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Hello freesurfer experts ,
I change the command and reduce the threads from 200 to 50 , seems ok now ,
I use the cluster to run the jobs and submit jobs to cluster, I found there
have several jobs assigned to the same node , do this be ok to run
different subjects in one node with the same time ? Thanks.
Yp Ben <benyoup...@gmail.com> 于2024年2月6日周二 13:39写道：
> Hello FreeSurfer Developers,
>
> I'm want to run HCP T1W data of recon-all , but it always failed on step
> " WhitePreAparc lh", below is my run information:
> OS: Ubuntu 22.04.2 LTS
> MEM: 32G
> CPU: 16
>
> Freesurfer Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
>
> Command:
> export SUBJECTS_DIR=$(pwd)
> nohup recon-all -s $1 -i $(ls *${1}*) -all -qcache -3T -parallel -openmp
> 16 -threads 200 > nohup_${1}.log 2> nohup_${1}.log &
>
> Error messages as below:
> mris_autodet_gwstats done
> @#@FSTIME 2024:02:06:05:28:14 mris_autodet_gwstats N 8 e 5.75 S 1.02 U
> 8.70 P 169% M 277604 F 3 R 131626 W 0 c 403 w 6466 I 0 O 8 L 1.96 14.01
> 13.54
> @#@FSLOADPOST 2024:02:06:05:28:20 mris_autodet_gwstats N 8 1.96 13.81 13.47
> #--------------------------------------------
> #@# WhitePreAparc lh 2024年 02月 06日 星期二 05:28:20 CST
> cd /home/tben/ds000102/HCA6139970_V1_MR/mri
> mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz
> --threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o
> ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
> 7.4.1
> 7.4.1
>
> cd /home/tben/ds000102/HCA6139970_V1_MR/mri
> setenv SUBJECTS_DIR /home/tben/ds000102
> mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz
> --threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o
> ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
>
> Command terminated by signal 11
> @#@FSTIME 2024:02:06:05:28:20 mris_place_surface N 18 e 24.22 S 4.47 U
> 1.71 P 25% M 185596 F 9 R 46047 W 0 c 184 w 12734 I 1296 O 0 L 1.96 13.81
> 13.47
> @#@FSLOADPOST 2024:02:06:05:28:44 mris_place_surface N 18 69.96 28.86 18.46
> Linux tben-dev-server 6.5.0-15-generic #15~22.04.1-Ubuntu SMP
> PREEMPT_DYNAMIC Fri Jan 12 18:54:30 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s HCA6139970_V1_MR exited with ERRORS at 2024年 02月 06日 星期二
> 05:28:45 CST
>
> For more details, see the log file
> /home/tben/ds000102/HCA6139970_V1_MR/scripts/recon-all.log
> To report a problem, see
> http://secure-web.cisco.com/1soATQZ1AnuA1BePnpvsKZY6noRO1D_NKP3ktYxdGpbc46jBBfb66Kk98nQEd7cToAZ6xkufBDAKaKj5XLVlmrIynx34OuetEvx16iA_ThaYlazxCjgmHQSI1HNVHJYpFCVCyIXo09mcghcvrig74kIa8IJ_ZOswsGw26wXfp-uVF8_uqzISA12elH7ySeiKMSeUzlFkwRbB914-sYkfzS-GCYEsFOJ9edd9ADaXEd5h4fF19wOVzezr1402ZtXv9QRui034tHyTU45jCYH_FARrGm-k6T4P-MTamv9JkFWxBr2mv54wRbVir8NRVFEFD/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
>
>
> Check the core dump file under /var/crash
> vim _opt_freesurfer_bin_mris_place_surface.1000.crash
> ProcStatus:
> Name: mris_place_surf
> Umask: 0002
> State: S (sleeping)
> Tgid: 23410
> Ngid: 0
> Pid: 23410
> PPid: 22657
> TracerPid: 0
> Uid: 1000 1000 1000 1000
> Gid: 1000 1000 1000 1000
> FDSize: 64
> Groups: 4 24 27 30 46 122 134 135 1000
> NStgid: 23410
> NSpid: 23410
> NSpgid: 23410
> NSsid: 22657
> Kthread: 0
> VmPeak: 10878292 kB
> VmSize: 10394436 kB
> VmLck: 0 kB
> VmPin: 0 kB
> VmHWM: 185500 kB
> VmRSS: 185500 kB
> RssAnon: 179356 kB
> RssFile: 6144 kB
> RssShmem: 0 kB
> VmData: 2068316 kB
> VmStk: 132 kB
> VmExe: 3084 kB
> VmLib: 3820 kB
> VmPTE: 1772 kB
> VmSwap: 0 kB
> HugetlbPages: 0 kB
> CoreDumping: 1
> THP_enabled: 1
> untag_mask: 0xffffffffffffffff
> Threads: 200 SigQ: 0/128234
> SigPnd: 0000000000000000
> ShdPnd: 0000000000000000
> SigBlk: 0000000000000000
> SigIgn: 0000000000000000
> SigCgt: 0000000100000000
> CapInh: 0000000000000000
> CapPrm: 0000000000000000
> CapEff: 0000000000000000
> CapBnd: 000001ffffffffff
> CapAmb: 0000000000000000
> NoNewPrivs: 0
> Seccomp: 0
> Seccomp_filters: 0
> Speculation_Store_Bypass: thread vulnerable
> SpeculationIndirectBranch: conditional enabled
> Cpus_allowed: ffff
> Cpus_allowed_list: 0-15
> Mems_allowed:
>
> 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
> Mems_allowed_list: 0-1
> voluntary_ctxt_switches: 21
> nonvoluntary_ctxt_switches: 17
> Signal: 11
> Uname: Linux 6.5.0-15-generic x86_64
> UserGroups: adm cdrom dip lpadmin lxd plugdev sambashare sudo
> CoreDump: base64
>
> I use 3 different VMs to run the same sample with different freesurfer
> versions , 2 are 7.4.1 and another one is 7.2 , but always failed on this
> step , I don't know what's the reason cause this failed , can you please
> help to have a look ? Thanks a lot .
>
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