User:Stuekero/GROMACS
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A new section for the GROMACS page, that I'm working on:
Environment modules[edit]
| GROMACS version | modules for running on CPUs | modules for running on GPUs (CUDA) | Notes |
|---|---|---|---|
| gromacs/2022.2 | StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2022.2 |
GCC, FlexiBLAS & FFTW | |
| gromacs/2021.6 | StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.6 |
StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 gromacs/2021.6 |
GCC, FlexiBLAS & FFTW |
| gromacs/2021.4 | StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.4 |
StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 gromacs/2021.4  |
GCC, FlexiBLAS & FFTW |
| gromacs/2021.2 | StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 gromacs/2021.2 |
GCC, FlexiBLAS & FFTW | |
| gromacs/2021.2 | StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.2 |
StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 gromacs/2021.2 |
GCC & MKL |
| gromacs/2020.6 | StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2020.6 |
StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 gromacs/2020.6 |
GCC, FlexiBLAS & FFTW |
| gromacs/2020.4 | StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 gromacs/2020.4 |
GCC, FlexiBLAS & FFTW | |
| gromacs/2020.4 | StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2020.4 |
StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 gromacs/2020.4 |
GCC & MKL |
Notes:
GROMACS versions 2020.0 up to and including 2021.5 contain a bug when used on GPUs of Volta or newer generations (i.e. V100, T4 and A100) with mdrunoption-update gputhat could have perturbed the virial calculation and, in turn, led to incorrect pressure coupling. The GROMACS developers state in the 2021.6 Release Notes: "The GPU update is not enabled by default, so the error can only appear in simulations where it was manually selected, and even in this case the error might be rare since we have not observed it in practice in the testing we have performed."[1] Further discussion of this bug can be found in the GitLab issue #4393 of the GROMACS project.[2]- Version 2020.4 and newer have been compiled for the new Standard software environment
StdEnv/2020. - Version 2018.7 and newer have been compiled with GCC compilers and the MKL-library, as they run a bit faster.
- Older versions have been compiled with either with GCC compilers and FFTW or Intel compilers, using Intel MKL and Open MPI 2.1.1 libraries from the default environment as indicated in the table above.
- CPU (non-GPU) versions are available in both single- and double precision, with the exception of 2019.3 (‡), where double precision not available for AVX512.
Further Reading[edit]
References[edit]
- ↑ "Fix missing synchronization in CUDA update kernels" in GROMACS 2021.6 Release Notes [1]
- ↑ Issue #4393 in GROMACS Project on GitLab.com [2]
- ↑ Larsson P, Hess B, Lindahl E. Algorithm improvements for molecular dynamics simulations. Wiley Interdiscip Rev Comput Mol Sci. 2011;1: 93–108. doi:10.1002/wcms.3