GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions many groups are also using it for research on non-biological systems.
Some test cases to start with can be found at ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz.
Refereneces
Build and Install Gromacs
Download the source code
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.2.tar.gz |
Build Gromacs for CPU only
tar xfz gromacs-2020.2.tar.gz
cd gromacs-2020.2
module load intel/2019.5.281
module load mkl/2019.5.281
module load gcc/8.4.0
module load cmake/3.13.4
module load hpcx/2.6.0
mkdir build install run
cd build
cmake .. -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=-mkl \
-DMKL_INCLUDE_DIR=$MKLROOT/include \
-DGMX_SIMD=AVX2_256 \
-DGMX_MPI=ON \
-DGMX_BUILD_MDRUN_ONLY=on \
-DBUILD_SHARED_LIBS=on \
-DGMX_HWLOC=off \
-DCMAKE_INSTALL_PREFIX=../install \
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
make -j 16 install
|
Check the install directory for the file mdrun_mpi
$ ls ../install/ bin include lib64 share $ ls ../install/bin gmx-completion-mdrun_mpi.bash mdrun_mpi
Build Gromacs with GPU support
tar xfz gromacs-2020.2.tar.gz
cd gromacs-2020.2
module load intel/2019.5.281
module load mkl/2019.5.281
module load gcc/8.4.0
module load cmake/3.13.4
module load hpcx/2.6.0
module load cuda/10.1
mkdir build install run
cd build
cmake .. -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=-mkl \
-DMKL_INCLUDE_DIR=$MKLROOT/include \
-DGMX_SIMD=AVX2_256 \
-DGMX_MPI=ON \
-DGMX_GPU=ON \
-DGMX_BUILD_MDRUN_ONLY=on \
-DBUILD_SHARED_LIBS=on \
-DGMX_HWLOC=off \
-DCMAKE_INSTALL_PREFIX=../install \
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
make -j 16 install
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Run Gromacs
To run Gromacs with CPU only using stmv case
% mpirun -np 40 -x UCX_NET_DEVICES=mlx5_0:1 -bind-to core -report-bindings \
mdrun_mpi -v -s stmv.tpr -nsteps 10000 -noconfout -nb cpu -pin on
Command line:
mdrun_mpi -v -s stmv.tpr -nsteps 10000 -noconfout -nb cpu -pin on
Reading file stmv.tpr, VERSION 2018.1 (single precision)
Note: file tpx version 112, software tpx version 119
Overriding nsteps with value passed on the command line: 10000 steps, 20 ps
Changing nstlist from 10 to 80, rlist from 1.2 to 1.316
Using 40 MPI processes
Using 1 OpenMP thread per MPI process
...
step 9900, remaining wall clock time: 6 s
vol 0.96 imb F 1% pme/F 0.81 step 10000, remaining wall clock time: 0 s
Dynamic load balancing report:
DLB was turned on during the run due to measured imbalance.
Average load imbalance: 0.9%.
The balanceable part of the MD step is 94%, load imbalance is computed from this.
Part of the total run time spent waiting due to load imbalance: 0.8%.
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 %
Average PME mesh/force load: 0.790
Part of the total run time spent waiting due to PP/PME imbalance: 2.0 %
Core t (s) Wall t (s) (%)
Time: 27556.777 688.921 4000.0
(ns/day) (hour/ns)
Performance: 2.509 9.567
To run Gromacs with GPU
% mpirun -np 4 -x UCX_NET_DEVICES=mlx5_0:1 -bind-to none --map-by node:PE=2 \
mdrun_mpi -v -s stmv.tpr -nsteps 10000 -noconfout -nb gpu -pin on
Command line:
mdrun_mpi -v -s stmv.tpr -nsteps 10000 -noconfout -nb gpu -pin on
Reading file stmv.tpr, VERSION 2018.1 (single precision)
Note: file tpx version 112, software tpx version 119
Overriding nsteps with value passed on the command line: 10000 steps, 20 ps
Changing nstlist from 10 to 100, rlist from 1.2 to 1.339
On host ops003.hpcadvisorycouncil.com 2 GPUs selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 2 ranks on this node:
PP:0,PP:1
PP tasks will do (non-perturbed) short-ranged and most bonded interactions on the GPU
PP task will update and constrain coordinates on the CPU
Using 4 MPI processes
Using 2 OpenMP threads per MPI process
...
imb F 0% step 9900, remaining wall clock time: 3 s
imb F 0% step 10000, remaining wall clock time: 0 s
Dynamic load balancing report:
DLB was off during the run due to low measured imbalance.
Average load imbalance: 0.2%.
The balanceable part of the MD step is 59%, load imbalance is computed from this.
Part of the total run time spent waiting due to load imbalance: 0.1%.
Core t (s) Wall t (s) (%)
Time: 2581.428 322.681 800.0
(ns/day) (hour/ns)
Performance: 5.356 4.481
Other command options
OPTIONS
Options to specify input files:
-s [<.tpr>] (topol.tpr)
Portable xdr run input file
-cpi [<.cpt>] (state.cpt) (Opt.)
Checkpoint file
-table [<.xvg>] (table.xvg) (Opt.)
xvgr/xmgr file
-tablep [<.xvg>] (tablep.xvg) (Opt.)
xvgr/xmgr file
-tableb [<.xvg> [...]] (table.xvg) (Opt.)
xvgr/xmgr file
-rerun [<.xtc/.trr/...>] (rerun.xtc) (Opt.)
Trajectory: xtc trr cpt gro g96 pdb tng
-ei [<.edi>] (sam.edi) (Opt.)
ED sampling input
-multidir [<dir> [...]] (rundir) (Opt.)
Run directory
-awh [<.xvg>] (awhinit.xvg) (Opt.)
xvgr/xmgr file
-membed [<.dat>] (membed.dat) (Opt.)
Generic data file
-mp [<.top>] (membed.top) (Opt.)
Topology file
-mn [<.ndx>] (membed.ndx) (Opt.)
Index file
Options to specify output files:
-o [<.trr/.cpt/...>] (traj.trr)
Full precision trajectory: trr cpt tng
-x [<.xtc/.tng>] (traj_comp.xtc) (Opt.)
Compressed trajectory (tng format or portable xdr format)
-cpo [<.cpt>] (state.cpt) (Opt.)
Checkpoint file
-c [<.gro/.g96/...>] (confout.gro)
Structure file: gro g96 pdb brk ent esp
-e [<.edr>] (ener.edr)
Energy file
-g [<.log>] (md.log)
Log file
-dhdl [<.xvg>] (dhdl.xvg) (Opt.)
xvgr/xmgr file
-field [<.xvg>] (field.xvg) (Opt.)
xvgr/xmgr file
-tpi [<.xvg>] (tpi.xvg) (Opt.)
xvgr/xmgr file
-tpid [<.xvg>] (tpidist.xvg) (Opt.)
xvgr/xmgr file
-eo [<.xvg>] (edsam.xvg) (Opt.)
xvgr/xmgr file
-px [<.xvg>] (pullx.xvg) (Opt.)
xvgr/xmgr file
-pf [<.xvg>] (pullf.xvg) (Opt.)
xvgr/xmgr file
-ro [<.xvg>] (rotation.xvg) (Opt.)
xvgr/xmgr file
-ra [<.log>] (rotangles.log) (Opt.)
Log file
-rs [<.log>] (rotslabs.log) (Opt.)
Log file
-rt [<.log>] (rottorque.log) (Opt.)
Log file
-mtx [<.mtx>] (nm.mtx) (Opt.)
Hessian matrix
-if [<.xvg>] (imdforces.xvg) (Opt.)
xvgr/xmgr file
-swap [<.xvg>] (swapions.xvg) (Opt.)
xvgr/xmgr file
Other options:
-deffnm <string>
Set the default filename for all file options
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-dd <vector> (0 0 0)
Domain decomposition grid, 0 is optimize
-ddorder <enum> (interleave)
DD rank order: interleave, pp_pme, cartesian
-npme <int> (-1)
Number of separate ranks to be used for PME, -1 is guess
-nt <int> (0)
Total number of threads to start (0 is guess)
-ntmpi <int> (0)
Number of thread-MPI ranks to start (0 is guess)
-ntomp <int> (0)
Number of OpenMP threads per MPI rank to start (0 is guess)
-ntomp_pme <int> (0)
Number of OpenMP threads per MPI rank to start (0 is -ntomp)
-pin <enum> (auto)
Whether mdrun should try to set thread affinities: auto, on, off
-pinoffset <int> (0)
The lowest logical core number to which mdrun should pin the first
thread
-pinstride <int> (0)
Pinning distance in logical cores for threads, use 0 to minimize
the number of threads per physical core
-gpu_id <string>
List of unique GPU device IDs available to use
-gputasks <string>
List of GPU device IDs, mapping each PP task on each node to a
device
-[no]ddcheck (yes)
Check for all bonded interactions with DD
-rdd <real> (0)
The maximum distance for bonded interactions with DD (nm), 0 is
determine from initial coordinates
-rcon <real> (0)
Maximum distance for P-LINCS (nm), 0 is estimate
-dlb <enum> (auto)
Dynamic load balancing (with DD): auto, no, yes
-dds <real> (0.8)
Fraction in (0,1) by whose reciprocal the initial DD cell size will
be increased in order to provide a margin in which dynamic load
balancing can act while preserving the minimum cell size.
-nb <enum> (auto)
Calculate non-bonded interactions on: auto, cpu, gpu
-nstlist <int> (0)
Set nstlist when using a Verlet buffer tolerance (0 is guess)
-[no]tunepme (yes)
Optimize PME load between PP/PME ranks or GPU/CPU
-pme <enum> (auto)
Perform PME calculations on: auto, cpu, gpu
-pmefft <enum> (auto)
Perform PME FFT calculations on: auto, cpu, gpu
-bonded <enum> (auto)
Perform bonded calculations on: auto, cpu, gpu
-update <enum> (auto)
Perform update and constraints on: auto, cpu, gpu
-[no]v (no)
Be loud and noisy
-pforce <real> (-1)
Print all forces larger than this (kJ/mol nm)
-[no]reprod (no)
Try to avoid optimizations that affect binary reproducibility
-cpt <real> (15)
Checkpoint interval (minutes)
-[no]cpnum (no)
Keep and number checkpoint files
-[no]append (yes)
Append to previous output files when continuing from checkpoint
instead of adding the simulation part number to all file names
-nsteps <int> (-2)
Run this number of steps (-1 means infinite, -2 means use mdp
option, smaller is invalid)
-maxh <real> (-1)
Terminate after 0.99 times this time (hours)
-replex <int> (0)
Attempt replica exchange periodically with this period (steps)
-nex <int> (0)
Number of random exchanges to carry out each exchange interval (N^3
is one suggestion). -nex zero or not specified gives neighbor
replica exchange.
-reseed <int> (-1)
Seed for replica exchange, -1 is generate a seed
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