Hi James,
thanks for the careful analysis. Not sure why it's not using swap, but
we'll get back to you soon.
have a good weekend,
Bruce
On Sat, 2 Feb 2008, James N. Porter wrote:
So, I believe I have isolated the problem. The failure happens during the
mri_concat phase of make_average_volumes. The seg-subj#.mgh temp files
that are being concatenated are 65 MB each and I can successfully run 59
subjects, but for 60 subjects and up, mri_concat exits immediately with
the error message as written below. I have 4GB of memory, and 65*59 is
less than 4 GB so that works; add any more subjects and the process is
shut down. It appears that mri_concat checks to see how much memory will
be needed to hold all those .mgh files in active use, then checks the
machine to see how much physical memory is available. I can easily set up
a larger swap file to handle the full 175*65 that is needed (it will be
insanely slow, but that's better than nothing). However, I can't get
FreeSurfer to utilize the swap space I already have available.
I watched the whole make_average_volumes process play out on my resource
monitor (I imagine that's what watching NASCAR is like--Come on, just
crash already!) and while it came very close to using all 4GB--leaving a
paltry 19 MB free at most points--it didn't touch the swap at any point
during the run. This is not the case with Matlab and other programs,
which will greedily eat up physical memory then seek out the swap. While
I appreciate that the FreeSurfer programs are set up to be judicious
consumers of resources, is there some sort of environmental variable in
FreeSurfer or line of code in mri_concat that I can modify that would
allow the programs to reach out and use the swap space?
Thanks,
Jim
---------
Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota
James N. Porter wrote:
Juergen--Have you had successful resolution to this problem?
Nick--I'm attempting to average 175 subjects, but
make_average_volume returns the same error as Juergen
reports.
> Allocing output
> MRIalloc(256,256,256): could not allocate 262144 bytes
for 15547th slice
I'm running freesurfer-Linux-rh9-stable-pub-v4.0.1 on SUSE
Linux 9.3 2.6.11.4-21.17-smp x86_64, with a pair of Pentium
3.20 GHz processors, 4 GB of physical memory and 8 GB of swap
memory. My limits are also quite liberal.
> cputime unlimited
> filesize unlimited
> datasize unlimited
> stacksize unlimited
> coredumpsize 0 kbytes
> memoryuse unlimited
> vmemoryuse unlimited
> descriptors 1024
> memorylocked 32 kbytes
> maxproc 28660
I've tried to also use the alternative script posted by Doug
Greve
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html).
That also returns the same error.
Any suggestions?
Many thanks,
---------
Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota
Nick Schmansky wrote:
Juergen,
Edit the 'make_average_subject' script removing (or commenting-out) the
line 'limit descriptors unlimited'. You may have to do the same for
'make_average_surface' and 'make_average_volume'. Although in v4.0,
these should already be commented-out.
Nick
On Mon, 2008-01-28 at 16:29 +0100, Juergen Haenggi wrote:
Dear FS experts
I tried to run make_average_subject in the past with 92 subjects and got the
following error: Cannot allocate memory. This is now on the to-do list of
the FS website. Then I bought some additional RAM and changed from OS X
tiger to leopard. Now I tried it again and get this error:
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit
descriptors 4096
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit
cputime unlimited
filesize unlimited
datasize 6144 kbytes
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 4096
memorylocked unlimited
maxproc 266
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
make_average_subject --subjects SNPs_Vp*
limit: descriptors: Can't remove limit (Invalid argument)
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
I set the descriptor limit to 4096, but the make_average_subject command
will not start anymore.
Any idea what is wrong here?
Thanks in advance
Best regards
Juergen
-----------------------------------------------------------
Juergen Haenggi
Ph.D. (Dr. des.)
Division of Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
[EMAIL PROTECTED] (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
-----------------------------------------------------------
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