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 > > > > > > > > > > > > > > > > > > _________________________________________________________________ > > > Hotmail� has ever-growing storage! 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