How to do parallel search of smi files on the cluster: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
Line 18: | Line 18: | ||
-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 | input.txt \ # The input file names and directory | ||
./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 | ||
</pre> | |||
'''input.txt''' | |||
The input file names and directory. An example of input.txt is shown below. You can use ls *.smi > input.txt to generate this file. | |||
<pre> | |||
/nfs/home/jizhou/ex7/2D/CD/CDAA.smi | |||
/nfs/home/jizhou/ex7/2D/CD/CDAB.smi | |||
/nfs/home/jizhou/ex7/2D/CD/CDAC.smi | |||
/nfs/home/jizhou/ex7/2D/CD/CDAD.smi | |||
/nfs/home/jizhou/ex7/2D/CD/CDAE.smi | |||
/nfs/home/jizhou/ex7/2D/CD/CDAF.smi | |||
... | |||
</pre> | </pre> |
Revision as of 17:23, 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 directory ./search_smi.sh \ # The searching function to be performed -q "CS(=O)(=O)CCNCc1ccccc1" # Parameter for search_smi.sh, the input query for searching
input.txt
The input file names and directory. An example of input.txt is shown below. You can use ls *.smi > input.txt to generate this file.
/nfs/home/jizhou/ex7/2D/CD/CDAA.smi /nfs/home/jizhou/ex7/2D/CD/CDAB.smi /nfs/home/jizhou/ex7/2D/CD/CDAC.smi /nfs/home/jizhou/ex7/2D/CD/CDAD.smi /nfs/home/jizhou/ex7/2D/CD/CDAE.smi /nfs/home/jizhou/ex7/2D/CD/CDAF.smi ...