[gmx-users] MDRun Compile issue

Weiner, Michael weinerm at ccf.org
Sun Jul 15 21:40:20 CEST 2018

I am trying to build gromacs 2018.2 on an intel-based HPC that i manage. i have the main program built but i want to build MDrun openmp support. I am using the latest version of Intel Parallel Studio XE (2018.3) in order to compile, as well as the latest boost (1.67.0), gsl (2.5) and openmil (3.1.1) sources. Here is my attemt/configuration to build mdrun with openmpi:


rm -rf *
export CC=icc
export CXX=icpc

export  GROMACS_INSTALL_DIR=/cm/shared/apps/gromacs/2018.2

export CMAKE_PREFIX_PATH=/cm/shared/apps/boost/1.67.0:/cm/shared/apps/gsl/2.5

export CFLAGS="-O3 -fast-transcendentals -ftz -fma -fp-model fast=2 -qopt-calloc  -fp-speculation=fast -fpic -ip -no-prec-div -xHOST -qopenmp"


export MPICC=mpiicc

cmake \
-DGMX_FFT_LIBRARY=fftw3  -DGMX_BUILD_OWN_FFTW=ON  .. && make -j25 mdrun && make  install-mdrun


It gets 95% of the way through the build and fails with the following:

[ 93%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tpi.cpp.o
cd /root/temp/gromacs-2018.2/build/src/gromacs && /cm/shared/apps/intel/parallelstudio/2018/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc  -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -isystem /root/temp/gromacs-2018.2/src/external/lmfit -I/root/temp/gromacs-2018.2/build/src/contrib/fftw/fftwBuild-prefix/include -I/root/temp/gromacs-2018.2/build/src -isystem /root/temp/gromacs-2018.2/src/external/thread_mpi/include -I/root/temp/gromacs-2018.2/src -isystem /cm/shared/apps/openmpi/gcc/64/3.1.1/include -I/root/temp/gromacs-2018.2/src/external/tng_io/include -I/root/temp/gromacs-2018.2/build/tng/include  -mavx   -O3 -fast-transcendentals -ftz -fma -fp-model fast=2 -qopt-calloc  -fp-speculation=fast -fpic -ip -no-prec-div -xHOST -qopenmp -std=c++11  -wd3180  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits     -o CMakeFiles/libgromacs.dir/mdlib/tpi.cpp.o -c /root/temp/gromacs-2018.2/src/gromacs/mdlib/tpi.cpp
/root/temp/gromacs-2018.2/src/gromacs/mdlib/nbnxn_search.cpp(2853): error: identifier "nthreads" is undefined
  #pragma omp parallel for num_threads(nthreads) schedule(static)

compilation aborted for /root/temp/gromacs-2018.2/src/gromacs/mdlib/nbnxn_search.cpp (code 2)
make[3]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o] Error 2

Can anyone provide any insights as to why this is failing and perhaps give me some pointers to get it to  compile?

Thank you

Michael Weiner

Lead Analyst/UNIX Systems Administrator

Lerner Research Institute Computing Services

Lerner Research Institute

Cleveland Clinic


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