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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-IUAB7paWJo1QUb0Vj4ezaR...
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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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 benyoupeng@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_NKP3ktYxdGpbc46jB...
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 .
freesurfer@nmr.mgh.harvard.edu
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Yp Ben