External Email - Use Caution
Hi, I'm trying to open freeview in a linux node in my institution's
computing cluster and an error is coming up consistently - see below. Can
you please advise? Thank you.
agc01:~ moana004$ module list
> No Modulefiles Currently Loaded.
> agc01:~ moana004$ module load freesurfer/6.0.0
> agc01:~ moana004$
> study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex02; \
> > subjID_list="20005 10015 11012"; \
> > for subjID in ${subjID_list}; do freeview
> ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/brainmask.gcuts.mgz:colormap=heat
> ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/T1.mgz:opacity=0.5;
> done
> libGL error: unable to load driver: swrast_dri.so
> libGL error: failed to load driver: swrast
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXbinUuAdIwcI0iRqe6KosyMKzWJq_kkReHZMfQMDhUHX3sHlUgUCEkU4XEOVVn-u2KtOf9LJ4sVNsGrNoauhQO_onuf_mvcuPTFxx8o39H4zCrl3lYXguL-r0BVaoORQIfA7PHqlLGpQ6qwCRVzlLs7A8q_mmDyyBbnpSu-VuQ5AtLTNeBRL5wKhCcIzIM4cSYpsztm9q1QVbHUuobd8L4mlLPi8jdsfTbOr0AiELvxbRPWPA_17c3xezx4gOAo7leN4se5Lw_dJq88bFxbg/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal[0]PETSC
> ERROR:
> or try
> http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwPz-rO-J1FzW6RPFhzjZ_DXULTjfDx7Tl3HkIFUWssfo_12FO0ZDaoyOkaJJ9NA3KDFT-WUV0Vs02nlPzcZsSaxemALkmavfAuE5-faK5-MEB5BmObdCUTf9A-8aEVtc3hW_Pd4BapjsUgSwXmzP5SIr4EIvObSju9mketw_eQ6rgURbuk78DM5GPWoKe1RErdc8mN8OMlJQXHLLfcPHZppsgwx7JIiD6kyDjxXzidtVNKt5K8snPYU12Id4NiL_KDUUCsAAtaunRZcJC9Lv/http%3A%2F%2Fvalgrind.org
> on linux or man libgmalloc on Apple to find
> memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Unknown Name on a linux-gnu named agc01 by moana004 Fri
> Mar 10 11:22:48 2023
> [0]PETSC ERROR: Libraries linked from
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> libGL error: unable to load driver: swrast_dri.so
> libGL error: failed to load driver: swrast
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXbinUuAdIwcI0iRqe6KosyMKzWJq_kkReHZMfQMDhUHX3sHlUgUCEkU4XEOVVn-u2KtOf9LJ4sVNsGrNoauhQO_onuf_mvcuPTFxx8o39H4zCrl3lYXguL-r0BVaoORQIfA7PHqlLGpQ6qwCRVzlLs7A8q_mmDyyBbnpSu-VuQ5AtLTNeBRL5wKhCcIzIM4cSYpsztm9q1QVbHUuobd8L4mlLPi8jdsfTbOr0AiELvxbRPWPA_17c3xezx4gOAo7leN4se5Lw_dJq88bFxbg/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal[0]PETSC
> ERROR:
> or try
> http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwPz-rO-J1FzW6RPFhzjZ_DXULTjfDx7Tl3HkIFUWssfo_12FO0ZDaoyOkaJJ9NA3KDFT-WUV0Vs02nlPzcZsSaxemALkmavfAuE5-faK5-MEB5BmObdCUTf9A-8aEVtc3hW_Pd4BapjsUgSwXmzP5SIr4EIvObSju9mketw_eQ6rgURbuk78DM5GPWoKe1RErdc8mN8OMlJQXHLLfcPHZppsgwx7JIiD6kyDjxXzidtVNKt5K8snPYU12Id4NiL_KDUUCsAAtaunRZcJC9Lv/http%3A%2F%2Fvalgrind.org
> on linux or man libgmalloc on Apple to find
> memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Unknown Name on a linux-gnu named agc01 by moana004 Fri
> Mar 10 11:22:50 2023
> [0]PETSC ERROR: Libraries linked from
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> libGL error: unable to load driver: swrast_dri.so
> libGL error: failed to load driver: swrast
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXbinUuAdIwcI0iRqe6KosyMKzWJq_kkReHZMfQMDhUHX3sHlUgUCEkU4XEOVVn-u2KtOf9LJ4sVNsGrNoauhQO_onuf_mvcuPTFxx8o39H4zCrl3lYXguL-r0BVaoORQIfA7PHqlLGpQ6qwCRVzlLs7A8q_mmDyyBbnpSu-VuQ5AtLTNeBRL5wKhCcIzIM4cSYpsztm9q1QVbHUuobd8L4mlLPi8jdsfTbOr0AiELvxbRPWPA_17c3xezx4gOAo7leN4se5Lw_dJq88bFxbg/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal[0]PETSC
> ERROR:
> or try
> http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwPz-rO-J1FzW6RPFhzjZ_DXULTjfDx7Tl3HkIFUWssfo_12FO0ZDaoyOkaJJ9NA3KDFT-WUV0Vs02nlPzcZsSaxemALkmavfAuE5-faK5-MEB5BmObdCUTf9A-8aEVtc3hW_Pd4BapjsUgSwXmzP5SIr4EIvObSju9mketw_eQ6rgURbuk78DM5GPWoKe1RErdc8mN8OMlJQXHLLfcPHZppsgwx7JIiD6kyDjxXzidtVNKt5K8snPYU12Id4NiL_KDUUCsAAtaunRZcJC9Lv/http%3A%2F%2Fvalgrind.org
> on linux or man libgmalloc on Apple to find
> memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Unknown Name on a linux-gnu named agc01 by moana004 Fri
> Mar 10 11:22:51 2023
> [0]PETSC ERROR: Libraries linked from
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> agc01:~ moana004$
>
--
Estephan J. Moana-Filho, DDS, MS, PhD
Assistant Professor
Division of TMD, Orofacial Pain and Dental Sleep Medicine
Graduate Faculty in Oral Biology
Department of Diagnostic and Biological Sciences
UMN School of Dentistry
moana...@umn.edu
6-320d Moos Tower
515 Delaware St. SE
Minneapolis, MN 55455-0329
Office: (612) 624-3338 Clinic: (612) 626-0140 Fax: (612) 626-0138
Clinical referrals: z.umn.edu/TMDrefer
UMN profile:
https://secure-web.cisco.com/1qDzqxV8A0saK5iVzOb_YFpj8bFrtMnaV7PlkTYT0_-gJxAabtJwshqpK5rL_1Ll91imEtniqiWzosl0EhfZ5rq_WJZkv3ZL_LD3V0tIhdx-Nq2Vu8-qAunoVzARNb5NAQUd1sQpag1HaIQL4i6J1ucknmH1sYG8Hcqp_Gc7bwb3PJmu7BM-wO7RGXnWZghgIsNi_E-2hxQXkAR1AoG7-qUeswH-eGsbsU8OP6iemHUtWHRMK2RXT7z36RT3TPbVCuNsDNxK3H07UPKR9DQ5pzcOWO99peFCSh3Ksfvx_cMEC6MqOQmVndlB89BuuBG5h/https%3A%2F%2Fexperts.umn.edu%2Fen%2Fpersons%2Festephan-j-moana-filho
ORCID ID:
http://secure-web.cisco.com/1_aaPiXWbc5YByvuEhM2gYDWPGPbSIFVNqn8PmXWXc3hUEsDf8EkIIUYq_PDIt5j8JesaT5fhTDIU0pd7cez8tCH1gjh3Ir-H_Eesf-bY_dI6irFkXprK52W70UQcyRFgeWZ9Ffdyrb6jFlEZWd8CZSJKo4yXNfwuLeBiHQEq4gRPZytSYXYEO_2DVzUk-ii_keopZ0hBJzD6Wucz4k_6uEThstj5cx73e9tzY_9w81zU68cuGvrkX9lj5_uqv6r8NLqAhGTsUD8ehXMBYp86thWp0tUjao8BjpY8AsMrQX-mWt5Oagj7gbODORUKXWwv/http%3A%2F%2Forcid.org%2F0000-0001-9642-944X
Publons:
https://secure-web.cisco.com/1xpdcvUYZasLT9y5HJGpNs2tmC4cot__gVR6i_BeYNss6zR52hlbPVQHDwHE2Sc7velXCRzOAF0Ynf_25xaok8hxqZnEVmvd6FHo30yVW1zfcXKOUoHVeXZ2jtyZW2cr49nii0p1JobNJb6R_aPORO_fxmgiAuxJ31ZOIV3svLNIT6S__0afTVbKCkb9SXSafVHGZF8DQu6MXbaMm7R9MEdXakV_gTZwZLJg4VKeusLM3clDpfv__ZDz01snc5hmrFBWzPCPNPkvwhdzYB0fYzKUHG5Z3uctcJbqNZPG5_PJa2optqAmq1uLNG0pswhnG/https%3A%2F%2Fpublons.com%2Fresearcher%2FO-9726-2016%2F
My Bibliography (NCBI):
https://secure-web.cisco.com/107k1mETeQHnb4m4TKKH4M_6g4tY9rwD3cvRPnRFwNezv_CtoA6SN-la_RUhMeyq8po5acluIBCXITSovz15Ru_Pea_eEoK3jQ9mDuf_oiJsBdbYVsdNBxsVPWqJ0CgeSpfvEmPNMPiYgkuL2bHnzQ_8bFw5fvQthrCOzK1PjG4w0hKP8ibefqB5GaFER6iacrB_c9GRldS9Gg1KQdDskfTR_tYtqFQdzBEYLxxUMcZlzhYLD-rgS21u1GBpZ6nDfIit0zygnOQIgSu6d3Pul8ey2gcflwB35ze52SvCyCEWtCOB4W837sooLweaIzUGX/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fmyncbi%2Festephan.moana-filho.1%2Fbibliography%2Fpublic%2F
The information transmitted in this e-mail is intended only for the person
or entity to which it is addressed and may contain confidential and/or
privileged material, including "protected health information." If you are
not the intended recipient, you are hereby notified that any review,
retransmission, dissemination, distribution, or copying of this message is
strictly prohibited. If you have received this communication in error,
please destroy and delete this message from any computer and contact us
immediately by return e-mail.
_______________________________________________
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.
