From 10a54f7b22174909956385dcd386e0d43e704dd0 Mon Sep 17 00:00:00 2001 From: Steffen Bollmann Date: Fri, 8 Nov 2024 11:15:11 +1000 Subject: [PATCH] added mriqc workaround --- content/en/docs/Getting Started/Hosted/bunya.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/content/en/docs/Getting Started/Hosted/bunya.md b/content/en/docs/Getting Started/Hosted/bunya.md index 0e72b9fdf..e13493fcf 100644 --- a/content/en/docs/Getting Started/Hosted/bunya.md +++ b/content/en/docs/Getting Started/Hosted/bunya.md @@ -8,7 +8,7 @@ description: > -Neurodesk is already installed at UQ's Bunya supercomputer. To access neurodesk tools you need to be in an interactive job (so either start a virtual desktop via Open On-Demand: https://bunya-ondemand.rcc.uq.edu.au/pun/sys/dashboard) or run: +Neurodesk is installed at the University of Queensland's supercomputer "Bunya". To access neurodesk tools you need to be in an interactive job (so either start a virtual desktop via Open On-Demand: https://bunya-ondemand.rcc.uq.edu.au/pun/sys/dashboard) or run: ``` salloc --nodes=1 --ntasks-per-node=1 --cpus-per-task=1 --mem=5G --job-name=TinyInteractive --time=01:00:00 --partition=debug --account=REPLACE_THIS_WITH_YOUR_AccountString srun --export=PATH,TERM,HOME,LANG --pty /bin/bash -l ``` @@ -35,4 +35,9 @@ If you want to use GUI applications (fsleyes, afni, suma, ...) you need to overw export TMPDIR=/tmp ``` +NOTE: MRIQC has its $HOME variable hardcoded to be /home/mriqc. This leads to problems on Bunya. A workaround is to run this before mriqc: +``` +export neurodesk_singularity_opts="--home $HOME:/home" +``` + If you are missing an application, please contact mail.neurodesk@gmail.com and ask for the neurodesk installation to be updated on Bunya :)