Re: [AMBER] huge memory consumption when running nab simulations

From: David A Case via AMBER <>
Date: Mon, 12 Jun 2023 20:57:16 -0400

On Mon, Jun 12, 2023, Dominik Brandstetter via AMBER wrote:
>a quick update on this topic. When I try to run the same simulation
>described in my previous message using hcp = 0, the simulation runs fine
>with a low memory consumption. The huge memory consumption, that eventually
>leads to failure of the run, occurs only when I use hcp = 4. This makes me
>think that my parallelization scheme works fine, and that there might be a
>sort of memory leak in the HCP implementation? What do you think?

Thanks for the extra info. I'm cc-ing this to Alexey Onufriev, who may have
some insight here. (I don't have any personal experience with HCP). But I
still suspect (hope) that one doesn't really need HCP for a system with only
4000 atoms.


>From: Dominik Brandstetter <>
>Sent: Tuesday, June 6, 2023 2:32 PM
>To: <>
>Subject: huge memory consumption when running nab simulations
>I am new to NAB, and I am running some implicit solvent simulations with it on a cluster having 2x 64-core nodes and with ~940 GiB of RAM memory per node.
>I am using the and files attached to start my simulations, which are nicely parallelized and run fine, but I notice a huge memory consumption, which often leads to a failure of the simulations, as you can see in the following error message for the run:
>Slurm Job_id=25014708 Name=3U_1_64 Failed, Run time 00:47:53, OUT_OF_MEMORY
>Name : 3U_1_64
>Cores : 64
>Submit : 2023-06-05T08:42:07
>Start : 2023-06-05T10:19:49
>End : 2023-06-05T11:07:42
>Reserved walltime : 03:00:00
>Used walltime : 00:47:53
>Used CPU time : 2-02:08:17
>% User (Computation): 99.76%
>% System (I/O) : 0.24%
>Mem reserved : 900G
>Max Mem used : 897.41G (node4113.gallade.os)
>Max Disk Write : 194.56K (node4113.gallade.os)
>Max Disk Read : 42.54M (node4113.gallade.os)
>The system I am trying to simulate has 3696 atoms. Do you think this high memory consumption is normal for this size? Or is there a way I can modify e.g. my or file to reduce the RAM usage and have a successful completion of my run?

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Received on Mon Jun 12 2023 - 18:00:02 PDT
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