Re: [Freesurfer] Command terminated by signal 11 when execute mris_place_surface
External Email - Use Caution
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 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: 1000100010001000
> Gid: 1000100010001000
> 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:0x
> Threads: 200 SigQ: 0/128234
> SigPnd:
> ShdPnd:
> SigBlk:
> SigIgn:
> SigCgt:0001
> CapInh:
> CapPrm:
> CapEff:
> CapBnd:01ff
> CapAmb:
> NoNewPrivs:0
> Seccomp: 0
> Seccomp_filters: 0
> Speculation_Store_Bypass: thread vulnerable
> SpeculationIndirectBranch: conditional enabled
> Cpus_allowed:
> Cpus_allowed_list: 0-15
> Mems_allowed:
>
> ,,,,,,,,,,,,,000
Re: [Freesurfer] Command terminated by signal 11 when execute mris_place_surface
External Email - Use Caution Hello there, Thanks for quickly response, due to email size limit ,I can't upload dump file via email , how can I provide my dump file ? Thanks. fsbuild 于2024年2月6日周二 14:33写道： > > I would look for the core file under /var/crash as close to the time to > the command failure and see what it says. > > Signal 11 is a segmentation violation meaning invalid memory access. It > could be that a VM on your machine does not have enough memory to run > recon-all. Or I assume the 32G RAM listed below is the total physical > RAM on the machine and the VM has some portion of that assigned to it. If > you did not assign the VM say 16G-24G of RAM out of that 32G total, then it > might be having a memory issue. You could try not running anything else on > the machine, giving the VM 24G and that would leave 8G for the host > machine. You could also try giving the VM 4 out of the 16 CPUs as well. > > - R. > > On Feb 6, 2024, at 00:39, Yp Ben wrote: > > External Email - Use Caution > > 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 > …. > > Command terminated by signal 11 > ... > Check the core dump file under /var/crash > ... > 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 . > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1qmLFE12eP5SRWEwkdnsUn16tH_GgBJOBbknqMeGTv8piaOThSgMRl4zSasTs1_2CWvRliLfg9q8k4DvRzuGoJ2dfH0yvCX4deMwGovCEO4dt9W2_hab6IfPmEg7poBNS8anem2ZSN5p2kfMVckj22qludJhWVwGu3qQSNQDNqc7hqS3kMInfBQ93cw-5cref8LuZTNWGIacdccV6181mAHb-2nPIsEbMargDTTutDtaWldmko3QXV7yn9-0SlPCHewbRoWGDHokAJ23nG2lgv7bPiJ1TBn4VQcGSYPn_ODpZK6x3nfjeJHN4oXPCTwWu/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Command terminated by signal 11 when execute mris_place_surface
External Email - Use Caution
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/1gYb-2hE-QjkoVlTlGmx1IVV7-IUAB7paWJo1QUb0Vj4ezaR8LII1FERoMOISc_G5vLoz5lviLvaCMZaELkJ2MygS0ul9Dn3JBIV1RtRd1vO54v1TRxAu-YgSDRTI8jIR5W27dmKjmog1Kek_A2-1Id2MidRaj88bWYvsm5ySBraq1DqvrdRXiG6yRjd-L0lIxzODdeWhPhlWqqCqndfjUT9Mm83VdOTTiDipArhYBg_JDQOFt-a5vfYqkg8TKn9EKe15CHXj-qtEEhOAM07Skpg607mhQ025411Y-LcyB7XJRl8KoQ09R1Ii0aUZ88PVvmqTx3p-JAPVS-SuSu8npQ/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: 1000100010001000
Gid: 1000100010001000
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:0x
Threads: 200 SigQ: 0/128234
SigPnd:
ShdPnd:
SigBlk:
SigIgn:
SigCgt:0001
CapInh:
CapPrm:
CapEff:
CapBnd:01ff
CapAmb:
NoNewPrivs:0
Seccomp: 0
Seccomp_filters: 0
Speculation_Store_Bypass: thread vulnerable
SpeculationIndirectBranch: conditional enabled
Cpus_allowed:
Cpus_allowed_list: 0-15
Mems_allowed:
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0003
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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