[gmx-users] how to generate executable file "g_energy_mpi" ?

[Justin Lemkul]

On 10/23/14 8:03 AM, Vinson Leung wrote:
> But I remove the option "-DGMX_BUILD_MDRUN_ONLY=ON" and can only get
> "gmx_mpi" and "template". There is no those analysis tools and my Gromacs
> version is 5.0.2.
> My build congfiure is like below:
> =====================================================================
> export CCDIR=/opt/intel/composer_xe_2013_sp1.2.144/bin/intel64
> export CMAKE_PREFIX_PATH=/opt/mpich
> export ZLIB_DIR=/usr
>
> ../../cmake-3.0.2/bin/cmake .. \
> -DBUILD_SHARED_LIBS=OFF \
> -DGMX_PREFER_STATIC_LIBS=ON \
> -DGMX_FFT_LIBRARY=mkl \
> -DCMAKE_INSTALL_PREFIX=/home/vincent/gromacs-5.0.2/build-all \
> -DGMX_MPI=ON \
> -DGMX_GPU=OFF \
> -DGMX_XML=OFF \
> -DGMX_SOFTWARE_INVSQRT=OFF \
> -DGMX_SKIP_DEFAULT_CFLAGS=ON \
> -DCMAKE_EXE_LINKER_FLAGS="-L${ZLIB_DIR}/lib64 -mkl=sequential" \
> -DCMAKE_CXX_COMPILER="icpc" \
> -DCMAKE_C_COMPILER="icc" \
> -DCMAKE_C_FLAGS=" -xAVX -O3 -vec-report1   -fno-alias -g  -DNDEBUG -ip
> -funroll-all-loops -fimf-domain-exclusion=15  -I${ZLIB_DIR}/include " \
> -DCMAKE_CXX_FLAGS=" -xAVX -O3 -vec-report1  -fno-alias -g  -DNDEBUG -ip
> -funroll-all-loops -fimf-domain-exclusion=15 -I${ZLIB_DIR}/include"
> ======================================================================
> Is there anything I miss?
>

In version 5.0, every Gromacs program is now a module of the gmx binary, so 
g_energy is just a symlink to "gmx energy," which is now the actual command. 
There is no point in compiling anything other than mdrun with MPI support, so 
set -DGMX_MPI=OFF unless doing an mdrun-only build.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================