fsl_usage
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fsl_usage [2016/05/24 22:17] mgstauff [Commands that Use SGE] |
fsl_usage [2016/05/24 22:23] (current) mgstauff |
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| ====== Using FSL ====== | ====== Using FSL ====== | ||
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| + | ===== Requesting More Memory ===== | ||
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| + | If your jobs are killed because of insufficient memory, it means most likely that the portions run via SGE are hitting the default memory limit. To request more, do so via the [[using_ogs_sge# | ||
| + | |||
| + | **NOTE** however that this will make the request for **all** jobs your run, which is an inefficient use of memory for you and everyone else, so be careful to always change this file before running other jobs that don't need as much memory (e.g. simply comment-out or deactivate any lines by adding a hash mark (#) by itself at the beginning of the line in your .sge_request file). I'm hoping to work out a more flexible way to request more memory and will let everyone know if I work it out. | ||
| ===== Commands that Use SGE ===== | ===== Commands that Use SGE ===== | ||
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| ==== Using FSL WITHOUT SGE ==== | ==== Using FSL WITHOUT SGE ==== | ||
| - | You may need to tell FSL to __not__ use SGE for one of the above commands. Typically this will be because you have a more involved script that does some other analysis steps along with the FSL commands that run SGE jobs, and you want to or need to run the whole script as a qsub or qlogin job. | + | You may need to tell FSL to __not__ use SGE for one of the above commands. |
| To tell FSL not to use SGE, you must clear the '' | To tell FSL not to use SGE, you must clear the '' | ||
| Line 40: | Line 47: | ||
| If your command gets killed because it takes too much CPU time running on chead, email the admin to learn how to work around this. This is very unlikely to be an issue. | If your command gets killed because it takes too much CPU time running on chead, email the admin to learn how to work around this. This is very unlikely to be an issue. | ||
| - | |||
| - | ===== Requesting More Memory ===== | ||
| - | |||
| - | If your jobs are killed because of insufficient memory, it means most likely that the portions run via SGE are hitting the default memory limit. To request more, do so via the [[using_ogs_sge# | ||
| - | |||
| - | **NOTE** however that this will make the request for **all** jobs your run, which is an inefficient use of memory for you and everyone else, so be careful to always change this file before running other jobs that don't need as much memory (e.g. simply comment-out or deactivate any lines by adding a hash mark (#) by itself at the beginning of the line in your .sge_request file). I'm hoping to work out a more flexible way to request more memory and will let everyone know if I work it out. | ||
fsl_usage.1464128262.txt.gz ยท Last modified: 2016/05/24 22:17 by mgstauff
