Re: Background load problem

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 26 2009 - 07:50:36 CST

Hi Anirban,
namd is generally able to scale efficiently in parallel up to 100-1000
atoms per processor, depending on your exact system. Trying to run a 45
particle system on more than one processor is unlikely to give
significant returns, and certainly running on more than one node (where
network latency comes into play) is right out. Have you tried
benchmarking with different numbers of processors?

How is your system so small? Do you not have cg water?

Best,
Peter

Anirban Ghosh wrote:
> Hi ALL,
>
> I am running a CGMD simulation of a system comprising of 45 beads using
> NAMD. I am using 16 processors (4 nodes) to run the job. Although no other
> jobs are running on this node and CPU usage % is only 10-11%, but still I
> am getting the following error messages related to background loads.
> Because of this the log files are becoming too large and the run-times are
> increasing exponentially.
> -----------------------------------------------------------------------------
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000100000
> OPENING COORDINATE DCD FILE
> WRITING COORDINATES TO DCD FILE AT STEP 1000100000
> WRITING COORDINATES TO RESTART FILE AT STEP 1000100000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 1000100000
> FINISHED WRITING RESTART VELOCITIES
> LDB: LOAD: AVG 0.00873701 MAX 0.0428593 MSGS: TOTAL 15 MAXC 1 MAXP 15
> None
> Warning: 1 processors are overloaded due to high background load.
> LDB: LOAD: AVG 0.00873701 MAX 0.0428593 MSGS: TOTAL 15 MAXC 1 MAXP 15
> Refine
> LDB: LOAD: AVG 0.00786597 MAX 0.0348988 MSGS: TOTAL 15 MAXC 1 MAXP 15
> None
> Warning: 2 processors are overloaded due to high background load.
> LDB: LOAD: AVG 0.00786597 MAX 0.031147 MSGS: TOTAL 15 MAXC 1 MAXP 15
> Refine
> LDB: LOAD: AVG 0.00806749 MAX 0.034482 MSGS: TOTAL 15 MAXC 1 MAXP 15
> None
> Warning: 2 processors are overloaded due to high background load.
> LDB: LOAD: AVG 0.00806749 MAX 0.0327935 MSGS: TOTAL 15 MAXC 1 MAXP 15
> Refine
> LDB: LOAD: AVG 0.00822078 MAX 0.0371771 MSGS: TOTAL 15 MAXC 1 MAXP 15
> None
> Warning: 1 processors are overloaded due to high background load.
> LDB: LOAD: AVG 0.00822078 MAX 0.0339828 MSGS: TOTAL 15 MAXC 1 MAXP 15
> Refine
> LDB: LOAD: AVG 0.00878559 MAX 0.0362875 MSGS: TOTAL 15 MAXC 1 MAXP 15
> None
> -----------------------------------------------------------------------------
>
> How can I solve this problem? Any suggestion is appreciated.
>
>
> Regards,
>
>

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