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: hranilovich@ucla.edu [hranilovich@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 dhaglerjr@hotmail.com ----- Date: Mon, 8 Jun 2009 11:19:43 -0700 From: Don Hagler dhaglerjr@hotmail.com Reply-To: Don Hagler dhaglerjr@hotmail.com Subject: RE: [Freesurfer] vtkMultiThreader error To: nicks@nmr.mgh.harvard.edu, martin.kavec@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: nicks@nmr.mgh.harvard.edu To: martin.kavec@gmail.com; dhaglerjr@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
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