[gmx-users] Excessive memory usage of mdrun

Sotirios Dionysios I. Papadatos si.papadatos at edu.cut.ac.cy
Tue Oct 6 16:39:46 CEST 2015

Hi, though your system is not that small, you shouldn't have any problem running lysozyme tutorial. Although the number of CPU's only affect the ns/day a simulation runs, it is a matter of your HPC system. Did you install gromacs yourself??

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of mpignata at bidmc.harvard.edu <mpignata at bidmc.harvard.edu>
Sent: Monday, September 28, 2015 9:12 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Excessive memory usage of mdrun

Good morning,

I'm trying to simulate a protein system on an HPC cluster called Orchestra, that use gromacs 5.0.4.

The system size is 39126 atoms and is made by the protein, 12160 water molecules, one Na+ and one Cl-. Of this system I've already made a run of 50 ns on my workstation without any problems, but every time that I've tried to simulate it on the cluster my job get killed for excessive memory usage (more than 64 GB).

I've tried to use different numbers of CPU (from 4 to 12) and I've tried to use a single node all for myself, but every time I had the same problem.

I've even tried the lysozyme benchmark, both with my .mdp and with a .mdp from a gromacs tutorial, and the same problem occurred every time.

I've talked with one of the administrator and they don't have a clue about what's happening, also because they usually don't have gromacs user on it.

Have this kind of things happened to someone before? Any clue?




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