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cluster:88 [2010/08/10 20:24] hmeij |
cluster:88 [2010/08/11 14:25] hmeij |
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* make a backup copy of / | * make a backup copy of / | ||
* edit file, delete everything but queue ' | * edit file, delete everything but queue ' | ||
- | * (if you rename queue normal you also need to edit lsb.params) | + | * (if you rename queue normal you also need to edit lsb.params |
* remove most queue definitions and set the following | * remove most queue definitions and set the following | ||
- | * QJOBLIMIT | + | * QJOB_LIMIT |
- | * UJOBLIMIT | + | * UJOB_LIMIT |
* INTERACTIVE = no (only batch is allowed) | * INTERACTIVE = no (only batch is allowed) | ||
* EXCLUSIVE = Y (allow the bsub -x flag) | * EXCLUSIVE = Y (allow the bsub -x flag) | ||
- | * PRE_EXEC = / | + | * PRE_EXEC = / |
* POST_EXEC = / | * POST_EXEC = / | ||
- | * make the directories /home/apps and / | + | * make the directories / |
+ | * make the directory / | ||
+ | * be sure / | ||
* create the pre/post exec files (post does an rm -rf against the created directories) | * create the pre/post exec files (post does an rm -rf against the created directories) | ||
+ | * for example: | ||
< | < | ||
#!/bin/bash | #!/bin/bash | ||
Line 204: | Line 207: | ||
fi | fi | ||
</ | </ | ||
+ | |||
+ | * ' | ||
+ | * ' | ||
+ | |||
+ | Now we're ready to submit a serial jobs. As a non-privilege user create two files: | ||
+ | |||
+ | * run | ||
+ | |||
+ | < | ||
+ | #!/bin/bash | ||
+ | |||
+ | rm -f out err job3.out | ||
+ | |||
+ | #BSUB -q normal | ||
+ | #BSUB -J test | ||
+ | #BSUB -n 1 | ||
+ | #BSUB -e err | ||
+ | #BSUB -o out | ||
+ | |||
+ | export MYSANSCRATCH=/ | ||
+ | export MYLOCALSCRATCH=/ | ||
+ | |||
+ | cd $MYLOCALSCRATCH | ||
+ | pwd | ||
+ | cp ~/job.sh . | ||
+ | time job.sh > job.out | ||
+ | |||
+ | cd $MYSANSCRATCH | ||
+ | pwd | ||
+ | cp $LOCALSCRATCH/ | ||
+ | |||
+ | cd | ||
+ | pwd | ||
+ | cp $MYSANSCRATCH/ | ||
+ | </ | ||
+ | |||
+ | * job.sh | ||
+ | * | ||
+ | < | ||
+ | #!/bin/bash | ||
+ | |||
+ | sleep 10 | ||
+ | echo Done sleeping. | ||
+ | |||
+ | for i in `seq 1 100` | ||
+ | do | ||
+ | date | ||
+ | done | ||
+ | |||
+ | </ | ||
+ | |||
+ | * 'bsub < run' (submits) | ||
+ | * ' | ||
+ | |||
+ | |||
+ | ===== Step 6 ===== | ||
+ | |||
+ | More fun. | ||
+ | |||
\\ | \\ | ||
**[[cluster: | **[[cluster: |