[gmx-users] MPI-specific compile problem finding fftwf_plan_r2r_1d in libfftw3f.a -- undefined reference to `_intel_fast_memset'

Christopher Neale chris.neale at alum.utoronto.ca
Thu Dec 21 23:28:09 CET 2017


I resolved the issue. I forget to use -DGMX_MPI=ON , though fixing that did not resolve the issue. The issue appears to be that the intel mpi compilers are not called mpicc and mpicxx so I was mixing things in a strange way that happened to cause problems with fftw loading.

The following script worked just fine to compile, where the key change was to remove -DCMAKE_C_COMPILER=mpicc and -DCMAKE_CXX_COMPILER=mpicxx

module purge
module load intel/17.0.4
module load cmake/3.9.0
module load intel-mpi/2017.1

mkdir -p $edir

export FFTW_LOCATION=/net/scratch3/cneale/exe/KODIAK/FFTW/fftw-3.3.4_intel/exec

cmake ../../../source/gromacs-5.1.2 \
      -DCMAKE_INSTALL_PREFIX=$(pwd)/$edir \
      -DGMX_X11=OFF \
      -DGMX_MPI=ON \

make -j 8

make install -j 8
} > output.cn_compile 2>&1

Thank you,

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