External Email - Use Caution Hi R,
Unfortunately, those changes did not work. It looks like it might just be too much for my computer to handle because the entire VM system slows down completely when trying to run the parallel command, and after an hour nothing new has appeared under the command. I will stick to 1 subject at a time if there is nothing else I can do (other than get a better computer!) Thank you for your help! Joanna ________________________________ From: fsbuild <[email protected]> Sent: Monday, May 9, 2022 4:00 PM To: [email protected] <[email protected]> Cc: Joanna L Eckhardt <[email protected]> Subject: Re: [Freesurfer] Recon-all Freezes on Parallel 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 <[email protected]> wrote: External Email - Use Caution Oops, I meant to reply all: Hi R , See below, I gave 8 GB and 2 CPU in settings. <image.png> <image.png> -- Joanna Eckhardt Neurosciences Graduate Program University of California, San Diego ________________________________ Sent: Monday, May 9, 2022 2:41 PM To: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> Cc: Joanna L Eckhardt <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> wrote: External Email - Use Caution 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! 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