Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
External Email - Use Caution Hello Developers! I am getting the same error in several patients (not all). The common error between all of them is this line Waiting for PID 2778 of (2778 2781) to complete... /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 Segmentation fault (core dumped) exec $JOB >> $LOG 2>&1 Waiting for PID 2781 of (2778 2781) to complete... Any idea? Thanks in advance! Emanuel On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo wrote: > Hello FreeSurfer Developers, > > I am running de following command > > /usr/local/freesurfer/subjects/SOME_SUBJECT > /usr/local/freesurfer/bin/recon-all > -s SOME_SUBJECT -i > /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 > - > all -parallel > > > I've searched the list and no similar errors have been reported. Does anyone > have any thoughts on how to trouble-shoot this one? Also, Ive attached the > recon-all.log in case it's of any use. > I have checked the log but I dont find de cause. > > 1) FreeSurfer > version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu > Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > 4) recon-all.log: see attached > > Thanks in advance > Emanuel > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
Hi Emanuel can you give us more details. What was your command line? What was the full job output? What is in the recon-all.log? Does this happen if you run directly instead of through some type of batch server? cheers Bruce On Wed, 30 Oct 2019, Emanuel Alvaredo wrote: External Email - Use Caution Hello Developers! I am getting the same error in several patients (not all). The common error between all of them is this line Waiting for PID 2778 of (2778 2781) to complete... /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 Segmentation fault (core dumped) exec $JOB >> $LOG 2>&1 Waiting for PID 2781 of (2778 2781) to complete... Any idea? Thanks in advance! Emanuel On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo wrote: Hello FreeSurfer Developers, I am running de following command /usr/local/freesurfer/subjects/SOME_SUBJECT /usr/local/freesurfer/bin/recon-all -s SOME_SUBJECT -i /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_ FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - all -parallel I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. I have checked the log but I dont find de cause. 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb 96c 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu S ep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thanks in advance Emanuel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
hmmm, does it always happen for this subject? What if you don't use -parallel? On Thu, 7 Nov 2019, Emanuel Alvaredo wrote: External Email - Use Caution Hi Bruce! Thanks for answer!! * The command line is recon-all -s SUBJECT_NAME -i /patients/SUBJECT_NAME/2_COGNITIVO/4_Accelerated_Ax_IR-FSPGR/i1602413.MRDC.127 -all -parallel * In this mail is attached the log. There is Segmentation fault (core dumped) * This happens running when I call a process from a Java application, but too if I run the command manually. I think this is the problem, but I dont know why. Thanks in advance Emanuel On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl wrote: Hi Emanuel can you give us more details. What was your command line? What was the full job output? What is in the recon-all.log? Does this happen if you run directly instead of through some type of batch server? cheers Bruce On Wed, 30 Oct 2019, Emanuel Alvaredo wrote: > > External Email - Use Caution > > Hello Developers! > I am getting the same error in several patients (not all). The common error > between all of them is this line > > Waiting for PID 2778 of (2778 2781) to complete... > /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 Segmentation fault > (core dumped) exec $JOB >> $LOG 2>&1 > Waiting for PID 2781 of (2778 2781) to complete... > > Any idea? > > Thanks in advance! > > > > Emanuel > > > On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo wrote: > > Hello FreeSurfer Developers, > > I am running de following command > /usr/local/freesurfer/subjects/SOME_SUBJECT > /usr/local/freesurfer/bin/recon-all > -s SOME_SUBJECT -i /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_ > FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - > all -parallel > I've searched the list and no similar errors have been reported. Does anyone > have any thoughts on how to trouble-shoot this one? Also, Ive attached the > recon-all.log in case it's of any use. > I have checked the log but I dont find de cause. > > 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb > 96c > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu S > ep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > 4) recon-all.log: see attached > Thanks in advance > Emanuel > > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
External Email - Use Caution Hi Bruce, same result. Question, Is it possible run two recon-all at the same time? Emanuel On Thu, Nov 7, 2019 at 4:41 PM Bruce Fischl wrote: > hmmm, does it always happen for this subject? What if you don't use > -parallel? > On Thu, 7 Nov 2019, Emanuel Alvaredo wrote: > > > > > External Email - Use Caution > > > > Hi Bruce! Thanks for answer!! > > * The command line is > > > > recon-all -s SUBJECT_NAME -i > > > /patients/SUBJECT_NAME/2_COGNITIVO/4_Accelerated_Ax_IR-FSPGR/i1602413.MRDC.127 > -all -parallel > > > > > > > > * In this mail is attached the log. There is > > > > Segmentation fault (core dumped) > > > > * This happens running when I call a process from a Java application, > but too if I run the > > command manually. > > > > > > > > I think this is the problem, but I dont know why. > > > > Thanks in advance > > > > > > Emanuel > > > > > > On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl < > fis...@nmr.mgh.harvard.edu> wrote: > > Hi Emanuel > > > > can you give us more details. What was your command line? What was > the > > full job output? What is in the recon-all.log? Does this happen if > you > > run directly instead of through some type of batch server? > > > > cheers > > Bruce > > On Wed, 30 Oct > > 2019, Emanuel Alvaredo wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello Developers! > > > I am getting the same error in several patients (not all). The > common error > > > between all of them is this line > > > > > > Waiting for PID 2778 of (2778 2781) to complete... > > > /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 > Segmentation fault > > > (core dumped) exec $JOB >> $LOG 2>&1 > > > Waiting for PID 2781 of (2778 2781) to complete... > > > > > > Any idea? > > > > > > Thanks in advance! > > > > > > > > > > > > Emanuel > > > > > > > > > On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo < > ealvar...@gmail.com> wrote: > > > > > > Hello FreeSurfer Developers, > > > > > > I am running de following command > > > /usr/local/freesurfer/subjects/SOME_SUBJECT > > > /usr/local/freesurfer/bin/recon-all > > > -s SOME_SUBJECT -i > /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_ > > > FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - > > > all -parallel > > > I've searched the list and no similar errors have been reported. > Does anyone > > > have any thoughts on how to trouble-shoot this one? Also, Ive > attached the > > > recon-all.log in case it's of any use. > > > I have checked the log but I dont find de cause. > > > > > > 1) FreeSurfer > version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb > > > 96c > > > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz > > > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic > #31~18.04.1-Ubuntu SMP Thu S > > > ep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > > > 4) recon-all.log: see attached > > > Thanks in advance > > > Emanuel > > > > > > > > >___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
Sure, if you have enough ram and cores > On Nov 7, 2019, at 10:23 PM, Emanuel Alvaredo wrote: > > External Email - Use Caution > > Hi Bruce, same result. > > Question, Is it possible run two recon-all at the same time? > > Emanuel > > >> On Thu, Nov 7, 2019 at 4:41 PM Bruce Fischl >> wrote: >> hmmm, does it always happen for this subject? What if you don't use >> -parallel? >> On Thu, 7 Nov 2019, Emanuel Alvaredo wrote: >> >> > >> > External Email - Use Caution >> > >> > Hi Bruce! Thanks for answer!! >> > * The command line is >> > >> > recon-all -s SUBJECT_NAME -i >> > /patients/SUBJECT_NAME/2_COGNITIVO/4_Accelerated_Ax_IR-FSPGR/i1602413.MRDC.127 >> > -all -parallel >> > >> > >> > >> > * In this mail is attached the log. There is >> > >> > Segmentation fault (core dumped) >> > >> > * This happens running when I call a process from a Java application, but >> > too if I run the >> > command manually. >> > >> > >> > >> > I think this is the problem, but I dont know why. >> > >> > Thanks in advance >> > >> > >> > Emanuel >> > >> > >> > On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl >> > wrote: >> > Hi Emanuel >> > >> > can you give us more details. What was your command line? What was >> > the >> > full job output? What is in the recon-all.log? Does this happen if >> > you >> > run directly instead of through some type of batch server? >> > >> > cheers >> > Bruce >> > On Wed, 30 Oct >> > 2019, Emanuel Alvaredo wrote: >> > >> > > >> > > External Email - Use Caution >> > > >> > > Hello Developers! >> > > I am getting the same error in several patients (not all). The >> > common error >> > > between all of them is this line >> > > >> > > Waiting for PID 2778 of (2778 2781) to complete... >> > > /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 >> > Segmentation fault >> > > (core dumped) exec $JOB >> $LOG 2>&1 >> > > Waiting for PID 2781 of (2778 2781) to complete... >> > > >> > > Any idea? >> > > >> > > Thanks in advance! >> > > >> > > >> > > >> > > Emanuel >> > > >> > > >> > > On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo >> > wrote: >> > > >> > > Hello FreeSurfer Developers, >> > > >> > > I am running de following command >> > > /usr/local/freesurfer/subjects/SOME_SUBJECT >> > > /usr/local/freesurfer/bin/recon-all >> > > -s SOME_SUBJECT -i >> > /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_ >> > > FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - >> > > all -parallel >> > > I've searched the list and no similar errors have been reported. >> > Does anyone >> > > have any thoughts on how to trouble-shoot this one? Also, Ive >> > attached the >> > > recon-all.log in case it's of any use. >> > > I have checked the log but I dont find de cause. >> > > >> > > 1) FreeSurfer >> > version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb >> > > 96c >> > > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz >> > > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu >> > SMP Thu S >> > > ep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux >> > > 4) recon-all.log: see attached >> > > Thanks in advance >> > > Emanuel >> > > >> > > >> > >___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> >___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
