... | ... | @@ -45,6 +45,14 @@ If your job gets killed, you will often see in your job output a line similar to |
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In addition, your job will have the exit status 127. To retrieve the exit status of your job using qacct, please see the next section.
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### Segfaults and core dumped for some jobs ###
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If you run programs that are quite large and depend on a lot of libraries from the system (dyn-libs) and the programs segfaults. Try to set the `-l h_stack` to a higher number. This error mostly occurs with applications that are using multithreading and working on large datasets (e.g. samtools, sambamba )
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`qsub -l h_stack=32M test_script.sh`
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By default, this setting is very low ( about 8MB max, and 2MB per thread ) (lookup with: `ulimit -s`)
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### Figure out how much memory you need
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You can find out the amount of memory used for any finished job with the following command:
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