How to do parallel search of smi files on the cluster: Difference between revisions
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-N test \ # The name of the queue to submit to | -N test \ # The name of the queue to submit to | ||
input.txt \ # The input file names and i | input.txt \ # The input file names and i | ||
./search_smi.sh \ | ./search_smi.sh \ # The searching function to be performed | ||
-q "CS(=O)(=O)CCNCc1ccccc1" # Parameter for search_smi.sh, the input query for searching | -q "CS(=O)(=O)CCNCc1ccccc1" # Parameter for search_smi.sh, the input query for searching | ||
</pre> | </pre> |
Revision as of 17:18, 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 \ # the qsub command -l 5 \ # The number of lines to be handled by each task, here is 5 -N test \ # The name of the queue to submit to input.txt \ # The input file names and i ./search_smi.sh \ # The searching function to be performed -q "CS(=O)(=O)CCNCc1ccccc1" # Parameter for search_smi.sh, the input query for searching