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If your host machine has 32G of RAM, then it should work to give the VM 16G or perhaps even 24G of RAM. If most all swap space is in use, then it’s likely something is under-running or exhausting the available physical RAM. Some machines start to swap what’s in memory out to disk files when only 80% of RAM is in use. But disk I/O from loading swap files in/out of memory can cause the machine to slow down or thrash and never finish processing. With no consequential or RAM hungry applications running on the host, then the host should be able to essentially run idle with 8G of RAM leaving 24G to assign to the VM. - R.
On Oct 3, 2023, at 02:01, Pål Gunnar Larsson <pall@ous-hf.no> wrote: External Email - Use Caution Thank you for fast reply..The computer has 32Gb. The virtual machine has 8Gb. According to ‘top’ all is used, except 140Mb. Swap has 1Gb of which 780Mb is used. Does swapping use lots of CPU? It is 100% most of the time. Fra: fsbuild <fsbuild@contbay.com> Sendt: 3. oktober 2023 04:33Til: freesurfer@nmr.mgh.harvard.eduKopi: Pål Gunnar Larsson <pall@ous-hf.no>Emne: Re: [Freesurfer] Slow processing of large defect Not clear if "8G of RAM" below means 8G is assigned to the VM, or the host machine has 8G RAM total. Assuming the VM has ~8G assigned then the host should have 16-24G RAM total.It reads like the VM is thrashing, e.g., swapping out to disk due to lack of RAM - which can cause a crash. I would try running the VM on a host machine that can provide more RAM. So if the VM is currently running with 8G, then try doubling it to 16G (on a host with at least 24 or 32G RAM).- R.On 10/2/23 10:31, Pål Gunnar Larsson (pall@ous-hf.no) wrote: External Email - Use Caution Hello I am running FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10, having 8Gb of ram. I am running a child-MRI where I got a message about a large defect which would run slowly or crash. FS is still running after more than 10 days (70%-100% CPU use), but there are nothing written to disk for 10 days. It is working on retesselation of defect 162.Is there any reason to wait it out? Or will the results be unpredictable? Best Pål G. Larsson Ikke sensitiv _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1aeEAtzSDgvMg67gOnpL-fUlNHOFDsR1OYOQuJbl5mIkHQv... note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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OK. Did make a new setup with 16Gb. Restarted. Hope I can give you positive feedback tomorrow. Best Pål
Pål G. Larsson M.D., PhD. Senior Medical Officer Department of Neurosurgery Division of Surgery and Clinical Neuroscience
Oslo University Hospital Po.box 4950 Nydalen 0424 Oslo Norway Tel: (+47) 23074407 Mobile: (+47) 93429791 E-mail: pall@ous-hf.nomailto:pall@ous-hf.no
Ikke sensitiv
Fra: fsbuild fsbuild@contbay.com Sendt: 3. oktober 2023 08:29 Til: freesurfer@nmr.mgh.harvard.edu Kopi: Pål Gunnar Larsson pall@ous-hf.no Emne: Re: [Freesurfer] Slow processing of large defect
If your host machine has 32G of RAM, then it should work to give the VM 16G or perhaps even 24G of RAM.
If most all swap space is in use, then it’s likely something is under-running or exhausting the available physical RAM. Some machines start to swap what’s in memory out to disk files when only 80% of RAM is in use. But disk I/O from loading swap files in/out of memory can cause the machine to slow down or thrash and never finish processing. With no consequential or RAM hungry applications running on the host, then the host should be able to essentially run idle with 8G of RAM leaving 24G to assign to the VM.
- R.
On Oct 3, 2023, at 02:01, Pål Gunnar Larsson <pall@ous-hf.nomailto:pall@ous-hf.no> wrote:
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Thank you for fast reply. The computer has 32Gb. The virtual machine has 8Gb. According to ‘top’ all is used, except 140Mb. Swap has 1Gb of which 780Mb is used. Does swapping use lots of CPU? It is 100% most of the time.
Fra: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sendt: 3. oktober 2023 04:33 Til: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Kopi: Pål Gunnar Larsson <pall@ous-hf.nomailto:pall@ous-hf.no> Emne: Re: [Freesurfer] Slow processing of large defect
Not clear if "8G of RAM" below means 8G is assigned to the VM, or the host machine has 8G RAM total. Assuming the VM has ~8G assigned then the host should have 16-24G RAM total.
It reads like the VM is thrashing, e.g., swapping out to disk due to lack of RAM - which can cause a crash. I would try running the VM on a host machine that can provide more RAM. So if the VM is currently running with 8G, then try doubling it to 16G (on a host with at least 24 or 32G RAM)..
- R.
On 10/2/23 10:31, Pål Gunnar Larsson (pall@ous-hf.nomailto:pall@ous-hf.no) wrote: External Email - Use Caution Hello
I am running FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10, having 8Gb of ram.
I am running a child-MRI where I got a message about a large defect which would run slowly or crash. FS is still running after more than 10 days (70%-100% CPU use), but there are nothing written to disk for 10 days. It is working on retesselation of defect 162. Is there any reason to wait it out? Or will the results be unpredictable?
Best
Pål G. Larsson
Ikke sensitiv
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On 10/3/2023 5:23 AM, Pål Gunnar Larsson wrote:
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OK.
Did make a new setup with 16Gb. Restarted. Hope I can give you positive feedback tomorrow.
Best
Pål
Pål G. Larsson M.D., PhD.
Senior Medical Officer
Department of Neurosurgery
Division of Surgery and Clinical Neuroscience
Oslo University Hospital
Po.box 4950 Nydalen
0424 Oslo
Norway
Tel: (+47) 23074407
Mobile: (+47) 93429791
E-mail: pall@ous-hf.no
Ikke sensitiv
*Fra:*fsbuild fsbuild@contbay.com *Sendt:* 3. oktober 2023 08:29 *Til:* freesurfer@nmr.mgh.harvard.edu *Kopi:* Pål Gunnar Larsson pall@ous-hf.no *Emne:* Re: [Freesurfer] Slow processing of large defect
If your host machine has 32G of RAM, then it should work to give the VM 16G or perhaps even 24G of RAM.
If most all swap space is in use, then it’s likely something is under-running or exhausting the available physical RAM. Some machines start to swap what’s in memory out to disk files when only 80% of RAM is in use. But disk I/O from loading swap files in/out of memory can cause the machine to slow down or thrash and never finish processing. With no consequential or RAM hungry applications running on the host, then the host should be able to essentially run idle with 8G of RAM leaving 24G to assign to the VM.
R.
On Oct 3, 2023, at 02:01, Pål Gunnar Larsson pall@ous-hf.no wrote:
* External Email - Use Caution *
Thank you for fast reply.
The computer has 32Gb. The virtual machine has 8Gb. According to ‘top’ all is used, except 140Mb. Swap has 1Gb of which 780Mb is used. Does swapping use lots of CPU? It is 100% most of the time.
*Fra:*fsbuild <fsbuild@contbay.com mailto:fsbuild@contbay.com> *Sendt:*3. oktober 2023 04:33 *Til:*freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Kopi:*Pål Gunnar Larsson <pall@ous-hf.no mailto:pall@ous-hf.no> *Emne:*Re: [Freesurfer] Slow processing of large defect
Not clear if "8G of RAM" below means 8G is assigned to the VM, or the host machine has 8G RAM total. Assuming the VM has ~8G assigned then the host should have 16-24G RAM total.
It reads like the VM is thrashing, e.g., swapping out to disk due to lack of RAM - which can cause a crash. I would try running the VM on a host machine that can provide more RAM. So if the VM is currently running with 8G, then try doubling it to 16G (on a host with at least 24 or 32G RAM)..
- R.
On 10/2/23 10:31, Pål Gunnar Larsson (pall@ous-hf.no mailto:pall@ous-hf.no) wrote:
* External Email - Use Caution * Hello I am running FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10, having 8Gb of ram. I am running a child-MRI where I got a message about a large defect which would run slowly or crash. FS is still running after more than 10 days (70%-100% CPU use), but there are nothing written to disk for 10 days. It is working on retesselation of defect 162. Is there any reason to wait it out? Or will the results be unpredictable? Best Pål G. Larsson Ikke sensitiv _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard..edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be*https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/16EgItWPYDfCVSwUZzDPgEfWizghsFer00dulSsyOBjnylWrzmN2ogMGoAAn2yo66o8yDSx3bIxO3yqrBnQpJwmjp0rkKZqXMMRzodJ4exo9BHkNkZS_7esrJVV0IsbF_Ndpl4rsJnRXYoH3RnQevzZXnnuD_Y1wSo-iyXVH1UHl7oTRfiVZnwSZX7P_cth9wf6hU2aQoY9I6qGSx4U-lDd8hPCn0hqkqU2t43IbrYJq3T4I6o2MlhgsC6EV26ct6q_tTBBalfmUIlv-Uh5G117DrAZnOq4NxA82lNKbOHAzLQC5rgAsla6AgblwXEdb7LZWh88qP2hMDbeuBKqHXJg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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