How to do parallel search of smi files on the cluster

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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

Create a folder with the following files and scripts
input.txt contains bash code for qsub. specify the qsub command, parameters for qsub, input file, the function script, parameters for the function. A example is shown below.


/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
    ./ \                                      #  The searching function to be performed 
    -q "CS(=O)(=O)CCNCc1ccccc1"                            #  Parameter for, the input query for searching


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.


The searching function used by qsub. The core function of is mol2img_trial which is located in "/nfs/home/jizhou/work/Projects/smi_index/dotmatics/". mol2img_trial generates index for the smi file to speedup searching. requires an input query for searching. An example is shown below

-q "CS(=O)(=O)CCNCc1ccccc1"