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april2016_jim_gromacscompilecommands.txt
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april2016_jim_gromacscompilecommands.txt
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1) module
module load icc_15.0.3-impi_5.0.3
2) unpack plumed
3) configure plumed
./configure --prefix=$INST
4) install
make install
5) plumed environment
export PATH=$PATH:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/bin
export INCLUDE=$INCLUDE:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/include
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib
6) which versions of GMX is BayesBias tree v 2.2 compatible with?
-bash-4.1$ plumed patch -p
warning:regcache incompatible with malloc
PLUMED patching tool
1) amber14 4) gromacs-5.0.4 7) namd-2.8
2) gromacs-4.5.7 5) gromacs-5.1.2 8) namd-2.9
3) gromacs-4.6.7 6) lammps-6Apr13 9) qespresso-5.0.2
lets gry GMX 5.1.2. , maybe we will get lucky
7) unpack 5.1.2
8) run patch in the root directory
-bash-4.1$ cd ../gromacs-5.1.2
-bash-4.1$ plumed patch -p
warning:regcache incompatible with malloc
PLUMED patching tool
1) amber14 4) gromacs-5.0.4 7) namd-2.8
2) gromacs-4.5.7 5) gromacs-5.1.2 8) namd-2.9
3) gromacs-4.6.7 6) lammps-6Apr13 9) qespresso-5.0.2
Choose the best matching code/version:5
MD engine: gromacs-5.1.2
PLUMED location: /gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib/plumed
diff file: /gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib/plumed/patches/gromacs-5.1.2.diff
sourcing config file: /gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib/plumed/patches/gromacs-5.1.2.config
Linking Plumed.h and Plumed.inc (shared mode)
Patching with on-the-fly diff from stored originals
patching file ./src/gromacs/CMakeLists.txt
patching file ./src/gromacs/mdlib/force.cpp
patching file ./src/gromacs/mdlib/minimize.cpp
patching file ./src/programs/mdrun/md.cpp
patching file ./src/programs/mdrun/mdrun.cpp
patching file ./src/programs/mdrun/repl_ex.cpp
PLUMED is compiled with MPI support so you can configure gromacs-5.1.2 with MPI
9) plumed is patched, now try cmake and see if it works
mkdir bin build_gromacs
cd bin
export GMXINST=`pwd`
cd ../build_gromacs/
cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$GMXINST
NOTE: to add different versions (like hte 8core version) :
cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$GMXINST -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_8c -DGMX_LIBS_SUFFIX=_8c
10) cmake was successful - next build and install
make -j12 install
11) to use GMX 5.1.2 + PLUMED 2.2-BayesBias tree set these variables in your PBS file:
module load icc_15.0.3-impi_5.0.3
export PATH=$PATH:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/bin
export INCLUDE=$INCLUDE:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/include
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/gscratch/pfaendtner/codes/plumed2-BayesBias/bin/lib
source /gscratch/pfaendtner/codes/gromacs-5.1.2/inst/bin/GMXRC
12) things have changed if you are familiar only with the old version that had all the individual gromacs commands, now you will use "gmx_mpi grompp" instead of "grompp"
gmx_mpi grompp -c start.gro -p topol.top -f nvt.mdp
to run a 4 replica multiple walkers job:
mpiexec.hydra -np 8 gmx_mpi mdrun -plumed plumed.dat -multi 4
example = /gscratch/pfaendtner/codes/gromacs-5.1.2/multiple_walkers_test