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Slow gmx tools
- nanogod
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6 years 6 months ago #7407
by nanogod
Slow gmx tools was created by nanogod
Hi,
Have any of you noticed that the analysis tools have become very slow? they always were rather slow but in version 5.x it was possible to use only single cores which increased the performance about 10x. In version 2016.2 which I am using, this is not possible. I have 12 physical cores and all run of about 10% when I do anaylisis.
This is perticular problematic with martini simulations because I often have large trajectories and lot of them.
Any of you have this problem? or ideas?
Best regards
Morten
Have any of you noticed that the analysis tools have become very slow? they always were rather slow but in version 5.x it was possible to use only single cores which increased the performance about 10x. In version 2016.2 which I am using, this is not possible. I have 12 physical cores and all run of about 10% when I do anaylisis.
This is perticular problematic with martini simulations because I often have large trajectories and lot of them.
Any of you have this problem? or ideas?
Best regards
Morten
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- peterkroon
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6 years 6 months ago #7409
by peterkroon
Replied by peterkroon on topic Slow gmx tools
Hi Morten,
how large (in GB) are your trajectories? What kind of analysis are you trying to perform? Could you time to identical analyses with different gromacs versions (e.g. with `time`)?
I expect you are simply limited by disk I/O, and that there is no appreciable difference between the different versions of Gromacs.
how large (in GB) are your trajectories? What kind of analysis are you trying to perform? Could you time to identical analyses with different gromacs versions (e.g. with `time`)?
I expect you are simply limited by disk I/O, and that there is no appreciable difference between the different versions of Gromacs.
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