To disable running mris_volmask (and its downstream dependent stages), add these flags to recon-all:
-nocortribbon -noaparc2aseg -nowmparc refer to: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable Nick On Tue, 2009-06-09 at 10:16 -0700, Christopher Nunez wrote: > I am getting similar error messages when running on our grid and pipeline > systems (see below). Our tech people had previously thought this could be > related to memory capacity issues, but after increasing memory to 8gb when > submitting my jobs with a qsub command, the problem is still not resolved. > I'm beginning to have doubts about this being related to memory capacity. > > > Could somebody please provide instructions on disabling the ribbon > processing? Thank you. > > > #...@# Cortical ribbon mask Sun May 31 18:21:54 PDT 2009 > /ifs/edevel/CN_SAN_DIEGO/FREESURFER/OUTPUT/164/mri > \n mris_volmask --label_left_white 2 --label_left_ribbon 3 > --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance > 164 \n > ERROR: In > /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line > 372 > vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() > returned 12 > > ERROR: In > /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line > 372 > vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() > returned 12 > > ERROR: In > /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line > 372 > vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() > returned 12 > > ERROR: In > /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line > 372 > vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() > returned 12 > > ERROR: In > /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line > 372 > vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() > returned 12 > > ERROR: In > /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line > 372 > vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() > returned 12 > > ERROR: In > /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line > 372 > vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() > returned 12 > > > > > ------------------------------------------------------------------- > S. Christopher Nuñez, PhD > Postdoctoral Fellow > Developmental Cognitive Neuroimaging Group > Laboratory of Neuro Imaging > UCLA Dept of Neurology > Neuroscience Research Building 1, Suite 225 > 635 Charles Young Drive South > Los Angeles, CA 90095-7334 > (310) 267-5555 > ------------------------------------------------------------------- > ________________________________________ > From: hranilov...@ucla.edu [hranilov...@ucla.edu] > Sent: Monday, June 08, 2009 12:13 PM > To: Christopher Nunez > Subject: Fwd: RE: [Freesurfer] vtkMultiThreader error > > Pretty much what I was saying the other day. It looks like maybe you > can disable this step if you don't want this output, though? > > ----- Forwarded message from dhagle...@hotmail.com ----- > Date: Mon, 8 Jun 2009 11:19:43 -0700 > From: Don Hagler <dhagle...@hotmail.com> > Reply-To: Don Hagler <dhagle...@hotmail.com> > Subject: RE: [Freesurfer] vtkMultiThreader error > To: ni...@nmr.mgh.harvard.edu, martin.ka...@gmail.com > Cc: freesurfer maillist <freesurfer@nmr.mgh.harvard.edu> > > > Hi Nick, > > Thanks for the reply. I will look into the memory limit issue some > more (we recently instituted per job memory limits), but I have done a > test run with a 16GB memory limit (running one job per node). > > Meanwhile, thanks for the novtk suggestion. Our fallback option is to > just disable the ribbon generation. I don't think we ever use them > for anything. > > Don > > > > Subject: Re: [Freesurfer] vtkMultiThreader error > > From: ni...@nmr.mgh.harvard.edu > > To: martin.ka...@gmail.com; dhagle...@hotmail.com > > Date: Mon, 8 Jun 2009 11:15:51 -0400 > > CC: freesurfer@nmr.mgh.harvard.edu > > > > Don and Martin, > > > > I dont have a good solution for you to this problem. The error code > > indicates an 'out-of-memory' error returned by pthread_create, and I do > > know the mris_vol_mask uses a lot of memory (at least 1GB). > > > > I have not been able to find any clues to the source of this problem on > > the web either. The only curious thing to it is that in the source > > code, that section is conditionally compiled to ignore the return code > > if 'VTK_HP_PTHREADS' is defined, which implies some sort of odd behavior > > on some special HP platform build. > > > > mris_vol_mask has been a real thorn in the side of the recon-all stream, > > but its not easy to replace because it does a subjectively better job of > > finding the voxels which intersect the pial and white surfaces. For > > comparison, or even to solve your problem, you can use > > mris_vol_mask_novtk to create the ribbon.mgz files. The output is not > > the same as that produced by mris_vol_mask though. Perhaps you can run > > it, and compare the results side-by-side and give us your opinion on > > which is the better ribbon (as there is no objective measure on what a > > 'correct' ribbon.mgz should like like, ie, should it include voxels that > > intersect more than half way through a surface, or not at all?). > > > > Nick > > > > > > On Mon, 2009-06-08 at 09:16 +0200, Martin Kavec wrote: > > > Hi Don, > > > > I am in a similar situation. I am on a IBM BladeCenter cluster > > (though with > one blade only) with 2 Quad core Intels, and I > > experience intermittent > crashes of mri_volmask as well. Similarly > > as you, when I run the mri_volmask > on the crashed subject on a > > desktop, this passes perfectly fine and sometimes > also on the > > cluster as well. > > > > I am wonder whether how do you obtain the debug information > > about the cause of > the crash (being in the vtkMultiThreader)? > > > > I also wonder, whether the crashes could be due to different > > compilation > environments of the VTK libraries used in teh FS > > distribution (centos) and > your redhat. I went on the bug-report > > site of VTK and there really isn't > anythink major reported on this > > class. > > In my experience the mri_volmask runs fine for quite a > > while and then crashes. > >From the debug messages you show it would > > thus could be that the process may > hit some limit of the threads > > which could be allocated to a process. > > > > What do you think? > > > > Martin > > On Saturday 06 June 2009 04:19:51 Don Hagler wrote: > > > > When we run v430 on our cluster, running rocks redhat 4.3, we > > get the error > > > > message below when mris_volmask is run. From a google search, I see > > > > that > > > > someone had the same error message back in Oct 2007. Was a > > solution found > > > > for this? It runs fine on our desktop machines as well as when we log > > > > in > > > > directly to a node and run the job interactively. > > > > > > > > > > > > > > > > mris_volmask --label_left_white 2 --label_left_ribbon 3 > > > > --label_right_white 41 --label_right_ribbon 42 --save_ribbon > > > > --save_distance FREESURFERRECON_NTNU_PRE_095v2_20071126.173245.968000_1 > > > > > > > > SUBJECTS_DIR is /home/dhagler/data_test > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > > thread. > > pthread_create() returned 12 > > > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > > thread. > > pthread_create() returned 12 > > > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > > thread. > > pthread_create() returned 12 > > > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > > thread. > > pthread_create() returned 12 > > > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > > thread. > > pthread_create() returned 12 > > > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > > thread. > > pthread_create() returned 12 > > > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > > thread. > > pthread_create() returned 12 > > > > > > > > Segmentation fault > > > > Linux compute-0-12.local 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 > > 14:14:47 EDT > > > > 2007 x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > recon-all exited with ERRORS at Fri Jun 5 18:58:09 PDT 2009 > > > > > > > > > > > > > > > > > > > > > > > > _________________________________________________________________ > > > > Hotmail® has ever-growing storage! Don't worry about storage limits. > > > > > > http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutori > > > >al_Storage_062009 > > > > > _______________________________________________ > > > 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 > > _________________________________________________________________ > Insert movie times and more without leaving Hotmail®. > http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd_062009 > > ----- End forwarded message ----- > n > _______________________________________________ > 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
