Differences

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--- gromacs-software [2018/07/16 15:48] – created aorth
+++ gromacs-software [2019/11/11 14:48] (current) – aorth
@@ Line 17: / Line 17: @@
 <code>$ module load gromacs/2018.2
 $ gmx</code>
+**Note:** Please use the ''-nt'' option to limit the number of threads launched by gmx to be the same amount as in your SLURM sbatch allocation. See the [[http://manual.gromacs.org/2018-current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node|gromacs documentation for more information]].
 ===== Installation ======
@@ Line 35: / Line 37: @@
 $ sudo chown -R root:root /export/apps/gromacs/2018.2</code>
-Gromacs recommends using the ''GMXRC.bash'' script to set up the user's environment, but since we're using environment modules we can't do that. Instead, I compared the output ''env'' before and after loading the ''GMXRC.bash'' environment and then used that to create the module file.
+Gromacs recommends sourcing the ''GMXRC.bash'' script to set up the user's environment, but since we're using environment modules we can't do that. Instead, I compared the output ''env'' before and after loading the ''GMXRC.bash'' environment and then used that to create the module file.