[gmx-users] MDRun Compile issue

[Mark Abraham]

Hi,

Please do check out our installation guide... you're doing a few things
that make your life hard and perhaps the resulting simulations slow slow.
http://manual.gromacs.org/documentation/current/install-guide/index.html

On Sun, Jul 15, 2018 at 9:40 PM Weiner, Michael <weinerm at ccf.org> wrote:

> 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.


Neither boost or gsl have been dependencies for some years.


> 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"
>

None of these will help GROMACS, and by using them you risk poor
interactions with those we set that do help. But I don't see any harm,
except that you turned OpenMP support on here, and turned it off below.
Leave OpenMP alone, ie. on by default because it's basically always useful
to users.

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?
>

Be consistent with your OpenMP options (ie set none of them) and this works.

Mark


>
> Thank you
>
> Michael Weiner
>
> Lead Analyst/UNIX Systems Administrator
>
> Lerner Research Institute Computing Services
>
> Lerner Research Institute
>
> Cleveland Clinic
>
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