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The VirtualBox settings indicate you host machine has 4 real and 4 virtual cores with 16G of RAM.

You could try shutting down the VM, and then change the VirtualBox settings to give the VM 4 cores (instead of 2) and 12G of RAM (instead of 8G).  Then start the VM and try running your command again to see if performance improves maybe first with 2 jobs and then 4.   I would try not to run other applications on your host machine at this time.

- R.

On May 9, 2022, at 17:47, Joanna L Eckhardt <jeckhardt@health.ucsd.edu> wrote:

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Oops, I meant to reply all: 

Hi R ,

See below, I gave 8 GB and 2 CPU in settings.

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--
Joanna Eckhardt
Neurosciences Graduate Program
University of California, San Diego

Sent: Monday, May 9, 2022 2:41 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Joanna L Eckhardt <jeckhardt@health.ucsd.edu>
Subject: Re: [Freesurfer] Recon-all Freezes on Parallel
 
In the VirtualBox settings, did you give the VM both cores to use?

It would also be good to know much memory your machine has, and how much of that you gave to the VM in the VirtualBox settings.

- R.

On May 9, 2022, at 17:27, Joanna L Eckhardt <jeckhardt@health.ucsd.edu> wrote:

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Dear FreeSurfer Team, 

I have been trying to use the parallel command (following FreeSurfer tutorial) to run multiple subjects (Windows os running Ubuntu VM).

I only have 2 cores, so I have it set to 2 jobs instead of 8 as in the tutorial. When I use the code from the tutorial, there is an error with the .nii, and I assume it is because my files are .nii.gz.
developer@developer-VirtualBox:~/FreeSurfer/Cannabis_Reduced$ ls *.nii | parallel --jobs 3 recon-all -s {.} -i {} -all -qcache
ls: cannot access '*.nii': No such file or directory
So I changed the code to .gz with everything else the same, and FreeSurfer does nothing (it stalls/freezes). Is this just because my computer cannot handle the job? Is there anything else I can do to run parallel? If not, I can always just run 1 subject at a time, but I want to check and see if there is another way to get this to work. 

Thank you for your time!
Joanna
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