Usage

mzMine can be run in a batch mode according to mzMine Manual by calling startMZmine with a single argument corresponding to a saved batch script generated within the GUI.

We provide an alternate startMZmine script that correctly sets the HEAP memory based on either the HPC_MZMINE_MEM environment variable or, if that variable if absent, based on the total amount of requested memory within a job. Also it appears to be necessary to simulate a virtual X11 environment for mzMine to run in batch mode.

Note that HiPerGator2 nodes are diskless, so /tmp directory that mzMine uses by default for its temporary files cannot be used. See Temporary Directories for details on how to set $TMPDIR variable that points to a directory in your /blue space.

If you need to run mzMine GUI, you should use OOD and the HiPerGator Desktop application.