New subject: Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}

5 Nov 2020


      External Email - Use Caution
Hello Ali,
I would try using the RPM installer which should at least check some dependencies on X packages, system libraries, etc.,&nbsp;
https://secure-web.cisco.com/1QZVOusYuqG6pzgftW11woMO3J7wlOTz6CpOKDAkTB2PSKd...
- R.
On Nov 5, 2020, at 22:39, Snedden, Ali &lt;Ali.Snedden@nationwidechildrens.org&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello,&nbsp;&nbsp;I’ve seen a couple mentions on the list-serv about difficulties using Freesurfer on CentOS 8.&nbsp; &nbsp;My issue is likely similar, but I have a few more details.&nbsp; I downloaded freesurfer-linux-centos8_x86_64-7.1.0.tar.gz.&nbsp;&nbsp; When I launch `freeview`, it pops up a white/empty X window for a moment and then quickly disappears.&nbsp;&nbsp;&nbsp;E.g.&nbsp;$ freeviewMESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)libGL error: failed to load driver: swrastAborted (core dumped)&nbsp;I vaguely recall that the libGL errors _aren’t_ fatal.&nbsp; I’ve seen them with other X applications.&nbsp; Digging around the abort logs, I found the stack trace (see&nbsp;end&nbsp;of email).&nbsp;&nbsp;Do you have thoughts on this?&nbsp; I thought it might be a VTK compatibility issue, but that is a guess at best.&nbsp;Best regards,Ali&nbsp;&nbsp;###################### The stack trace ########################&nbsp;[ccpp-2020-11-05-09:15:34-22241]# cat core_backtrace{ &nbsp; "signal": 6, &nbsp; "executable": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview", &nbsp; "only_crash_thread": true, &nbsp; "stacktrace":&nbsp; &nbsp; &nbsp; [ { &nbsp; "crash_thread": true&nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "frames":&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; [ { &nbsp; "address": 140352624871839&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "build_id_offset": 227743&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "function_name": "raise"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "file_name": "/usr/lib64/libc-2.28.so"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; }&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , { &nbsp; "address": 140352624782581&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "build_id_offset": 138485&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "function_name": "abort"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "file_name": "/usr/lib64/libc-2.28.so"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; }&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , { &nbsp; "address": 140352824105729&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "build_id_offset": 1358593&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "function_name": "vtkXOpenGLRenderWindow::CreateAWindow()"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; }&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 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, &nbsp; "function_name": "QCoreApplication::exec()"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; }&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , { &nbsp; "address": 4615883&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "build_id": "0de18d9e888c309c18e5e9450078f0fa6f19efa3"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "build_id_offset": 421579&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; , &nbsp; "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; } ]&nbsp; &nbsp; &nbsp; &nbsp; } ]}&nbsp;_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}