probtrackx2 very slow and runs serially instead of in parallel

McIntosh-Lab / tvb-ukbb

TVB-UKBB Pipeline: TheVirtualBrain implementation of the UK Biobank pipeline

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probtrackx2 very slow and runs serially instead of in parallel #70

Closed noahfl closed 3 years ago

noahfl commented 3 years ago

Right now the only queue that supports probtrackx2 due to its size is bigmem_64. However bigmem_64 isn't accepting subjects in parallel and is super slow as a result. Will investigate

shen4brains commented 3 years ago

Parallelizing probtrackx is possible and likely necessary. See this post here for a solution: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;daca6637.1603

shen4brains commented 3 years ago

this can be modelled after the array job submission by bedpostx, where we create a .txt file of parallel probtrackx commands and use the -t flag in fsl_sub to submit it

shen4brains commented 3 years ago

parallelized tractography implemented in ADNI3 and PPMI branches

parallelization for Cam-CAN and master branches still needed

justinliuyuwang commented 3 years ago

master branch fixed with commit 6b9ace2617ddff82ad6e03c3371637fd821a7206 Cam_CAN branch to be fixed with merge with Cam-CAN_wQC where issue has been fixed with commit 27b0cca13aa28dbdee5e1805c7fce0f385dd9852