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