Re: Background load problem

From: Anirban (anirbang_at_cdac.in)
Date: Thu Feb 26 2009 - 08:15:04 CST

Hi Peter,

Actually that is a shape-based system, thats why the size is too small.
I also tried to run a RBCG model of 5622 CG beads and that is also not
scaling beyond 16 processors. And I am getting the same comment "High
background load" for this system also. What should I do?

Regards,

On Thu, 2009-02-26 at 07:50 -0600, Peter Freddolino wrote:
> 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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