Dear Gert,
It is definitely possible to run SPM on a cluster. From the rest of your
email, I understand the main issue is the absence of MATLAB on the
cluster you have access to?
If so, you have multiple options depending on what else is available on
the cluster or what you would be able to install:
* If Preprocessingsteponehpc.m is a single script (not a function) and
MATLAB Runtime R2010a is available on the cluster (or can be installed)
then you can use the SPM Standalone:
https://www.fil.ion.ucl.ac.uk/spm/software/download/
https://en.wikibooks.org/wiki/SPM/Standalone#Usage
./run_spm12.sh /path/to/MCR/ script Preprocessingsteponehpc.m
I can also give you a link to a version compatible with MATLAB Runtime
R2019b.
* If Preprocessingsteponehpc.m is or relies on extra functions that are
not part of SPM or you want to use a specific version of the MATLAB
Runtime because that's what has been installed by the admins on the
cluster, then use spm_make_standalone to compile a version yourself
(copy all your files somewhere within the SPM directory):
https://github.com/spm/spm12/blob/master/config/spm_make_standalone.m
and use the command line:
./run_spm12.sh /path/to/MCR/ function Preprocessingsteponehpc
* If Singularity is available on the cluster and
Preprocessingsteponehpc.m is a single script (as in item 1), then you
can use this image:
https://github.com/spm/spm-docker
singularity pull oras://ghcr.io/spm/spm-docker:matlab
./spm-docker_matlab.sif script Preprocessingsteponehpc.m
(this is fairly recent - names might change)
Let us know which situation you're in and I can expand on the
corresponding option if necessary.
Best regards,
Guillaume.
On 31/08/2021 15:32, Gert Vanhollebeke wrote:
> Hello Everybody,
>
> I am trying to run some SPM scripts on a supercomputer/cluster, but have
> some troubles getting it working. I saw on this website (Ohio
> supercomputer
> center: https://www.osc.edu/resources/available_software/software_list/matlab/spm
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.osc.edu%2Fresources%2Favailable_software%2Fsoftware_list%2Fmatlab%2Fspm&data=04%7C01%7Cg.flandin%40UCL.AC.UK%7C39b2a982fdb8422caeac08d96c8c5412%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637660172947099105%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Ndr82oQXi78hq1QK7liJXJifSV%2FxME8P5ubIcYRHhco%3D&reserved=0>)
> that spm is available, so it should be possible.
>
> I think the main problem is that I need to compile my batch script,
> which gives some problems sadly. I am currently using the /mcc/ command
> (link: https://www.mathworks.com/help/compiler/mcc.html
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mathworks.com%2Fhelp%2Fcompiler%2Fmcc.html&data=04%7C01%7Cg.flandin%40UCL.AC.UK%7C39b2a982fdb8422caeac08d96c8c5412%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637660172947109069%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=1z8AJPFgF%2BUh1QYCDgHy%2F83LPpqoAha15%2F5wMDq59Kc%3D&reserved=0>)
> to compile my script, the whole command is the following: mcc -mv
> Preprocessingsteponehpc.m -a '/location_to_spm12_folder' -I
> '/location_of_dataset'
>
> This however does not work. My question is thus the following: does
> anybody have experience regarding running SPM on a supercomputer/cluster
> and is willing to help me out? Secondly, is there a walktrough/tutorial
> online for this?
>
> Thanks in advance for any answer!
>
> Met vriendelijke groeten, with regards
>
> Gert Vanhollebeke
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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