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I would look for the core file under /var/crash as close to the time to the command failure and see what it says. Signal 11 is a segmentation violation meaning invalid memory access. It could be that a VM on your machine does not have enough memory to run recon-all. Or I assume the 32G RAM listed below is the total physical RAM on the machine and the VM has some portion of that assigned to it. If you did not assign the VM say 16G-24G of RAM out of that 32G total, then it might be having a memory issue. You could try not running anything else on the machine, giving the VM 24G and that would leave 8G for the host machine. You could also try giving the VM 4 out of the 16 CPUs as well. - R. On Feb 6, 2024, at 00:39, Yp Ben <benyoupeng@gmail.com> wrote: External Email - Use Caution Hello FreeSurfer Developers,I'm want to run HCP T1W data of recon-all , but it always failed on step " WhitePreAparc lh", below is my run information:OS: Ubuntu 22.04.2 LTSMEM: 32GCPU: 16….Command terminated by signal 11...Check the core dump file under /var/crash...I use 3 different VMs to run the same sample with different freesurfer versions , 2 are 7.4.1 and another one is 7.2 , but always failed on this step , I don't know what's the reason cause this failed , can you please help to have a look ? Thanks a lot . _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hello there, Thanks for quickly response, due to email size limit ,I can't upload dump file via email , how can I provide my dump file ? Thanks.
fsbuild fsbuild@contbay.com 于2024年2月6日周二 14:33写道：
I would look for the core file under /var/crash as close to the time to the command failure and see what it says.
Signal 11 is a segmentation violation meaning invalid memory access. It could be that a VM on your machine does not have enough memory to run recon-all. Or I assume the 32G RAM listed below is the total physical RAM on the machine and the VM has some portion of that assigned to it. If you did not assign the VM say 16G-24G of RAM out of that 32G total, then it might be having a memory issue. You could try not running anything else on the machine, giving the VM 24G and that would leave 8G for the host machine. You could also try giving the VM 4 out of the 16 CPUs as well.
- R.
On Feb 6, 2024, at 00:39, Yp Ben benyoupeng@gmail.com wrote:
External Email - Use CautionHello FreeSurfer Developers,
I'm want to run HCP T1W data of recon-all , but it always failed on step " WhitePreAparc lh", below is my run information: OS: Ubuntu 22.04.2 LTS MEM: 32G CPU: 16 ….
Command terminated by signal 11 ... Check the core dump file under /var/crash ... I use 3 different VMs to run the same sample with different freesurfer versions , 2 are 7.4.1 and another one is 7.2 , but always failed on this step , I don't know what's the reason cause this failed , can you please help to have a look ? Thanks a lot . _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1qmLFE12eP5SRWEwkdnsUn16tH_GgBJOBbknqMeGTv8piaO...
freesurfer@nmr.mgh.harvard.edu
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fsbuild -
Yp Ben