Dear FreeSurfer experts, Bruce/Doug,
I am running my analysis on a server. I have a total of 128 GB RAM, when I run my analysis and when it stops I'm consuming ~44, having about 83 free.
I can run 1224 subjects but no more than that. As soon as I have 1225 subjects the analysis won't run (but it does run for all the remaining subjects if I run them separately). I tried to run the analysis on different servers, some that had 72GB and some that had 128GB and the pattern stayed the same; none of the 12 servers could run 1225 subjects but all could run 1224 subjects. This may mean it's not a memory problem (?) but it doesn't seem to be a problem with subject files either as all of them work, just not all at the same time.
All the servers I have access to have a 24-core processor, if that's important.
Any further suggestions on what might be going on?
Best wishes,
Hanna
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Date: Fri, 25 Jul 2014 09:50:51 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1407250949560.20368@nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi Hanna
seems like you are running out of memory. How much RAM do you have on your machine? Are there other things running on it that you can kill, or is there a larger RAM machine you can use?
Doug will be back next week and perhaps will comment also. If you don't hear from him you should repost.
cheers Bruce
On Fri, 25 Jul 2014, Isotalus, Hanna wrote:
Dear FreeSurfer gurus,
I am using QDEC to run my analyses on a large data set. The analysis works fine with up to 1224 subjects but as soon as I add subject 1225 I get an error and the analysis stops. The error displays during 'concatenating volumes' and it just displays file names. When I try to run the analysis on the remaining subjects (around 360 of them) the analysis runs fine ? so I am inclined to think there's nothing wrong with the data files. I've tried rotating the order of subjects and it just doesn't seem to allow me to run the analysis on all of them. Do you have any suggestions?
Here's a link to a screenshot of the error I get:
https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif
I can't actually see all of the error message, here's it from the beginning of what I can see and it continues like that ? displaying all file names I think.
Thank you and best wishes, Hanna
I'm still not sure what is going on. I can run it with 2000 files, so I still suspect a memory problem. Try running it with /usr/bin/time, ie,
/usr/bin/time mri_concat ...
SEnd me the last line
On 07/28/2014 03:24 PM, Isotalus, Hanna wrote:
Dear FreeSurfer experts, Bruce/Doug,
I am running my analysis on a server. I have a total of 128 GB RAM, when I run my analysis and when it stops I'm consuming ~44, having about 83 free.
I can run 1224 subjects but no more than that. As soon as I have 1225 subjects the analysis won't run (but it does run for all the remaining subjects if I run them separately). I tried to run the analysis on different servers, some that had 72GB and some that had 128GB and the pattern stayed the same; none of the 12 servers could run 1225 subjects but all could run 1224 subjects. This may mean it's not a memory problem (?) but it doesn't seem to be a problem with subject files either as all of them work, just not all at the same time.
All the servers I have access to have a 24-core processor, if that's important.
Any further suggestions on what might be going on?
Best wishes,
Hanna
Date: Fri, 25 Jul 2014 09:50:51 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1407250949560.20368@nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi Hanna
seems like you are running out of memory. How much RAM do you have on your machine? Are there other things running on it that you can kill, or is there a larger RAM machine you can use?
Doug will be back next week and perhaps will comment also. If you don't hear from him you should repost.
cheers Bruce
On Fri, 25 Jul 2014, Isotalus, Hanna wrote:
Dear FreeSurfer gurus,
I am using QDEC to run my analyses on a large data set. The analysis works fine with up to 1224 subjects but as soon as I add subject 1225 I get an error and the analysis stops. The error displays during 'concatenating volumes' and it just displays file names. When I try to run the analysis on the remaining subjects (around 360 of them) the analysis runs fine ? so I am inclined to think there's nothing wrong with the data files. I've tried rotating the order of subjects and it just doesn't seem to allow me to run the analysis on all of them. Do you have any suggestions?
Here's a link to a screenshot of the error I get:
https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif
I can't actually see all of the error message, here's it from the beginning of what I can see and it continues like that ? displaying all file names I think.
Thank you and best wishes, Hanna
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Isotalus, Hanna