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Today's Topics:
- Re: reprocessing on FS4.0 takes much longer for some scans (Bruce Fischl)
- Re: reprocessing on FS4.0 takes much longer for some
scans
(Pedro Paulo Oliveira Jr)
- RE: reprocessing on FS4.0 takes much longer for some
scans
(Pedro Paulo Oliveira Jr)
- RE: reprocessing on FS4.0 takes much longer for some scans (Nicolas Cherbuin)
- RE: reprocessing on FS4.0 takes much longer for some scans (Bruce Fischl)
Message: 1 Date: Sun, 11 Nov 2007 16:30:22 -0500 (EST) From: Bruce Fischl fi schl@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans To: Nicolas Cherbuin herbuin@an u.edu.au>Cc: freesurfer@nmr.mgh.harvard.eduMessage-ID: .4.62.0711111627310.8527@gate.nmr.mgh.harvard.edu>Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Hi Nicolas,
- No, sorry, the amount of RAM is sometimes dependent on the
individual anatomy, and in any case can't be predefine.
- Not sure about the itaniums. We have no real experience. 72 hours
does sound pretty long. That's I think about what it used to take on our old athlons. Can you extend the time limit?
As for the random stopping of recon-all, we have seen that sometimes as well, and are trying to track it down. It seems pretty mysterious, as a binary will exit with a nonzero exit code according to the shell even though the last printf in the code has been executed and the next statement is an exit(0).
Bruce
On Mon, 12 Nov 2007, Nicolas Cherbuin wrote:
Hi,
At the beginning of the year I processed 400
scans on a linux cluster. It had a reported ram limit of 1 Gig but it could cope with the slight excess of FS3 and a processing time limit of 48 hours (which was fine for 99% of the scans). Most scans went through autorecon-all without problem.>
I am now trying to reprocess the scans with
the new version but I am running into a number of problems. On the same linux cluser processing the same scans, some scans (~30%) run without problem. The rest either fail because they exceed the memory limit or because they take much more than 48 hours (the jobs are being killed and the logs report only the left and sometimes part of the right hemisphere being processed).>
Since the documentation makes clear that FS
works best with 2 Gig of ram, I have switched to an Itinium cluster with 2 Gig ram limit and 48 hours processing time limit. When I compare the logs of the same scans processed on both systems the Itinium cluster seems to take longer and although I am still running tests it appears that for at least some scans autoreconall might take 70+ hours.>
Here are my questions:
- On the linux cluster can I tell
freesurfer not to exceed a certain ram allocation? and if yes how?>
- Do the problems I have on the Itinium
cluster suggest that FS is badly configured on this system? and if yes where should we look? (I don't have access to this system's configuration and I have to feedback to the system managers to fix eventual problems.)>
Thank you very much for your help and for
sharing these great tools with us.>
Nic
_______________________________________________> Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
Message: 2 Date: Mon, 12 Nov 2007 06:23:04 -0200 From: "Pedro Paulo Oliveira Jr" ppj@netf ilter.com.br>Subject: Re: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans To: Bruce Fischl fi schl@nmr.mgh.harvard.edu>Cc: freesurfer@nmr.mgh.harvard.edu,
Nicolas Cherbuin herbuin@an
u.edu.au>Message-ID: 5@mai l.netfilter.com.br>Content-Type: text/plain; charset=UTF-8
I'm sure Bruce has much more experience on the subject than me. Also I'm not part of Martinos development team. I'll just add my personal experience:
- Your running times seens very high. I never saw 72 hours in my
studies. Notice that Itanium (and Itanium 2) cpu are far distinct than x86 and x86-64, and even running correctly x86 code its performance in fpu falls in my experience to 50%. Since FS code is not compiled to Itanium arch I think the stated above can explain the problem. 2) Regarding memory my experience is that 1GB usually does fine if you have swap space. 3) about 3.0.5 and 4.0.1 differences in running time my data is: 22 hrs vs 31 hrs average. It depends on the "extended" topological fix 4.0.1 does.
It would be nice to know your cluster configuration and a sample of your data to give you a better advice. best regards,
Pedro Paulo Oliveira Jr.
-- mens. original -- Assunto: Re: [Freesurfer] reprocessing on FS4.0 takes much longer for some scansDe: Bruce Fischl fi schl@nmr.mgh.harvard.edu>Data: 11/11/2007 21:42
Hi Nicolas,
- No, sorry, the amount of RAM is sometimes dependent on the
individual anatomy, and in any case can't be predefine.
- Not sure about the itaniums. We have no real experience. 72 hours
does sound pretty long. That's I think about what it used to take on our old athlons. Can you extend the time limit?
As for the random stopping of recon-all, we have seen that sometimes as well, and are trying to track it down. It seems pretty mysterious, as a binary will exit with a nonzero exit code according to the shell even though the last printf in the code has been executed and the next statement is an exit(0).
Bruce
On Mon, 12 Nov 2007, Nicolas Cherbuin wrote:
Hi,
At the beginning of the year I processed 400
scans on a linux cluster. It had a reported ram limit of 1 Gig but it could cope with the slight excess of FS3 and a processing time limit of 48 hours (which was fine for 99% of the scans). Most scans went through autorecon-all without problem.>
I am now trying to reprocess the scans with
the new version but I am running into a number of problems. On the same linux cluser processing the same scans, some scans (~30%) run without problem. The rest either fail because they exceed the memory limit or because they take much more than 48 hours (the jobs are being killed and the logs report only the left and sometimes part of the right hemisphere being processed).>
Since the documentation makes clear that FS
works best with 2 Gig of ram, I have switched to an Itinium cluster with 2 Gig ram limit and 48 hours processing time limit. When I compare the logs of the same scans processed on both systems the Itinium cluster seems to take longer and although I am still running tests it appears that for at least some scans autoreconall might take 70+ hours.>
Here are my questions:
- On the linux cluster can I tell
freesurfer not to exceed a certain ram allocation? and if yes how?>
- Do the problems I have on the Itinium
cluster suggest that FS is badly configured on this system? and if yes where should we look? (I don't have access to this system's configuration and I have to feedback to the system managers to fix eventual problems.)>
Thank you very much for your help and for
sharing these great tools with us.>
Nic
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Message: 3 Date: Mon, 12 Nov 2007 10:16:06 -0200 From: "Pedro Paulo Oliveira Jr" ppj@netf ilter.com.br>Subject: RE: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans To: "'Bruce Fischl'" fi schl@nmr.mgh.harvard.edu>, freesurfer@nmr.mgh.harvard.edu>,
"'Nicolas Cherbuin'" herbuin@an
u.edu.au>Message-ID: Content-Type: text/plain; charset="UTF-8"
one correction: FS does have Itanium version. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-suse -ia64-stable-pub-v4.0.1-full.tar.gz So my guess for item (1) is check if all code running is for IA64 architecture. -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Pedro Paulo Oliveira JrSent: segunda-feira, 12 de novembro de 2007 06:23 To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu; Nicolas CherbuinSubject: Re: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans I'm sure Bruce has much more experience on the subject than me. Also I'm not part of Martinos development team. I'll just add my personal experience:
- Your running times seens very high. I never saw 72 hours in my
studies. Notice that Itanium (and Itanium 2) cpu are far distinct than x86 and x86-64, and even running correctly x86 code its performance in fpu falls in my experience to 50%. Since FS code is not compiled to Itanium arch I think the stated above can explain the problem. 2) Regarding memory my experience is that 1GB usually does fine if you have swap space. 3) about 3.0.5 and 4.0.1 differences in running time my data is: 22 hrs vs 31 hrs average. It depends on the "extended" topological fix 4.0.1 does.
It would be nice to know your cluster configuration and a sample of your data to give you a better advice. best regards,
Pedro Paulo Oliveira Jr.
-- mens. original -- Assunto: Re: [Freesurfer] reprocessing on FS4.0 takes much longer for some scansDe: Bruce Fischl fi schl@nmr.mgh.harvard.edu>Data: 11/11/2007 21:42
Hi Nicolas,
- No, sorry, the amount of RAM is sometimes dependent on the
individual anatomy, and in any case can't be predefine.
- Not sure about the itaniums. We have no real experience. 72 hours
does sound pretty long. That's I think about what it used to take on our old athlons. Can you extend the time limit?
As for the random stopping of recon-all, we have seen that sometimes as well, and are trying to track it down. It seems pretty mysterious, as a binary will exit with a nonzero exit code according to the shell even though the last printf in the code has been executed and the next statement is an exit(0).
Bruce
On Mon, 12 Nov 2007, Nicolas Cherbuin wrote:
Hi,
At the beginning of the year I processed 400
scans on a linux cluster. It had a reported ram limit of 1 Gig but it could cope with the slight excess of FS3 and a processing time limit of 48 hours (which was fine for 99% of the scans). Most scans went through autorecon-all without problem.>
I am now trying to reprocess the scans with
the new version but I am running into a number of problems. On the same linux cluser processing the same scans, some scans (~30%) run without problem. The rest either fail because they exceed the memory limit or because they take much more than 48 hours (the jobs are being killed and the logs report only the left and sometimes part of the right hemisphere being processed).>
Since the documentation makes clear that FS
works best with 2 Gig of ram, I have switched to an Itinium cluster with 2 Gig ram limit and 48 hours processing time limit. When I compare the logs of the same scans processed on both systems the Itinium cluster seems to take longer and although I am still running tests it appears that for at least some scans autoreconall might take 70+ hours.>
Here are my questions:
- On the linux cluster can I tell
freesurfer not to exceed a certain ram allocation? and if yes how?>
- Do the problems I have on the Itinium
cluster suggest that FS is badly configured on this system? and if yes where should we look? (I don't have access to this system's configuration and I have to feedback to the system managers to fix eventual problems.)>
Thank you very much for your help and for
sharing these great tools with us.>
Nic
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Message: 4 Date: Tue, 13 Nov 2007 06:08:00 +1100 From: "Nicolas Cherbuin" herbuin@an u.edu.au>Subject: RE: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans To: "Bruce Fischl" fi schl@nmr.mgh.harvard.edu>Cc: freesurfer@nmr.mgh.harvard.eduMessage-ID:
Content-Type: text/plain; charset="Windows-1252"
Hi Bruce,
Thanks for your answers. I am not sure how much more ram might be needed dependant on anatomy but my last job failed due to FS using more than 3 Gig PBS: job killed: per node vmem 34078384kb exceeded limit 2097152kb
or does it suggest there is a problem with our configuration?
Also, a related question. Since a number of jobs have failed after many hours of processing, I have had to investigate restarting jobs to finish processing the right hemisphere. For instance after the following log: status file for recon-all Thu Nov 8 23:13:39 EST 2007 #@# MotionCor Thu Nov 8 23:13:53 EST 2007 #@# Nu Intensity Correction Thu Nov 8 23:14:33 EST 2007 #@# Talairach Thu Nov 8 23:15:44 EST 2007 #@# Talairach Failure Detection Thu Nov 8 23:18:32 EST 2007 #@# Intensity Normalization Thu Nov 8 23:18:32 EST 2007 #@# Skull Stripping Thu Nov 8 23:25:47 EST 2007 #@# EM Registration Fri Nov 9 00:11:07 EST 2007 #@# CA Normalize Fri Nov 9 00:31:03 EST 2007 #@# CA Reg Fri Nov 9 00:37:06 EST 2007 #@# CA Reg Inv Fri Nov 9 16:56:14 EST 2007 #@# Remove Neck Fri Nov 9 16:59:57 EST 2007 #@# SkullLTA Fri Nov 9 17:04:39 EST 2007 #@# SubCort Seg Fri Nov 9 17:37:12 EST 2007 #@# CC Seg Fri Nov 9 18:57:34 EST 2007 #@# Intensity Normalization2 Fri Nov 9 18:59:22 EST 2007 #@# Mask BFS Fri Nov 9 19:08:32 EST 2007 #@# WM Segmentation Fri Nov 9 19:08:45 EST 2007 #@# Fill Fri Nov 9 19:17:29 EST 2007 #@# Tessellate lh Fri Nov 9 19:19:57 EST 2007 #@# Smooth1 lh Fri Nov 9 19:20:37 EST 2007 #@# Inflation1 lh Fri Nov 9 19:20:56 EST 2007 #@# QSphere lh Fri Nov 9 19:24:27 EST 2007 #@# Fix Topology lh Fri Nov 9 19:58:03 EST 2007 #@# Make Final Surf lh Sat Nov 10 03:17:04 EST 2007 #@# Smooth2 lh Sat Nov 10 07:11:02 EST 2007 #@# Inflation2 lh Sat Nov 10 07:11:19 EST 2007 #@# Sphere lh Sat Nov 10 07:19:55 EST 2007 #@# Surf Reg lh Sat Nov 10 10:29:15 EST 2007 #@# Jacobian white lh Sat Nov 10 17:43:19 EST 2007 #@# AvgCurv lh Sat Nov 10 17:43:29 EST 2007 #@# Cortical Parc lh Sat Nov 10 17:43:37 EST 2007 #@# Parcellation Stats lh Sat Nov 10 17:44:55 EST 2007 #@# Cortical Parc 2 lh Sat Nov 10 17:45:30 EST 2007 #@# Parcellation Stats 2 lh Sat Nov 10 17:47:12 EST 2007 #@# Tessellate rh Sat Nov 10 17:47:58 EST 2007 #@# Smooth1 rh Sat Nov 10 17:48:35 EST 2007 #@# Inflation1 rh Sat Nov 10 17:48:55 EST 2007 #@# QSphere rh Sat Nov 10 17:52:32 EST 2007 #@# Fix Topology rh Sat Nov 10 18:26:17 EST 2007
I initially thought I could restart with -autorecon3 but since this did not work I restarted with: recon-all -s subject -autorecon2 -hemi right
but this (log below) restarted with a number of (very lengthy!!!) processes that had been completed before. What is the most efficient way to restart a process and is there a way of restarting autorecon2 and have it automatically followed by autorecton3? Sun Nov 11 11:29:26 EST 2007 #@# EM Registration Sun Nov 11 11:29:26 EST 2007 #@# CA Normalize Sun Nov 11 11:48:51 EST 2007 #@# CA Reg Sun Nov 11 11:54:14 EST 2007 #@# CA Reg Inv Mon Nov 12 04:21:18 EST 2007 #@# Remove Neck Mon Nov 12 04:25:00 EST 2007 #@# SkullLTA Mon Nov 12 04:29:31 EST 2007 #@# SubCort Seg Mon Nov 12 05:01:49 EST 2007 #@# CC Seg Mon Nov 12 06:21:48 EST 2007 #@# Intensity Normalization2 Mon Nov 12 06:23:50 EST 2007 #@# Mask BFS Mon Nov 12 06:32:52 EST 2007 #@# WM Segmentation Mon Nov 12 06:33:05 EST 2007 #@# Fill Mon Nov 12 06:41:56 EST 2007 #@# Tessellate rh Mon Nov 12 06:44:23 EST 2007 #@# Smooth1 rh Mon Nov 12 06:45:00 EST 2007 #@# Inflation1 rh Mon Nov 12 06:45:19 EST 2007 #@# QSphere rh Mon Nov 12 06:48:48 EST 2007 #@# Fix Topology rh Mon Nov 12 07:22:02 EST 2007 #@# Make Final Surf rh Mon Nov 12 15:26:46 EST 2007 #@# Smooth2 rh Mon Nov 12 19:18:37 EST 2007 #@# Inflation2 rh Mon Nov 12 19:18:55 EST 2007 #@# ASeg Stats Mon Nov 12 19:27:09 EST 2007 #@# Cortical ribbon mask rh Mon Nov 12 20:03:45 EST 2007
Finally, what is the best way to restart it from the last memory exceeded failure which interupted processing towards the end of autorecon2? Thanks
Nic
-----Original Message----- From: Bruce Fischl [fi schl@nmr.mgh.harvard.edu]Sent: Sun 11/11/2007 4:30 PM To: Nicolas Cherbuin Cc: freesurfer@nmr.mgh.harvard.eduSubject: Re: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans Hi Nicolas,
- No, sorry, the amount of RAM is sometimes dependent on the
individual anatomy, and in any case can't be predefine.
- Not sure about the itaniums. We have no real experience. 72 hours
does sound pretty long. That's I think about what it used to take on our old athlons. Can you extend the time limit?
As for the random stopping of recon-all, we have seen that sometimes as well, and are trying to track it down. It seems pretty mysterious, as a binary will exit with a nonzero exit code according to the shell even though the last printf in the code has been executed and the next statement is an exit(0).
Bruce
On Mon, 12 Nov 2007, Nicolas Cherbuin wrote:
Hi,
At the beginning of the year I processed 400
scans on a linux cluster. It had a reported ram limit of 1 Gig but it could cope with the slight excess of FS3 and a processing time limit of 48 hours (which was fine for 99% of the scans). Most scans went through autorecon-all without problem.>
I am now trying to reprocess the scans with
the new version but I am running into a number of problems. On the same linux cluser processing the same scans, some scans (~30%) run without problem. The rest either fail because they exceed the memory limit or because they take much more than 48 hours (the jobs are being killed and the logs report only the left and sometimes part of the right hemisphere being processed).>
Since the documentation makes clear that FS
works best with 2 Gig of ram, I have switched to an Itinium cluster with 2 Gig ram limit and 48 hours processing time limit. When I compare the logs of the same scans processed on both systems the Itinium cluster seems to take longer and although I am still running tests it appears that for at least some scans autoreconall might take 70+ hours.>
Here are my questions:
- On the linux cluster can I tell
freesurfer not to exceed a certain ram allocation? and if yes how?>
- Do the problems I have on the Itinium
cluster suggest that FS is badly configured on this system? and if yes where should we look? (I don't have access to this system's configuration and I have to feedback to the system managers to fix eventual problems.)>
Thank you very much for your help and for
sharing these great tools with us.>
Nic
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Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
Message: 5 Date: Mon, 12 Nov 2007 14:40:35 -0500 (EST) From: Bruce Fischl fi schl@nmr.mgh.harvard.edu>Subject: RE: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans To: Nicolas Cherbuin herbuin@an u.edu.au>Cc: freesurfer@nmr.mgh.harvard.eduMessage-ID: .4.62.0711121440040.8310@gate.nmr.mgh.harvard.edu>Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
do you know what process it was running when it failed? You could use -autorecon2-cp and -autorecon3. Something else seems like it is wrong though - you shouldn't need 3G of ram.
On Tue, 13 Nov 2007, Nicolas Cherbuin wrote:
Hi Bruce,
Thanks for your answers. I am not sure how
much more ram might be needed dependant on anatomy but my last job failed due to FS using more than 3 Gig>
PBS: job killed: per node vmem 34078384kb
exceeded limit 2097152kb>
or does it suggest there is a problem with
our configuration?>
Also, a related question. Since a number of
jobs have failed after many hours of processing, I have had to investigate restarting jobs to finish processing the right hemisphere. For instance after the following log:>
status file for recon-all Thu Nov 8 23:13:39 EST 2007 #@# MotionCor Thu Nov 8 23:13:53 EST 2007 #@# Nu Intensity Correction Thu Nov 8
23:14:33 EST 2007> #@# Talairach Thu Nov 8 23:15:44 EST 2007
#@# Talairach Failure Detection Thu Nov 8
23:18:32 EST 2007> #@# Intensity Normalization Thu Nov 8 23:18:32 EST 2007> #@# Skull Stripping Thu Nov 8 23:25:47 EST 2007> #@# EM Registration Fri Nov 9 00:11:07 EST 2007> #@# CA Normalize Fri Nov 9 00:31:03 EST 2007> #@# CA Reg Fri Nov 9 00:37:06 EST 2007
#@# CA Reg Inv Fri Nov 9 16:56:14 EST 2007 #@# Remove Neck Fri Nov 9 16:59:57 EST 2007 #@# SkullLTA Fri Nov 9 17:04:39 EST 2007 #@# SubCort Seg Fri Nov 9 17:37:12 EST 2007 #@# CC Seg Fri Nov 9 18:57:34 EST 2007 #@# Intensity Normalization2 Fri Nov 9
18:59:22 EST 2007> #@# Mask BFS Fri Nov 9 19:08:32 EST 2007
#@# WM Segmentation Fri Nov 9 19:08:45 EST
2007> #@# Fill Fri Nov 9 19:17:29 EST 2007
#@# Tessellate lh Fri Nov 9 19:19:57 EST
2007> #@# Smooth1 lh Fri Nov 9 19:20:37 EST 2007
#@# Inflation1 lh Fri Nov 9 19:20:56 EST
2007> #@# QSphere lh Fri Nov 9 19:24:27 EST 2007
#@# Fix Topology lh Fri Nov 9 19:58:03 EST
2007> #@# Make Final Surf lh Sat Nov 10 03:17:04 EST 2007> #@# Smooth2 lh Sat Nov 10 07:11:02 EST 2007
#@# Inflation2 lh Sat Nov 10 07:11:19 EST
2007> #@# Sphere lh Sat Nov 10 07:19:55 EST 2007
#@# Surf Reg lh Sat Nov 10 10:29:15 EST 2007 #@# Jacobian white lh Sat Nov 10 17:43:19
EST 2007> #@# AvgCurv lh Sat Nov 10 17:43:29 EST 2007
#@# Cortical Parc lh Sat Nov 10 17:43:37 EST
2007> #@# Parcellation Stats lh Sat Nov 10 17:44:55 EST 2007> #@# Cortical Parc 2 lh Sat Nov 10 17:45:30 EST 2007> #@# Parcellation Stats 2 lh Sat Nov 10 17:47:12 EST 2007> #@# Tessellate rh Sat Nov 10 17:47:58 EST 2007> #@# Smooth1 rh Sat Nov 10 17:48:35 EST 2007
#@# Inflation1 rh Sat Nov 10 17:48:55 EST
2007> #@# QSphere rh Sat Nov 10 17:52:32 EST 2007
#@# Fix Topology rh Sat Nov 10 18:26:17 EST
2007>
I initially thought I could restart with
-autorecon3 but since this did not work I restarted with:>
recon-all -s subject -autorecon2 -hemi right
but this (log below) restarted with a number
of (very lengthy!!!) processes that had been completed before. What is the most efficient way to restart a process and is there a way of restarting autorecon2 and have it automatically followed by autorecton3?>
Sun Nov 11 11:29:26 EST 2007 #@# EM Registration Sun Nov 11 11:29:26 EST
2007> #@# CA Normalize Sun Nov 11 11:48:51 EST 2007> #@# CA Reg Sun Nov 11 11:54:14 EST 2007
#@# CA Reg Inv Mon Nov 12 04:21:18 EST 2007 #@# Remove Neck Mon Nov 12 04:25:00 EST 2007 #@# SkullLTA Mon Nov 12 04:29:31 EST 2007 #@# SubCort Seg Mon Nov 12 05:01:49 EST 2007 #@# CC Seg Mon Nov 12 06:21:48 EST 2007 #@# Intensity Normalization2 Mon Nov 12
06:23:50 EST 2007> #@# Mask BFS Mon Nov 12 06:32:52 EST 2007
#@# WM Segmentation Mon Nov 12 06:33:05 EST
2007> #@# Fill Mon Nov 12 06:41:56 EST 2007
#@# Tessellate rh Mon Nov 12 06:44:23 EST
2007> #@# Smooth1 rh Mon Nov 12 06:45:00 EST 2007
#@# Inflation1 rh Mon Nov 12 06:45:19 EST
2007> #@# QSphere rh Mon Nov 12 06:48:48 EST 2007
#@# Fix Topology rh Mon Nov 12 07:22:02 EST
2007> #@# Make Final Surf rh Mon Nov 12 15:26:46 EST 2007> #@# Smooth2 rh Mon Nov 12 19:18:37 EST 2007
#@# Inflation2 rh Mon Nov 12 19:18:55 EST
2007> #@# ASeg Stats Mon Nov 12 19:27:09 EST 2007
#@# Cortical ribbon mask rh Mon Nov 12
20:03:45 EST 2007>
Finally, what is the best way to restart it
from the last memory exceeded failure which interupted processing towards the end of autorecon2?>
Thanks
Nic
-----Original Message----- From: Bruce Fischl [fi
schl@nmr.mgh.harvard.edu]> Sent: Sun 11/11/2007 4:30 PM
To: Nicolas Cherbuin Cc: freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] reprocessing on
FS4.0 takes much longer for some scans>
Hi Nicolas,
- No, sorry, the amount of RAM is sometimes
dependent on the> individual anatomy, and in any case can't be predefine.>
- Not sure about the itaniums. We have no
real experience. 72 hours does> sound pretty long. That's I think about what it used to take on our old> athlons. Can you extend the time limit?
As for the random stopping of recon-all, we
have seen that sometimes as> well, and are trying to track it down. It seems pretty mysterious, as a> binary will exit with a nonzero exit code according to the shell even> though the last printf in the code has been executed and the next statement> is an exit(0).
Bruce
On Mon, 12 Nov 2007, Nicolas Cherbuin wrote:
Hi,
At the beginning of the year I processed
400 scans on a linux cluster. It had a reported ram limit of 1 Gig but it could cope with the slight excess of FS3 and a processing time limit of 48 hours (which was fine for 99% of the scans). Most scans went through autorecon-all without problem.>>
I am now trying to reprocess the scans with
the new version but I am running into a number of problems. On the same linux cluser processing the same scans, some scans (~30%) run without problem. The rest either fail because they exceed the memory limit or because they take much more than 48 hours (the jobs are being killed and the logs report only the left and sometimes part of the right hemisphere being processed).>>
Since the documentation makes clear that FS
works best with 2 Gig of ram, I have switched to an Itinium cluster with 2 Gig ram limit and 48 hours processing time limit. When I compare the logs of the same scans processed on both systems the Itinium cluster seems to take longer and although I am still running tests it appears that for at least some scans autoreconall might take 70+ hours.>>
Here are my questions:
- On the linux cluster can I tell
freesurfer not to exceed a certain ram allocation? and if yes how?>>
- Do the problems I have on the Itinium
cluster suggest that FS is badly configured on this system? and if yes where should we look? (I don't have access to this system's configuration and I have to feedback to the system managers to fix eventual problems.)>>
Thank you very much for your help and for
sharing these great tools with us.>>
Nic
_______________________________________________>> Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E%3E
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