AMBER Archive (2008)

Subject: AMBER: memory usage

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Sat Apr 26 2008 - 08:57:44 CDT

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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