| Auszug |
|---|
a versatile package to perform molecular dynamics for systems with hundreds to millions of particles. |
...
GROMACS provides extremely high performance compared to all other programs.
GROMACS can make simultaneous use of both CPU and GPU available in a system. There are options to statically and dynamically balance the load between the different resources.
GROMACS is user-friendly, with topologies and parameter files written in clear text format.
Both run input files and trajectories are independent of hardware endian-ness, and can thus be read by any version GROMACS.
GROMACS comes with a large selection of flexible tools for trajectory analysis.
GROMACS can be run in parallel, using the standard MPI communication protocol.
GROMACS contains several state-of-the-art algorithms.
GROMACS is Free Software, available under the GNU Lesser General Public License (LGPL).
Weaknesses
GROMACS does not do to much further analysis to get very high simulation speed.
Sometimes it is challenging to get non-standard information about the simulated system.
Different versions sometimes have differences in default parameters/methods. Reproducing older version simulations with a newer version can be difficult.
Additional tools and utilities provided by GROMACS are sometimes not the top quality.
...
Version | Module file | Thread-MPI (gmx) | MPI (gmx_mpi) | Plumed (gmx_mpi_plumed) | Prerequisites |
|---|---|---|---|---|---|
CPU CLX partition | |||||
2021.7 | gromacs/2021.7 |
|
|
| impi/2021.13 |
2023.0 | gromacs/2023.0 |
|
|
| impi/2021.13 |
CPU Genoa partition | |||||
GPU A100 partition | |||||
2022.5 | gromacs/2022.5 |
|
|
| gcc/11.3.0 cuda/11.8 impi/2021.11 |
2023.0 | gromacs/2023.0_tmpi |
|
|
| gcc/11.3.0 intel/2023.0.0 cuda/11.8 |
2024.0 | gromacs/2024.0_tmpi |
|
|
| gcc/11.3.0 intel/2023.0.0 cuda/12.3 |
GPU PVC partition | |||||
Version | Installation Path | modulefile | compiler | comment |
|---|
Deprecated versions | ||||
|
|
|
| |
|
|
|
|
|
|
|
|
| |
|
|
|
|
|
|
|
|
| |
|
|
|
|
|
|
|
|
| |
|
|
|
| |
with plumed
2023.0
/sw/chem/gromacs/2023/clx.el9/mpi & /sw/chem/gromacs/2023/clx.el9/mpi_plumed
gromacs/2023.0
gcc/g++ with Intel MPI
gmx_mpi binary and PLUMED-patched gmx_mpi_plumed binaryModules for running on GPUs
2022.5
/sw/chem/gromacs/2022.5/a100/impi
gromacs/2022.5
|
gmx_mpi binary and PLUMED-patched gmx_mpi_
|
2023.0
/sw/chem/gromacs/2023.0/a100/tmpi_gcc
gromacs/2023.0_tmpi
2024.0
/sw/chem/gromacs/2024.0/a100/tmpi
*Release notes can be found here.
...
Note: Settings of the Thread-MPI ranks and OpenMP threads is for achieve optimal performance. The number of ranks should be a multiple of the number of sockets, and the number of cores per node should be a multiple of the number of threads per rank.
Related Modules
Gromacs-Plumed
PLUMED is an open-source, community-developed library that provides a wide range of different methods, such as enhanced-sampling algorithms, free-energy methods and tools to analyze the vast amounts of data produced by molecular dynamics (MD) simulations. PLUMED works together with some of the most popular MD engines.
Gromacs/20XX.X-plumed modules are versions have been patched with PLUMED's modifications, and these versions are able to run meta-dynamics simulations.
Analyzing results
GROMACS Tools
...
Turbo-boost has been mostly disabled on Emmy at GWDG (partitions medium40, large40, standard96, large96, and huge96) in order to save energy. However, this has a particularly strong performance impact on GROMACS in the range of 20-40%. Therefore, we recommend that GROMACS jobs be submitted requesting turbo-boost to be enabled with the --constraint=turbo_on option given to srun or sbatch.