Hi Jon – This log file also has output only from trac-all –path, and not from trac-all –prep. I’ll have to see the output from all steps. Thanks!
a.y From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Whitney, Jon" <jon.whit...@ert.com<mailto:jon.whit...@ert.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, October 31, 2018 at 9:57 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Segmentation fault External Email - Use Caution Yes, here is the log file. Thanks for your help! -Jon On Tue, Oct 30, 2018 at 5:34 PM Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote: Hi Jon - I suspect that the source of the problem is before the -path step, but your trac-all.log only has output from that step. Did you by any chance move the original trac-all.log file somewhere else? Typically with every new invocation of trac-all the new output is just appended at the end of the log file. a.y ________________________________ From:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Whitney, Jon <jon.whit...@ert.com<mailto:jon.whit...@ert.com>> Sent: Monday, October 29, 2018 4:59:17 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: Walia, Piyush Subject: Re: [Freesurfer] Segmentation fault External Email - Use Caution I got someone to help me, and based on what they told me the trac-all.log is where the debug information gets stored (I tried using -x +x in my bash command script and it only gave me upper level debugging information), so I have attached the trac-all.log file. I also was able to get help from someone who was able to save the core dump for when the system crashed, but it is extremely large (1.7GB). I can upload the core dump file if that would be helpful. I watched the system resources while the program ran, and I noticed that the memory usage only got up to 4% while the CPU usage was 100%, so I don't think I'm running out of memory. We looked at the core dump file, and my linux expert friend suggested that it may be a memory overflow error because it references memory at 0x0000000etc. [image.png] unfortunately, without the source code to help us interpret the core dump, I don't think I can provide much more in the way of specific information. Please let me know if there's somewhere I can upload the core dump if you want to look at it. Thanks! On Mon, Oct 29, 2018 at 1:32 AM fsbuild <fsbu...@contbay.com<mailto:fsbu...@contbay.com>> wrote: External Email - Use Caution Hello Jon, Can you get any stack or backtrace information after the segfault occurs ?, e.g., Mac OS has the option to display the crash report with a trace. On Linux you could run thru gdb and get a back trace. This would help us to see where the code is exiting. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jon Whitney Image Analysis Engineer ERT | 26801 Miles Rd | Cleveland, OH 44128 | USA ert.com <https://www.ert.com/> [http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227/img]<http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227> Notice: This e-mail message, together with any attachments, contains information of ERT that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jon Whitney Image Analysis Engineer ERT | 26801 Miles Rd | Cleveland, OH 44128 | USA ert.com <https://www.ert.com/> [http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227/img]<http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227> Notice: This e-mail message, together with any attachments, contains information of ERT that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it.
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