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

Install package on Roar cluster without Root permission

Roar cluster runs RedHat Linux version 8.9

To install rpm file without root permission: rpm2cpio the_file_name.rpm | cpio -idv

Example on install ATOM Code editor:

1. `rpm2cpio atom.x86_64.rpm | cpio -idv`
This will extract rpm file to folder name ./usr . Move this folder to desired folder, e.g ~/programs:
2. `mv usr ~/programs/Atom`
3. Create Desktop link to application:
    Go to ~/.local/share/applications/
    create a desktop file: `Atom.desktop` with content:
    ```
    [Desktop Entry]
    Name=Atom Editor
    Comment=Code Editing. Redefined.
    GenericName=Text Editor
    Exec=/storage/home/qzv5006/programs/Atom/bin/atom %F
    Icon=/storage/home/qzv5006/programs/Atom/share/icons/hicolor/32x32/apps/atom.png
    Type=Application
    StartupNotify=false
    StartupWMClass=Code
    Categories=TextEditor;Development;IDE;
    MimeType=application/x-code-workspace;
    Actions=new-empty-window;
    Keywords=vscode;
    
    [Desktop Action new-empty-window]
    Name=New Empty Window
    Name[de]=Neues leeres Fenster
    Name[es]=Nueva ventana vacÃa
    Name[fr]=Nouvelle fenÃªtre vide
    Name[it]=Nuova finestra vuota
    Name[ja]=\u65b0\u3057\u3044\u7a7a\u306e\u30a6\u30a3\u30f3\u30c9\u30a6
    Name[ko]=\uc0c8 \ube48 \ucc3d
    Name[ru]=\u041d\u043e\u0432\u043e\u0435 \u043f\u0443\u0441\u0442\u043e\u0435 \u043e\u043a\u043d\u043e
    Name[zh_CN]=\u65b0\u5efa\u7a7a\u7a97\u53e3
    Name[zh_TW]=\u958b\u65b0\u7a7a\u8996\u7a97
    Exec=/storage/home/qzv5006/programs/Atom/bin/atom --new-window %F
    Icon=/storage/home/qzv5006/programs/Atom/share/icons/hicolor/32x32/apps/atom.png
    ```
4. Give executable permission for Desktop file: `chmod +x Atom.desktop`