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

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     -l 5 \                                                #  The number of lines to be handled by each task, here is 5
 
     -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
 
     -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 \                                                      #  The searching function to be performed  
 
     ./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
 
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</pre>

Revision as of 17:17, 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