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Dear Freesurfer developers and users,
Has anyone had experience running Freesurfer on Linux VM on Google Cloud Platform? I have a question about runtime of recon-all -all. The specs of VM on GCP as follows, Linux CentOS 6, 16 CPU(Intel(R) Xeon(R) @ 2.50GHz) with 60 G memory I installed Freesurfer v 6.0.0 and run recon-all -all -parallel -openmp num No matter what number I put (6,8,12,16 after openmp), the recon-all runtime of a single subject ranges 6-7 hours. It's just disappointing to compare to my own desktop. My own Desktop is Mac Pro (3.7 GHz quad-core intel xeon E5, 16G memory). The recon-all runtime (Freesurfer version 5.3.0, no parallel) for a single subject is usually 7~8 hours. Is this a reasonable runtime given the setting of VM? Only 1-2 hour shorter than my Mac Pro?? Or is there any configuration of VM I should pay attention to set up?
Thanks, Yi-Fang Chuang ᐧ ᐧ
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I do not have experience with running on Google Cloud, but from what I know, the common way is to run FreeSurfer in parallel over many subjects instead of using openmp to speed up the process for a single subject.
So your desktop should run 4 subjects in parallel, and the cloud instance 16. Not that bad.
Tim
On February 9, 2019 at 4:33 PM Yi-Fang Chuang chuangy@ym.edu.tw wrote:
External Email - Use CautionDear Freesurfer developers and users,
Has anyone had experience running Freesurfer on Linux VM on Google Cloud Platform? I have a question about runtime of recon-all -all. The specs of VM on GCP as follows, Linux CentOS 6, 16 CPU(Intel(R) Xeon(R) @ 2.50GHz) with 60 G memory I installed Freesurfer v 6.0.0 and run recon-all -all -parallel -openmp num No matter what number I put (6,8,12,16 after openmp), the recon-all runtime of a single subject ranges 6-7 hours. It's just disappointing to compare to my own desktop. My own Desktop is Mac Pro (3.7 GHz quad-core intel xeon E5, 16G memory). The recon-all runtime (Freesurfer version 5.3.0, no parallel) for a single subject is usually 7~8 hours. Is this a reasonable runtime given the setting of VM? Only 1-2 hour shorter than my Mac Pro?? Or is there any configuration of VM I should pay attention to set up?
Thanks, Yi-Fang Chuang ᐧ ᐧ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, but -openmp N should give significant imrpovements up to about N=4
On Sat, 9 Feb 2019, Tim Schäfer wrote:
External Email - Use CautionI do not have experience with running on Google Cloud, but from what I know, the common way is to run FreeSurfer in parallel over many subjects instead of using openmp to speed up the process for a single subject.
So your desktop should run 4 subjects in parallel, and the cloud instance 16. Not that bad.
Tim
On February 9, 2019 at 4:33 PM Yi-Fang Chuang chuangy@ym.edu.tw wrote:
External Email - Use CautionDear Freesurfer developers and users,
Has anyone had experience running Freesurfer on Linux VM on Google Cloud Platform? I have a question about runtime of recon-all -all. The specs of VM on GCP as follows, Linux CentOS 6, 16 CPU(Intel(R) Xeon(R) @ 2.50GHz) with 60 G memory I installed Freesurfer v 6.0.0 and run recon-all -all -parallel -openmp num No matter what number I put (6,8,12,16 after openmp), the recon-all runtime of a single subject ranges 6-7 hours. It's just disappointing to compare to my own desktop. My own Desktop is Mac Pro (3.7 GHz quad-core intel xeon E5, 16G memory). The recon-all runtime (Freesurfer version 5.3.0, no parallel) for a single subject is usually 7~8 hours. Is this a reasonable runtime given the setting of VM? Only 1-2 hour shorter than my Mac Pro?? Or is there any configuration of VM I should pay attention to set up?
Thanks, Yi-Fang Chuang ᐧ ᐧ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks~ I was asking this because the release note of v6.0.0 said the recon-all -all runtime of new-ish workstation is just under 3 hours!!! That makes me wonder if I missed something or did not set up the VM right.
Yi-Fang
Bruce Fischl fischl@nmr.mgh.harvard.edu 於 2019年2月10日 週日 上午9:21寫道：
yes, but -openmp N should give significant imrpovements up to about N=4
On Sat, 9 Feb 2019, Tim Schäfer wrote:
External Email - Use CautionI do not have experience with running on Google Cloud, but from what I
know, the common way is to run FreeSurfer in parallel over many subjects instead of using openmp to speed up the process for a single subject.
So your desktop should run 4 subjects in parallel, and the cloud
instance 16. Not that bad.
Tim
On February 9, 2019 at 4:33 PM Yi-Fang Chuang chuangy@ym.edu.tw
wrote:
External Email - Use CautionDear Freesurfer developers and users,
Has anyone had experience running Freesurfer on Linux VM on Google Cloud Platform? I have a question about runtime of recon-all -all. The specs of VM on GCP as follows, Linux CentOS 6, 16 CPU(Intel(R) Xeon(R) @ 2.50GHz) with 60 G memory I installed Freesurfer v 6.0.0 and run recon-all -all -parallel -openmp
num
No matter what number I put (6,8,12,16 after openmp), the recon-all
runtime
of a single subject ranges 6-7 hours. It's just disappointing to compare to my own desktop. My own Desktop is Mac Pro (3.7 GHz quad-core intel xeon E5, 16G memory). The recon-all runtime (Freesurfer version 5.3.0, no parallel) for a
single
subject is usually 7~8 hours. Is this a reasonable runtime given the setting of VM? Only 1-2 hour shorter than my Mac Pro?? Or is there any configuration of VM I should pay attention to set up?
Thanks, Yi-Fang Chuang ᐧ ᐧ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, that is correct, we see those runtimes commonly with openmp. Someone else will have to answer the VM question though.
Bruce
On Sun, 10 Feb 2019, Yi-Fang Chuang wrote:
External Email - Use Caution
Thanks~ I was asking this because the release note of v6.0.0 said the recon-all -all runtime of new-ish workstation is just under 3 hours!!! That makes me wonder if I missed something or did not set up the VM right.
Yi-Fang
Bruce Fischl fischl@nmr.mgh.harvard.edu 於 2019年2月10日 週日 上午9:21寫道： yes, but -openmp N should give significant imrpovements up to about N=4
On Sat, 9 Feb 2019, Tim Schäfer wrote: > External Email - Use Caution > > I do not have experience with running on Google Cloud, but from what I know, the common way is to run FreeSurfer in parallel over many subjects instead of using openmp to speed up the process for a single subject. > > So your desktop should run 4 subjects in parallel, and the cloud instance 16. Not that bad. > > Tim > >> On February 9, 2019 at 4:33 PM Yi-Fang Chuang <chuangy@ym.edu.tw> wrote: >> >> >> External Email - Use Caution >> >> Dear Freesurfer developers and users, >> >> Has anyone had experience running Freesurfer on Linux VM on Google Cloud >> Platform? >> I have a question about runtime of recon-all -all. >> The specs of VM on GCP as follows, >> Linux CentOS 6, 16 CPU(Intel(R) Xeon(R) @ 2.50GHz) with 60 G memory >> I installed Freesurfer v 6.0.0 and run recon-all -all -parallel -openmp num >> No matter what number I put (6,8,12,16 after openmp), the recon-all runtime >> of a single subject ranges 6-7 hours. >> It's just disappointing to compare to my own desktop. >> My own Desktop is Mac Pro (3.7 GHz quad-core intel xeon E5, 16G memory). >> The recon-all runtime (Freesurfer version 5.3.0, no parallel) for a single >> subject is usually 7~8 hours. >> Is this a reasonable runtime given the setting of VM? Only 1-2 hour >> shorter than my Mac Pro?? >> Or is there any configuration of VM I should pay attention to set up? >> >> Thanks, >> Yi-Fang Chuang >> ᐧ >> ᐧ >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Yi-Fang Chuang (莊宜芳), M.D., Ph.D. Assistant Professor Institute of Public Health, National Yang-Ming University No. 155, Sec. 2, Linong Street, Taipei, 11221 Taiwan (R.O.C) +886-2-28267000#7981 chuangy@ym.edu.tw Attending physician Department of Psychiatry, Far Eastern Memorial Hospital No.21, Sec. 2, Nanya S. Rd,. Banqiao Dist., New Taipei City 220, Taiwan (R.O.C) Special Volunteer NIA-Laboratory of Behavioral Neuroscience-Unit of Clinical and Translational Neuroscience BRC-Biomedical Research Center, 04C316 251 Bayview Blvd. Baltimore, MD chuangy@mail.nih.gov [t?sender=aZ3JhY2UueWlmYW5nY2h1YW5nQGdtYWlsLmNvbQ%3D%3D&type=zerocontent&guid=5cf2b1c3-2adc-4f8d-8d03-170b683d51a 5] ᐧ
freesurfer@nmr.mgh.harvard.edu
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