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 <fis...@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 <chua...@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
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--
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
chua...@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
chua...@mail.nih.gov
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