Tips and Tricks

Configuring automatic reservation cancellation

If you use the BioHPC reservation system or SLURM, it helps others if at the end of a long-running job, your reservation is cancelled as soon as possible. One way to do this is to add the following to the scripts you are running:

Stata

// Use the code below at the bottom of the Stata "main" or 
// "master" script to automatically sign out 

shell /programs/bin/labutils/endres.pl 

R

# Add to end of main or last script.
system("/programs/bin/labutils/endres.pl")

Matlab

%Use code below at end of MATLAB main script, or last script, to automatically sign out

system("/programs/bin/labutils/endres.pl")

Python

# Use code below at bottom of Python/Anaconda script 
# to automatically sign out

import os

os.system("/programs/bin/labutils/endres.pl")

Bash

#Use the code below at the bottom of the bash "main" or 
# "master" script to automatically sign out 
/programs/bin/labutils/endres.pl 

Unzipping large ZIP files fails

In some cases, unzipping large ZIP files (larger than 2GB) may fail (although the local unzip command has been compiled to handle large files).

error: invalid zip file with overlapped components (possible zip bomb)

If this is detected, you need to use a 64-bit version of a decompression program. This may vary by Linux host.

<literal>7z</literal>

Instead of zip, use 7z as follows:

FILENAME=something
/programs/bin/util/7z x -O${FILENAME} ${FILENAME}.zip

(which is the equivalent to the zip command zip -n ${FILENAME} -d ${FILENAME}). The first option (-O) is an upper-case letter O`, not zero.

Others

Other options include using jar, if available.