This post contains some bash code-snippet to make my daily work easier.

Loop through array

In case of looping through an continous list of number:

#!/bin/bash
for i in {1..100}
do
    # DO SOMETHING
done

If the list to loop is not continous, used the following form:

#!/bin/bash
arr=( 3 4 9 10)
for i in "${arr[@]}"
do
    echo $i       
    #DONE SOMETHING HERE
done

Note that arr definition is without whitespace.

Counting number of lines in file

Sometime, after perform a long analysis of many simulations. We want to make sure if the analysis is done automatically, instead of looking into single file one-by-one, we can use bash script to do so.

#!/bin/bash
for i in {1..100}
do
        #echo "$i"
        nl=$(wc -l < $i/G_traj_${i}.dat)
        if [ $nl -eq 400008 ]; then
                echo "traj $i :  $nl --- DONE"
        else
                echo "traj $i :  $nl --- Has not been DONE"
        fi

done

In this example, we loop through all simulations (1 to 100) and use command: wc -l < $i/G_traj_${i}.dat to count the number of lines in file. we assign the output from this command to nl variable by packing previous command by $(command)

Search and replace in file

#!/bin/bash
cur_dir=`pwd`
for i in {1..100}
do
        if [ -f "/net/people/plgqvuvan/plggligroup/qvuvan/10proj/synthesize/cat3/wt/$i/traj/1/prot_l213_dissociation_final.cor" ]; then
                echo "copy cor and vel file for run $i"
                rm -rf $i && mkdir $i
                cp /net/people/plgqvuvan/plggligroup/qvuvan/10proj/synthesize/cat3/wt/$i/traj/1/prot_l213_dissociation_final.cor $i/
                cp /net/people/plgqvuvan/plggligroup/qvuvan/10proj/synthesize/cat3/wt/$i/traj/1/prot_l213_dissociation_final.vel $i/
                cp template/* $i/
                sed "s/SETINDEX/${i}/g" -i ${i}/job_plgrid_gpu.sh
                sed "s/SETINDEX/${i}/g" -i ${i}/control.cntrl
        else
                echo "simulation $i is not finished"
        fi
done

line 5: check if file prot_l213_dissociation_final.cor in specified directory existed. If yes, then run the code block.
line 11-12: sed command used to search and replace pattern SETINDEX in file ${i}/job_plgrid_gpu.sh by value of variable $i

Sync data between local and cluster computer

#!/bin/bash
rsync -avzhP plgqvuvan@pro.cyfronet.pl:/net/people/plgqvuvan/plggligroup/qvuvan/10proj/post_trans/cat3/stride_by5/combine_trajs/ post_trans/

The above command sync the data from cluster pro.cyfronet.pl to local computer. To exclude files (e.g xtc file), add this: –exclude=*.xtc