End of line (EOL)

Different operating systems uses different special caracters to indicate EOL. You can read about it and the issues with it here. If you edit a file in Windows of Mac before transferring it to the cluster (or any linux system), you have to convert the EOL. There are certain editors which can help you in both identifying the EOL and convert the file, e.g.: Notepad++.

On Linux you can use these commands:

  • to identify EOL (it prints out the content of the text file while showing the special characters, such as EOL):
    cat -e <file>
    • for a Linux file: some text$
    • for a Windows file: some text^M$
    • for a Mac file: some text^M
  • to convert EOL:
    /usr/local/apps/psycapps/bin/dos2unix -n <Windows file> <new file>
    /usr/local/apps/psycapps/bin/mac2unix -n <Mac file> <new file>

Configurator wrappers

If you want to use programs such as FSL, and FreeSurfer in your job, you need to configure them in your main script by adding the corresponding configurator wrapper (see Software) and use -V switch for qsub (see How to submit jobs (linux)). If your main script uses arguments, then you have to specify the version or use “latest”. Use

source <configurator wrapper> help

to see available versions.


Where are the backups?

Backups of every storage spaces (/home, /MRIWork, /MRIRaw, /MRIArchive, /usr/local/apps) are created on a daily bases at 0.10am and kept for 30 days. They are available under <storage space>/.snapshot/daily.YYYY-MM-DD_0010 (e.g. /MRIWork/.snapshot/daily.2018-07-01_0010)



extension “GLX” missing on display (or similar)

Some applications (e.g. fsleyes, freeview) requires OpenGL. It cannot be loaded automatically but via vglrun, so these programs have to be executed in a follwing way:

vglrun <command/script to run>


OpenGL rendering in MATLAB is slow and/or advanced functions are not supperted even when started via vglrun

MATLAB considers software-emulated OpenGL as default, which is not as powerfull as hardware-based. Our login node psyclogin has a dedicated GPU, therefore you can use hardware-based OpenGL. To force MATLAB to use it, you have to call it in a following way:

vglrun matlab -nosoftwareopengl

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