[gmx-users] MDRun Compile issue

[Weiner, Michael]

I apologilize, it looks like auto-correct hit me again, should be openmpi not openmp
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Weiner, Michael <weinerm at ccf.org>
Sent: Sunday, July 15, 2018 3:22 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [EXT] [gmx-users] MDRun Compile issue

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 CXXFLAGS=$CFLAGS
export LDFLAGS=$CFLAGS

export MPICC=mpiicc

cmake \
-DCMAKE_VERBOSE_MAKEFILE=TRUE \
-DCMAKE_INSTALL_PREFIX=$GROMACS_INSTALL_DIR \
-DGMX_GPU=OFF  -DGMX_MPI=ON -DGMX_OPENMP=OFF \
-DGMX_EXTERNAL_BLAS=OFF \
-DGMX_BUILD_MDRUN_ONLY=ON \
-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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 Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.