Differences

This shows you the differences between two versions of the page.

--- fsl_usage [2015/06/30 21:07]
mgstauff [Commands that Use SGE]
+++ fsl_usage [2016/05/24 22:23] (current)
mgstauff
@@ Line 2: / Line 2: @@
 ====== Using FSL ======
+===== 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#setting_default_options_for_all_scripts|.sqe_request file]] in your home directory.
+**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 =====
-Several compute-intensive commands use OGS/SGE to run portions of the processing in parallel. They submit qsub jobs using your username:
+Several compute-intensive commands use SGE to run portions of the processing in parallel. They submit qsub jobs using your username.
+These are the commands:
   FEAT    will run multiple first-level analyses in parallel if they are setup all together in one GUI setup. At second level, if full FLAME (stages 1+2) is selected then all the slices are processed in parallel.
@@ Line 19: / Line 28: @@
   POSSUM  will process all slices in parallel.
-Because they call qsub, **YOU MUST RUN THESE COMMANDS ON THE FRONT-END DIRECTLY**. That is, call them or the script that calls them from chead directly, without using qlogin or qsub.
+If you get an error like this:
-If you run one of these commands from a compute node, you'll get an error like this:
   denied: host "compute-0-6.local" is no submit host
-We are working on a safe way to run these commands from qsub and qlogin.
+tell the admin. This shouldn't happen as of May 2016.
-==== CPU Time Limit Issues ====
-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.
+==== Using FSL WITHOUT SGE ====
-===== Requesting More Memory =====
+You may need to tell FSL to __not__ use SGE for one of the above commands.
-If your jobs are killed because of insufficient memory, it means most likely that the portions run via OGS/SGE are hitting the default memory limit. To request more, do so via the [[using_ogs_sge#setting_default_options_for_all_scripts|.sqe_request file]] in your home directory.
+To tell FSL not to use SGE, you must clear the ''SGE_ROOT'' environment variable for your script. Add this line to your script, before you call an FSL command that normally uses 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.
+  unset SGE_ROOT
+When the FSL scripts see that ''SGE_ROOT'' is not defined (i.e. it is unset), it will run its analysis portions on the same computer that the script was run from.
+==== CPU Time Limit Issues ====
+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.

Computing

User Tools

Site Tools

Differences

Page Tools