Can you try it with -threads instead? We don't typically use -parallel
On 2/23/2024 2:44 PM, Horn, Mitchell Jacob wrote:
This is all with ‘recon-all -parallel’
Thanks,
Mitch
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
*Sent:* Friday, February 23, 2024 2:30 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] consistency in recon-all parallel pipeline
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
<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
*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
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