Thanks again, Bruce. The time problem precludes running with a single cpu. But you jogged my memory and I was fooling around with freeview while recon-all was running. I might have overrun the memory with it as I was loading 10's of 1000's of points to plot which really pushes it. I'll try with 5 cpus again since my time is so short and leave the machine idle otherwise.
Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, February 11, 2015 9:53 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] time critical problem: mri_ca_register failure > during > recon-all run > > Hi Don > > does it repeatably die in the same place when you run it with openmp 5? Are > you sure nothing else was running at the time? Try running it with openmp 1 > and make sure nothing else is running and see if it finishes sorry, not sure > what > else to suggest. If it dies in the same spot, upload the entire subject dir > and let > us know > > good luck > Bruce > > > On > Wed, 11 Feb 2015, Krieger, Donald N. wrote: > > > Thanks for responding so quickly, Bruce. > > Yes I was running a single job on the 6-core machine and have used it and > this version of recon-all successfully before. > > The freesurfer instance was downloaded a few weeks ago - it is the Centos6 > one. > > I don't know how to tell which version of the entire package it is. > > recon-all -version returns: > > $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ > > mri_ca_register -version returns: > > stable5 > > nu_estimate_np_and_em -version returns: > > Package MNI N3, version 1.10, compiled by nicks@minerva > > (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 preceded by a bunch > of deprecation notices. > > > > ??? > > > > Regards, > > > > Don > > > > > > Don Krieger, Ph.D. > > Department of Neurological Surgery > > University of Pittsburgh > > (412)648-9654 Office > > (412)521-4431 Cell/Text > > > > > >> -----Original Message----- > >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > >> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > >> Sent: Wednesday, February 11, 2015 9:39 AM > >> To: Freesurfer support list > >> Subject: Re: [Freesurfer] time critical problem: mri_ca_register > >> failure during recon-all run > >> > >> Hi Don > >> > >> are you running a single job on the 8G machine? What FS version? We > >> haven't seen any core dumps in mri_ca_register recently. If you run > >> it without openmp does it work? Kind of worrisome that it dies in a > >> different place on a different machine Bruce > >> > >> > >> On Wed, 11 Feb 2015, Krieger, Donald N. wrote: > >> > >>> > >>> Dear list: > >>> > >>> > >>> > >>> We are under a significant deadline on which this freesurfer run depends. > >>> > >>> I’m reposting from last night along with a bit of additional information. > >>> > >>> A 2nd run on a different box yielded: > >>> > >>> nu_correct: crashed while running nu_estimate_np_and_em > >>> (termination > >>> status=256) > >>> > >>> > >>> Also, the box on which the run detailed below was done has 8 GBytes > >>> of RAM, not 8 Mbytes – sorry about that. > >>> > >>> > >>> > >>> Any help and direction you can provide with this error would be > appreciated. > >>> > >>> The full log is attached. > >>> > >>> I was running with –openmp 5 on a machine with 6 cores and 8 Mbytes > >>> of > >> RAM. > >>> > >>> > >>> > >>> 0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777 > >>> > >>> 0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=96777 > >>> > >>> 0035: dt=73.984000, rms=0.640 (0.095%), neg=0, invalid=96777 > >>> > >>> 0036: dt=517.888000, rms=0.639 (0.162%), neg=0, invalid=96777 > >>> > >>> 0037: dt=23.120000, rms=0.639 (-0.002%), neg=0, invalid=96777 > >>> > >>> blurring input image with Gaussian with sigma=0.500... > >>> > >>> 0000: dt=0.000, rms=0.639, neg=0, invalid=96777 > >>> > >>> 0038: dt=92.480000, rms=0.638 (0.081%), neg=0, invalid=96777 > >>> > >>> Segmentation fault (core dumped) > >>> > >>> ERROR: mri_ca_register with non-zero status 139 > >>> > >>> but continuing despite the error > >>> > >>> #-------------------------------------- > >>> > >>> #@# CA Reg Inv Tue Feb 10 19:24:19 EST 2015 > >>> > >>> /home/kriegerd/Contrib/freesurfer/subjects/175/mri > >>> > >>> > >>> > >>> mri_ca_register -invert-and-save transforms/talairach.m3z > >>> > >>> > >>> > >>> Loading, Inverting, Saving, Exiting ... > >>> > >>> Reading transforms/talairach.m3z > >>> > >>> ERROR: cannot find or read transforms/talairach.m3z > >>> > >>> ERROR: mri_ca_register with non-zero status 0 > >>> > >>> Linux OfficeFedora21 3.17.4-301.fc21.x86_64 #1 SMP Thu Nov 27 > >>> 19:09:10 UTC > >>> 2014 x86_64 x86_64 x86_64 GNU/Linux > >>> > >>> > >>> > >>> recon-all -s 175 exited with ERRORS at Tue Feb 10 19:24:19 EST 2015 > >>> > >>> > >>> > >>> Regards, > >>> > >>> > >>> > >>> Don > >>> > >>> > >>> > >>> Signature0001 > >>> > >>> Don Krieger, Ph.D. > >>> > >>> Department of Neurological Surgery > >>> > >>> University of Pittsburgh > >>> > >>> > >>> > >>> > >>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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