2015 intel-mkl/2015 mvapich2/2.0.1__intel-2015 | |
| compilervars.sh intel64 | |
| PREFIX=/opt/plumed/2.1-hrex | |
| make clean | |
| # ideally you only need to do | |
| ./configure --prefix=$PREFIX | |
| # in practice, what you find... | |
| ./configure --enable-mpi CXX=mpicxx --prefix=$PREFIX | |
| sed -i s#'DYNAMIC_LIBS=-lstdc++'#'DYNAMIC_LIBS=-lstdc++ -mkl'# Makefile.conf | |
| make -j8 | |
| make install | |
| # verify the compilation | |
| $ ldd `which plumed` | |
| linux-vdso.so.1 => (0x00007fff895ff000) | |
| libdl.so.2 => /lib64/libdl.so.2 (0x000000381dc00000) | |
| libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003a1c400000) | |
| libmkl_intel_lp64.so => /system/software/linux-x86_64/compilers/intel/intelPS-2016/mkl/lib/intel64/libmkl_intel_lp64.so (0x00007f0655909000) | |
| libmkl_intel_thread.so => /system/software/linux-x86_64/compilers/intel/intelPS-2016/mkl/lib/intel64/libmkl_intel_thread.so (0x00007f06545b1000) | |
| libmkl_core.so => /system/software/linux-x86_64/compilers/intel/intelPS-2016/mkl/lib/intel64/libmkl_core.so (0x00007f0652ccc000) | |
| libiomp5.so => /system/software/linux-x86_64/compilers/intel/intelPS-2015/lib/intel64/libiomp5.so (0x00007f0652990000) | |
| libz.so.1 => /lib64/libz.so.1 (0x000000381f000000) | |
| libmpicxx.so.12 => /system/software/linux-x86_64/compilers/intel/intelPS-2016/impi/5.1.1.109/lib64/libmpicxx.so.12 (0x00007f065276f000) | |
| libmpifort.so.12 => /system/software/linux-x86_64/compilers/intel/intelPS-2016/impi/5.1.1.109/lib64/libmpifort.so.12 (0x00007f06523de000) | |
| libmpi.so.12 => /system/software/linux-x86_64/compilers/intel/intelPS-2016/impi/5.1.1.109/lib64/libmpi.so.12 (0x00007f0651c25000) | |
| librt.so.1 => /lib64/librt.so.1 (0x000000381e800000) | |
| libpthread.so.0 => /lib64/libpthread.so.0 (0x000000381e400000) | |
| libm.so.6 => /lib64/libm.so.6 (0x000000381ec00000) | |
| libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003a1c000000) | |
| libc.so.6 => /lib64/libc.so.6 (0x000000381e000000) | |
| /lib64/ld-linux-x86-64.so.2 (0x000000381d800000) | |
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| #!/usr/bin/env bash | |
| module purge | |
| module add intel-compilers/2015 intel-mkl/2015 mvapich2/2.0.1__intel-2015 | |
| compilervars.sh intel64 | |
| wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz | |
| tar xf gromacs-4.6.7.tar.gz ; cd gromacs-4.6.7 | |
| mkdir build ; cd build | |
| PREFIX=/opt/gromacs | |
| cmake .. \ | |
| -DGMX_USE_RDTSCP=OFF \ # better timing | |
| -DGMX_FFT_LIBRARY=mkl \ # only with intel compilers, not with GCC, will give you BLAS/LAPACK/FFTW | |
| -DGMX_MPI=ON \ # mpi-gromacs to run on multiple nodes | |
| -DGMX_BUILD_MDRUN_ONLY=ON \ # it will only compile 'mdrun', much faster compilation | |
| -DGMX_DEFAULT_SUFFIX=OFF \ # matter of style | |
| -DCMAKE_INSTALL_PREFIX=$PREFIX \ # where to install | |
| -DGMX_GPU=OFF \ # no need for a GPU in my scenario | |
| -DGMX_SIMD=AVX_256 # important: will depend on the architecture of your cluster nodes | |
| # optional | |
| -DMKL_INCLUDE_DIR=${MKLROOT}/include \ | |
| -DMKL_LIBRARIES="${MKLROOT}/lib/intel64/libmkl_intel_lp64.so; ${MKLROOT}/lib/intel64/libmkl_sequential.so; ${MKLROOT}/lib/intel64/libmkl_core.so" \ | |
| # optional, important: will depend on the architecture of your cluster nodes | |
| -DGMX_SIMD=AVX2_256 \ | |
| -DCMAKE_C_FLAGS="-O3 -xCORE-AVX2 -ip" \ | |
| -DCMAKE_CXX_FLAGS="-O3 -xCORE-AVX2 -ip" \ | |
| make -j16 | |
| cd .. | |
| plumed patch -p << EOF | |
| 3 | |
| EOF | |
| cd build | |
| make -j16 | |
| make install | |
| # verify the compilation | |
| source /opt/gromacs/bin/GMXRC.bash | |
| ldd `which mdrun ` | |
| linux-vdso.so.1 => (0x00007ffff97ff000) | |
| libmkl_intel_lp64.so => /system/software/linux-x86_64/compilers/intel/intelPS-2016/mkl/lib/intel64/libmkl_intel_lp64.so (0x00007fc2bb948000) | |
| libmkl_intel_thread.so => /system/software/linux-x86_64/compilers/intel/intelPS-2016/mkl/lib/intel64/libmkl_intel_thread.so (0x00007fc2ba5f1000) | |
| libmkl_core.so => /system/software/linux-x86_64/compilers/intel/intelPS-2016/mkl/lib/intel64/libmkl_core.so (0x00007fc2b8d0c000) | |
| libiomp5.so => /system/software/linux-x86_64/compilers/intel/intelPS-2015/lib/intel64/libiomp5.so (0x00007fc2b89cf000) | |
| libgmxpreprocess.so.8 => /home/sbcb-membr/jdomanski/privateopt/gromacs-4.6.7_plumed2.1-hrex-wenwei-icc/bin/../lib/libgmxpreprocess.so.8 (0x00007fc2b86fe000) | |
| libmd.so.8 => /home/sbcb-membr/jdomanski/privateopt/gromacs-4.6.7_plumed2.1-hrex-wenwei-icc/bin/../lib/libmd.so.8 (0x00007fc2b81c5000) | |
| libgmx.so.8 => /home/sbcb-membr/jdomanski/privateopt/gromacs-4.6.7_plumed2.1-hrex-wenwei-icc/bin/../lib/libgmx.so.8 (0x00007fc2b7ac0000) | |
| libdl.so.2 => /lib64/libdl.so.2 (0x000000381dc00000) | |
| libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003a1c400000) | |
| libz.so.1 => /lib64/libz.so.1 (0x000000381f000000) | |
| libmpifort.so.12 => /system/software/linux-x86_64/compilers/intel/intelPS-2016/impi/5.1.1.109/intel64/lib/libmpifort.so.12 (0x00007fc2b7717000) | |
| libmpi.so.12 => /system/software/linux-x86_64/compilers/intel/intelPS-2016/impi/5.1.1.109/intel64/lib/libmpi.so.12 (0x00007fc2b6f5f000) | |
| librt.so.1 => /lib64/librt.so.1 (0x000000381e800000) | |
| libpthread.so.0 => /lib64/libpthread.so.0 (0x000000381e400000) | |
| libm.so.6 => /lib64/libm.so.6 (0x000000381ec00000) | |
| libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003a1c000000) | |
| libc.so.6 => /lib64/libc.so.6 (0x000000381e000000) | |
| /lib64/ld-linux-x86-64.so.2 (0x000000381d800000) | |
| libmkl_sequential.so => /system/software/linux-x86_64/compilers/intel/intelPS-2016/mkl/lib/intel64/libmkl_sequential.so (0x00007fc2b66b5000) | |
| libimf.so => /system/software/linux-x86_64/compilers/intel/intelPS-2015/lib/intel64/libimf.so (0x00007fc2b61fa000) | |
| libsvml.so => /system/software/linux-x86_64/compilers/intel/intelPS-2015/lib/intel64/libsvml.so (0x00007fc2b5327000) | |
| libirng.so => /system/software/linux-x86_64/compilers/intel/intelPS-2015/lib/intel64/libirng.so (0x00007fc2b511f000) | |
| libintlc.so.5 => /system/software/linux-x86_64/compilers/intel/intelPS-2015/lib/intel64/libintlc.so.5 (0x00007fc2b4ec4000) | |
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Thank you so much for such nice instructions.