[FieldTrip] Question using fieldtrip on a HPC cluster

Schoffelen, J.M. (Jan Mathijs) janmathijs.schoffelen at donders.ru.nl
Mon Feb 14 08:47:26 CET 2022

Hi April,

I am privy to the details of the job management on your HPC cluster, so I can only guess a bit about what’s going on on your end.

My frame if reference is our local compute cluster. When I send off a matlab job to the cluster, this consists of an instruction to the job scheduler to start a (non-interactive) matlab session on one of the compute nodes, followed by the execution of a few matlab commands, the most relevant of which obviously is the analysis script/function that you want to have executed. Naively, the compute node on which the matlab session is started, does not necessarily ‘know’ about the path settings that the user may assume to have been specified. In other words, you may want to investigate whether this is the case for you.

Again, not inhibited by any knowledge on how you interact with the HPC-cluster, I think you might need to add some addpath(<path-to-fieldtrip>), followed by ft_defaults to you matlab m-file. Also, I would check with your local IT-support to get some idea how the job deployment works at your place. It could even be that the functions in fieldtrip/qsub might be a way forward for you. Please have a look at https://www.fieldtriptoolbox.org/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing/ , https://www.fieldtriptoolbox.org/faq/how_to_get_started_with_distributed_computing_using_qsub/ and links therein

Best wishes,

On 12 Feb 2022, at 01:03, April Luo via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:


I'm trying to run fieldtrip package on sEEG data on a HPC cluster, but when I was running ft_preprocessing function, it gave an error for ft_preamble init, saying 'Could not run %s - does not seem to exist, full_cmd,' I checked further and it seems like it's looking for ft_preamble_init.m file, I checked to make sure it's under /utilities/private, but it still gave this error. Running on a local matlab works. but I wanted to run on a HPC cluster because of the large datafile. Could you help me solve this issue? Thank you so much!

My matlab version on both my local computer and HPC cluster is 2021a and my fieldtrip version is 20210501.

April Luo
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