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I have a multi-core workstation running Windows 7. When I submit a job to run on 12 cores, things go fine, but after some time the percent of the cpu the job occupies decreases from ~30% to 3% even when I set the priority of the job to high. Essentially, the process gets shifted to run on only 1 core rather than 12, but not as a result of other processes needing the resources (there are still cores available and no other processes are started over that time). Is there a way to prevent this from happening?

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What do you mean submit a job? Are you a REXX or JCL programmer? –  Brad Patton Mar 13 '13 at 20:27
    
We need to know more about jour job. Most likly is that the job uses so much memory that all the CPU caches fill up and the job end ups bottle necking at your RAM, with one CPU easily able to process the data as it comes in from the slower RAM. Can you use task manager to post more details like memory size and page faults? (Also does you hdd light come on and stay on? Some data may be cached with the rest having to read from disk at a much slower speed). –  Mundi Mar 13 '13 at 20:33
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The job may not be suitable for parallel processing for all or part of the work. –  BJ292 Mar 13 '13 at 20:41
    
The job is a molecular dynamics simulation using the software package Gromacs. The process is definitely not memory limited as the max memory usage is ~50MB, and I have 256 GB installed. –  Mike Mar 18 '13 at 21:25

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