Hi,
This error suggests that your cluster instance is not able to find the swrast
drivers:
libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
swrast is a software renderer. It is provided by libgl1-mesa-dri library. If
the library is not installed, you can install it - though the exact
installation steps would depend on your OS. I'd advice to contact the
maintainers of your compute cluster for this error.
________________________________
From: [email protected]
<[email protected]> on behalf of Estephan Moana Filho
<[email protected]>
Sent: Friday, March 10, 2023 12:59 PM
To: [email protected] <[email protected]>
Subject: [Freesurfer] Freeview error
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 MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC<http://secure-web.cisco.com/1xBVMH7lnCEhUq9J5hsq5IuQWk3qEq0TYSuhzQe5BEwAIcoo_Ph2jMDpJW_bezKEUUHzz2fK7dDhSW-8id6Oueij27SJdAkDwBYIzlcFoGyiueE_dDjwDmC8QsYLEzRzKJaqJbvS-bSde41-Qb-iRAR4E_QYNC7Vr4rQztWhIKfMAMsp0fVxhLNiJAJcy2CLdAamFubSkH5DzggwUbrtTL-dR9xM5y1GVB9dYuSejFn4Tc7Kd4uAaso_mjMivlvhIymCnKQD1ZK-RPcczxUc8pjQaIItJqR6ivhNv_2RnyAaoBL8wqxRydIJ-5dSy6q3y/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal%5B0%5DPETSC>
ERROR: or try MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://valgrind.org<http://secure-web.cisco.com/1koEldMN_Nux-AKyw6PB_HunrQTVcL6gNek0fymq4gNBgw_YlwUMFxL-HyUhOj8Y1H1Q1fZOnwvnWg9pYU3FNe6PP_Br-JPQM-PbaDqHdx7n2uMOFpFQhbtXbQwdTqXM6F_Y-_S5b79yCDLf4wpTVf26VqQwJgd7wwahUBtPXI_IJo7FdAqAbKynBkix5oLK_DYGI67GqYJC3PmALEekgeRYfuXueJqL_VbtuS15bXwKoDCjgKmLRhXqWp5fb6mVozKd5pXpXH4X_ZN9DWSal7bTva3ln5LI01McljU-CpxN-JqrVPmilgUFw1oFiHM1p/http%3A%2F%2Fvalgrind.org%2F>
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 MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC<http://secure-web.cisco.com/1xBVMH7lnCEhUq9J5hsq5IuQWk3qEq0TYSuhzQe5BEwAIcoo_Ph2jMDpJW_bezKEUUHzz2fK7dDhSW-8id6Oueij27SJdAkDwBYIzlcFoGyiueE_dDjwDmC8QsYLEzRzKJaqJbvS-bSde41-Qb-iRAR4E_QYNC7Vr4rQztWhIKfMAMsp0fVxhLNiJAJcy2CLdAamFubSkH5DzggwUbrtTL-dR9xM5y1GVB9dYuSejFn4Tc7Kd4uAaso_mjMivlvhIymCnKQD1ZK-RPcczxUc8pjQaIItJqR6ivhNv_2RnyAaoBL8wqxRydIJ-5dSy6q3y/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal%5B0%5DPETSC>
ERROR: or try MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://valgrind.org<http://secure-web.cisco.com/1koEldMN_Nux-AKyw6PB_HunrQTVcL6gNek0fymq4gNBgw_YlwUMFxL-HyUhOj8Y1H1Q1fZOnwvnWg9pYU3FNe6PP_Br-JPQM-PbaDqHdx7n2uMOFpFQhbtXbQwdTqXM6F_Y-_S5b79yCDLf4wpTVf26VqQwJgd7wwahUBtPXI_IJo7FdAqAbKynBkix5oLK_DYGI67GqYJC3PmALEekgeRYfuXueJqL_VbtuS15bXwKoDCjgKmLRhXqWp5fb6mVozKd5pXpXH4X_ZN9DWSal7bTva3ln5LI01McljU-CpxN-JqrVPmilgUFw1oFiHM1p/http%3A%2F%2Fvalgrind.org%2F>
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 MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC<http://secure-web.cisco.com/1xBVMH7lnCEhUq9J5hsq5IuQWk3qEq0TYSuhzQe5BEwAIcoo_Ph2jMDpJW_bezKEUUHzz2fK7dDhSW-8id6Oueij27SJdAkDwBYIzlcFoGyiueE_dDjwDmC8QsYLEzRzKJaqJbvS-bSde41-Qb-iRAR4E_QYNC7Vr4rQztWhIKfMAMsp0fVxhLNiJAJcy2CLdAamFubSkH5DzggwUbrtTL-dR9xM5y1GVB9dYuSejFn4Tc7Kd4uAaso_mjMivlvhIymCnKQD1ZK-RPcczxUc8pjQaIItJqR6ivhNv_2RnyAaoBL8wqxRydIJ-5dSy6q3y/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal%5B0%5DPETSC>
ERROR: or try MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://valgrind.org<http://secure-web.cisco.com/1koEldMN_Nux-AKyw6PB_HunrQTVcL6gNek0fymq4gNBgw_YlwUMFxL-HyUhOj8Y1H1Q1fZOnwvnWg9pYU3FNe6PP_Br-JPQM-PbaDqHdx7n2uMOFpFQhbtXbQwdTqXM6F_Y-_S5b79yCDLf4wpTVf26VqQwJgd7wwahUBtPXI_IJo7FdAqAbKynBkix5oLK_DYGI67GqYJC3PmALEekgeRYfuXueJqL_VbtuS15bXwKoDCjgKmLRhXqWp5fb6mVozKd5pXpXH4X_ZN9DWSal7bTva3ln5LI01McljU-CpxN-JqrVPmilgUFw1oFiHM1p/http%3A%2F%2Fvalgrind.org%2F>
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
[email protected]<mailto:[email protected]>
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<http://secure-web.cisco.com/1h7mq5tvgz97pw6FhgTn5E5w9xg59cSgBfhbhpcFRnDwlxgECKz74z_O4HC5Vpauq9Bzb1aqW-K6cpQfacSUHWWcoPurmSgBotx4DPy1p3lXXthec-vIppj04wl5kLg5RKinZY92y_Hpcr3vawnmvAVqvcW12UfGj1vGxBMMkqJIy3gRqZe2g6zYoWH1LM6OZtCUFr7IzYC2u7mm0o0ErHFzm60EPh3-_MfMhHu3cF6IHfjKqJLpj5rpw1_tj3p79LzrLisY2hPVOO-nO-aJD6AcVQmGYy-XdCxDQ90CoRCwQHCIUgaA0zvaaUmSOmTie/http%3A%2F%2Fz.umn.edu%2FTMDrefer>
UMN profile: MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://experts.umn.edu/en/persons/estephan-j-moana-filho<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: MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://orcid.org/0000-0001-9642-944X<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: MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://publons.com/researcher/O-9726-2016/<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): MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://www.ncbi.nlm.nih.gov/myncbi/estephan.moana-filho.1/bibliography/public/<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>
[https://secure-web.cisco.com/1BxJ_p0ZQgo1xyQ3uU4jDmtvSdjCubmCd8DNmWuWm9BUvfdm_m85DEzWqzRJaNbJEQ621srhdF5nllp9T_w7m_7MJ6iqpiSE-_F4XzDm-RNEcF5Say1NDK67RYIcGjkAbyRItxLaipQ8Dicj6JBZ45B9qPQz5T6xNXkgX94c-N-iuGfgZjKpKGRIbL33cCrqAX-2qeVWXCjg2Ztrgz2nPHy2cYQm-ZEh8afFoIBAS_HdG0Plf_sXexTyd11ILPvHiTW5q7g5ktNWrC1MSrujD68bXK8cHHEe0H6RYLVqT_JuzKtp1Z-SNHVeFFFYpSbkB/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4yncn7TuIgDhP7nzTlrzSXcMdNPTNU61-9fu4ds8CUtmxZTcCv30qC68X-dNsNtkybgsL3PH3s]
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