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Hi April,
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<div class="">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.</div>
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<div class="">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. </div>
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<div class="">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 <a href="https://www.fieldtriptoolbox.org/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing/" class="">https://www.fieldtriptoolbox.org/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing/</a> ,
<a href="https://www.fieldtriptoolbox.org/faq/how_to_get_started_with_distributed_computing_using_qsub/" class="">
https://www.fieldtriptoolbox.org/faq/how_to_get_started_with_distributed_computing_using_qsub/</a> and links therein</div>
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<div>Best wishes,</div>
<div>Jan-Mathijs</div>
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<div class="">On 12 Feb 2022, at 01:03, April Luo via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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<div dir="ltr" class="">Hello,
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<div class="">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!</div>
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<div class="">My matlab version on both my local computer and HPC cluster is 2021a and my fieldtrip version is 20210501.</div>
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<div class="">Best,</div>
<div class="">April Luo</div>
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