AMBER Archive (2008)

Subject: RE: AMBER: memory usage

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Apr 27 2008 - 01:07:04 CDT

Hi Ye,

>10513 chem 25 0 15.7g 161m 57m R 100 0.2 2028:17 sander.MPI

This doesn't look like much memory to me. 0.2% seems perfectly reasonable.
The 15.7GB of virtual memory seems a bit strange though. Are you sure this
is not some strange problem with reporting of memory usage? Why did the
administrator ask you to check things? Is it causing problems? The jobs are
all running at 100% cpu usage so it isn’t clear that it is swapping, more
likely there is 15.7 GB that got swapped out immediately.

This is AMBER 9 I assume? If so then this is weird for a 4000 atom run,
although I suppose if you were using Generalized Born it might use a lot,
but not that much. Can you post details of the actual calculation you are
running.

Of course if this is an earlier version of sander which used to have static
memory then it is possible it was compiled with a "huge" sizes.h file that
requests 16GB of static memory. Then even if you run a tiny job it still
allocates 16GB and then of course the memory manager then swaps out the
15.7GB or so that is not being used. This doesn't correlate with the
executable being called sander.MPI though...

Thus I am a little confused. It will probably be easier to see your input
script etc. And the first part of the output. Also what is the performance
like? Very slow or inline with what you'd expect?

All the best
Ross

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Ye Mei
Sent: Saturday, April 26, 2008 6:58 AM
To: amber mailing list
Subject: AMBER: memory usage

Dear amber users,

I got quite confused about memory usage by sander.MPI running on SGI Altix.
As far as I know, sander does not use much memory, especially for a tiny
system with less than 4000 atoms. It is true on PC. But it is not the case
on SGI Altix 4700 running SuSE Linux Enterprise Server 10 with patch level
1. The top command shows that it occupies more than 15GB virtual memory as
following.
  PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
10513 chem 25 0 15.7g 161m 57m R 100 0.2 2028:17 sander.MPI
10514 chem 25 0 15.7g 120m 14m R 100 0.2 2028:06 sander.MPI
10515 chem 25 0 15.7g 161m 57m R 100 0.2 2028:07 sander.MPI
10516 chem 25 0 15.7g 160m 56m R 100 0.2 2028:19 sander.MPI
10517 chem 25 0 15.7g 160m 57m R 100 0.2 2028:07 sander.MPI
10518 chem 25 0 15.7g 158m 55m R 100 0.2 2028:19 sander.MPI
10519 chem 25 0 15.7g 160m 57m R 100 0.2 2028:19 sander.MPI
10520 chem 25 0 15.7g 159m 56m R 100 0.2 2028:07 sander.MPI

The server administrator ordered me to check my jobs. But I have no idea how
this could happen. Does anyone know how to solve this problem?
BTW, jobs are managed by PBS Pro.

　　　　　　

Best regards,

Ye Mei
ymei_at_itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry of MOE
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2008-04-26

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