Difference between revisions of "How to do parallel search of smi files on the cluster"

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search_smi.sh
 
search_smi.sh
 
merge.sh
 
merge.sh
 +
</pre>
 +
 +
'''SUBMIT.sh'''
 +
SUBMIT.sh contains bash code for qsub. SUBMIT.sh specify the qsub command, parameters for qsub, input file, the function script, parameters for the function. A example is shown below.
 +
<pre>
 +
#!/bin/bash
 +
 +
/nfs/soft/tools/utils/qsub-slice/qsub-mr \
 +
    -l 5 \
 +
    -N test \
 +
    all.input \
 +
    ./search_smi.sh \
 +
    -q "CS(=O)(=O)CCNCc1ccccc1"
 
</pre>
 
</pre>

Revision as of 17:10, 19 July 2018

This tutorial shows how to do parallel search of smi files on the cluster. The files and scripts can be found in /nfs/home/jizhou/ex7/2D/test-parallel @gimel.compbio.ucsf.edu

Create a folder with the following files and scripts

SUBMIT.sh
input.txt
search_smi.sh
merge.sh

SUBMIT.sh SUBMIT.sh contains bash code for qsub. SUBMIT.sh specify the qsub command, parameters for qsub, input file, the function script, parameters for the function. A example is shown below.

#!/bin/bash

/nfs/soft/tools/utils/qsub-slice/qsub-mr \
    -l 5 \
    -N test \
    all.input \
    ./search_smi.sh \
    -q "CS(=O)(=O)CCNCc1ccccc1"