Do you run ‘recon-all -parallel’ or ‘recon-all –threads <nthreads>’?
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Horn, Mitchell Jacob Sent: Friday, February 23, 2024 12:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline Bottom line is that when I run any FreeSurfer version 7+ in parallel on COS8 I get different results each time. Thanks, Mitch From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Douglas N. Greve Sent: Friday, February 23, 2024 11:03 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline So, is the bottom line that when you run 7.4.1 on COS8 in parallel that you get (slightly) different results each time? On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote: Hi FS Devs, I’m experiencing unreproducible thickness results when running any 7+ version with parallelization enabled. Running recon-all without parallelization produces consistent thickness results. I’m running this in AlmaLinux8 (a library-equivalent downstream OS to CentOS8). I’m attaching a table (table1) of 12 recons with bert: 1. 3 parallelized with CentOS8-compiled 7.4.1 2. 3 non-parallelized with CentOS8-compiled 7.4.1 3. 3 parallelized with CentOS7-compiled 7.4.1 4. 3 non-parallelized with CentOS7-compiled 7.4.1 I suspected the downstream CentOS8 libm was the culprit (because of testing I did this last 2023 summer). I ran 3 more recons parallelized with the CentOS7-compiled 7.4.1, but before running the recon-all command, set LD_PRELOAD to a copy of the CentOS7 libm libraries. The thickness results were then consistent, see the second table below (table2). I could not run this experiment on the CentOS8-compiled version, as that one is obviously not backward compatible with CentOS7 libm. As a quick test of the OS-dependency, I submitted 3 parallel recons on MLSC with 7.3.3. Each reported different thickness. See table 3 (table3). I’m asking if you can please confirm whether running any 7.+ version with parallelization is generating reproducible results for you in CentOS8 (or equivalent)? P.S. - I tested 6.0 (CentOS6-compilation) with parallelization, and the results were consistent. Best, Mitch _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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