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Since you are running in VirtualBox, you should try clicking on the SETTINGS wheel in the VirtualBox application window, then in the pop-up window click on SYSTEM, and look at the amount off memory you have allocated to the VM. I would try and increase the amount to 10 - 16G of RAM from the system, but also avoid giving it much more than 1/2 of the total memory available on your host system. VM’s sometimes will not start up if you give them too much RAM. Similarly, for the number of processors you allocate from the host system, i.e., you might not want to give it more than 1/2 depending upon what else is going on with the machine besides running VirtualBox. See the attached screenshot..
- R.
On Mar 8, 2021, at 10:25, Fischl, Bruce <BFISCHL@MGH.HARVARD.EDU> wrote:Hi Raquel The log says: Command terminated by signal 9 Which is a message from the Linux scheduler, and usually means you ran out of ram. It looks like you have 5G on that machine and some of it was in use at the time. Can you find a machine with more ram to try it on? Or free up the memory before running recon-all? CheersBruce From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Gool, Raquel van (Stud. FPN / Alumni FPN)Sent: Monday, March 8, 2021 9:26 AMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] mris_sphere error: terminated by signal 9 External Email - Use Caution Dear FreeSurfer experts, I'm attempting to use recon-all on my subjects and I have one of my subjects exit with errors after it is terminated by signal 9 during -sphere of autorecon3. I tried rerunning this particular step with command recon-all -autorecon3 -subjid subj07 -sphere. Unfortunately mris_sphere keeps being terminated. I experience this exact same problem with another one of my other subjects, whereas the rest of my subjects manage to finish recon-all. I use freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b on a virtual machine (VirtualBox) on my windows computer. Linux developer-VirtualBox 5.4.0-65-generic #73~18..04.1-Ubuntu SMP Tue Jan 19 09:02:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Any thoughts on how to troubleshoot this? Thanks a lot. Regards, _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B
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Hi,
Thank you for your advice. ?I have indeed already allocated as much memory as possible to the VM. I did manage to finish recon-all for another subject overnight, yet still not the subject that got terminated at this step.
I have now updated all software, rebooted the VM and freed up as much RAM as possible. I am currently running autorecon3 again for this subject. If this does not work out I will try a machine with more RAM. Thank you!
Best,
Raquel
________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens fsbuild fsbuild@contbay.com Verzonden: maandag 8 maart 2021 21:04 Aan: freesurfer@nmr.mgh.harvard.edu CC: Gool, Raquel van (Stud. FPN / Alumni FPN) Onderwerp: Re: [Freesurfer] mris_sphere error: terminated by signal 9
External Email - Use Caution
Since you are running in VirtualBox, you should try clicking on the SETTINGS wheel in the VirtualBox application window, then in the pop-up window click on SYSTEM, and look at the amount off memory you have allocated to the VM. I would try and increase the amount to 10 - 16G of RAM from the system, but also avoid giving it much more than 1/2 of the total memory available on your host system. VM's sometimes will not start up if you give them too much RAM. Similarly, for the number of processors you allocate from the host system, i.e., you might not want to give it more than 1/2 depending upon what else is going on with the machine besides running VirtualBox. See the attached screenshot.
- R.
On Mar 8, 2021, at 10:25, Fischl, Bruce BFISCHL@MGH.HARVARD.EDU wrote:
Hi Raquel
The log says:
Command terminated by signal 9
Which is a message from the Linux scheduler, and usually means you ran out of ram. It looks like you have 5G on that machine and some of it was in use at the time. Can you find a machine with more ram to try it on? Or free up the memory before running recon-all?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Gool, Raquel van (Stud. FPN / Alumni FPN) Sent: Monday, March 8, 2021 9:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_sphere error: terminated by signal 9
External Email - Use Caution
Dear FreeSurfer experts,
I'm attempting to use recon-all on my subjects and I have one of my subjects exit with errors after it is terminated by signal 9 during -sphere of autorecon3.
I tried rerunning this particular step with command recon-all -autorecon3 -subjid subj07 -sphere. Unfortunately mris_sphere keeps being terminated. I experience this exact same problem with another one of my other subjects, whereas the rest of my subjects manage to finish recon-all.
I use freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b on a virtual machine (VirtualBox) on my windows computer. Linux developer-VirtualBox 5.4.0-65-generic #73~18.04.1-Ubuntu SMP Tue Jan 19 09:02:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Any thoughts on how to troubleshoot this? Thanks a lot.
Regards,?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14STtTLvto_DST-Dhox6bOQFWT38XGq3Uj4S5Tv7MZIWUPK...
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freesurfer@nmr.mgh.harvard.edu
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Gool, Raquel van (Stud. FPN / Alumni FPN)