External Email - Use Caution Dear Paul:
Thank you so much for your quick response and we will test on your suggestion! Best regards Xin On Mon, Nov 8, 2021 at 1:15 PM Paul Wighton <[email protected]> wrote: > External Email - Use Caution > > Hi Xin, > > If I understand correctly, recon-all runs successfully in your docker > container when testing it on an EC2 instance, but when trying to run the > same container on AWS batch or fargate, it doesn't make it past the `-fill` > step. Is that correct? > > If so, the first thing I'd like to confirm is that the container has > enough resources (time and memory) when running on AWS batch or fargate. > The recon-all.log you attached shows there is only 8.9Gb of free space > available (line 31). Can you try increasing that so there is 32Gb of space > available? Can you also try doubling the JobTimeout duration? > > Thanks, > > -Paul > > On Sat, Nov 6, 2021 at 12:10 PM Xin Qi <[email protected]> wrote: > >> External Email - Use Caution >> >> Hello FreeSurfer Developers, >> >> We are attempting to use recon-all -all on T1w MRI image analysis. We >> tested it on AWS EC2 in a docker container successfully. The uname -a >> output the EC2 is Linux ip-10-193-42-20 5.11.0-1019-aws #20~20.04.1-Ubuntu >> SMP Tue Sep 21 10:40:39 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux. The docker >> file entrypoint is a job_script.py python code to call a subprocess of bash >> script, like recon-all using a python library called subprocess. >> >> When we used the same docker image with AWS ECS or batch processing, from >> the files created inside the processed subject's mri folder,* the >> recon-all stuck at "-fill" step because the input files (wm.mgz, >> aseg.auto_noCCseg.mgz, and transforms/talairach.lta) are created, but NO >> filled.mgz was created as the output file of "-fill " step in recon-all >> -autorecon2. * >> >> I have searched the list and no similar errors have been reported. Does >> anyone have any thoughts on how to troubleshoot this? Also I have attached >> the reon-all.log in cas it is of any use. >> >> 1). FreeSurfer version: 7.2.0 >> 2). Platform: AWS EC2 batch or ECS Fargate >> >> Looking forward to your feedback. >> >> Best Regards >> Xin >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1Td8FQ5Z5s9j1VyD3HF_Zm2_9rEUvwUfVbzDZoHpDJhG8Hj4LgOniwuMeZJ3nrP8SznB2mZFL7u5WpwA1m8Z-Z2Mt_P20FhCGT2SvhS54rmUxHAGizUvNunfTbgDiZLSqEmSIccndlulP-ccK9XHAK-pwyQ246oMKHM8V--ZOkwK3FEcoe5Ss_vcvjYMgCrAaKpvTtqjifmfT1ifEJEFfRE4_jDN64OWR1T7ylUQJICt0yl4XWn9Uidl3X1eRueGmEJI0_m8-x368sFxQpFv8Fg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1SqeFzz1UKNQJUVqjoOsy-gI1ZvHNCGQk1wsyHVm3QjTWt1Bc4CrowVsrYwVcctL1Qeb_PlEU4reThHIvkNIwhX9sXbuGiXf5tkq6A0r07-_u7VLDOblNFU-953AL9byAdBrC20a6Xdo_s1NGPi0SJNv7mFmSOoBI_0u9_WigG70m1Bt04CJFIDKaz14KJVOycTzAJ0CnHfoSTPfgMpYgTaiKM41dA0pJDHVg8n25j4NicKi422VXWVCYqjwCUGGPfBLOfgFBWH-GEWR3vEFyEw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1Td8FQ5Z5s9j1VyD3HF_Zm2_9rEUvwUfVbzDZoHpDJhG8Hj4LgOniwuMeZJ3nrP8SznB2mZFL7u5WpwA1m8Z-Z2Mt_P20FhCGT2SvhS54rmUxHAGizUvNunfTbgDiZLSqEmSIccndlulP-ccK9XHAK-pwyQ246oMKHM8V--ZOkwK3FEcoe5Ss_vcvjYMgCrAaKpvTtqjifmfT1ifEJEFfRE4_jDN64OWR1T7ylUQJICt0yl4XWn9Uidl3X1eRueGmEJI0_m8-x368sFxQpFv8Fg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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