External Email - Use Caution        

Hello Ali,

The swrast error can happen if Nvidia grpahics drivers were installed using Nvidia’s own packages/download and then subsequently, your CentOS8 kernel was updated via the CentOS package management tools, i.e. the Nvidia software may then be incompatible with the upgraded system.  I think there are Nvidia packages in the CentOS package repos, and using those to re-install the Nvidia software could fix those kinds of errors.

Currently the freesurfer RPM install path is not relocatable.  I’m not sure relocation would help as I think admin/root privileges would still be needed to for the installation process to download and install any system system dependent packages the freesurfer RPM indicates are needed.

I would ask your IT folks (with root/admin privileges) to look into updating the Nvidia software and also install the freesurfer RPM for you.  They may already have a way to share/mount/mirror what the freesurfer RPM will install under the unique path /usr/local/freesurfer/7.1.1 from one machine to another.

-R.

On Nov 6, 2020, at 09:29, Snedden, Ali <Ali.Snedden@nationwidechildrens.org> wrote:

        External Email - Use Caution        


Hello,
 
Thank you for the response.  I am working on a computer cluster where we install all user software on a shared filesystem.  Looking at the RPM, it does not seem that I can install it in a path of my choosing (i.e. not in /usr).
 
i.e..
$ rpm -qpi freesurfer-CentOS8-7.1.0-1.x86_64.rpm | head -15 | grep Relocations
Relocations : (not relocatable)
 
Is there a strategy for installing the rpm in a custom path?
 
Best,
Ali
 
 
From: fsbuild <fsbuild@contbay.com>
Date: Thursday, November 5, 2020 at 11:47 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "Snedden, Ali" <Ali.Snedden@nationwidechildrens.org>
Subject: Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1
 
Hello Ali,
 
I would try using the RPM installer which should at least check some dependencies on X packages, system libraries, etc., 
 
 
- R.
 
 
On Nov 5, 2020, at 22:39, Snedden, Ali <Ali.Snedden@nationwidechildrens.org> wrote:
 
        External Email - Use Caution        
 
Hello, 
 
I’ve seen a couple mentions on the list-serv about difficulties using Freesurfer on CentOS 8.   My issue is likely similar, but I have a few more details.  I downloaded freesurfer-linux-centos8_x86_64-7.1.0.tar.gz.   When I launch `freeview`, it pops up a white/empty X window for a moment and then quickly disappears.  
 
E.g. 
$ freeview
MESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)
libGL error: failed to load driver: swrast
Aborted (core dumped)
 
I vaguely recall that the libGL errors _aren’t_ fatal.  I’ve seen them with other X applications.  Digging around the abort logs, I found the stack trace (see end of email). 
 
Do you have thoughts on this?  I thought it might be a VTK compatibility issue, but that is a guess at best.
 
Best regards,
Ali
 
 
###################### The stack trace ########################
 
[ccpp-2020-11-05-09:15:34-22241]# cat core_backtrace
{   "signal": 6
,   "executable": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"
,   "only_crash_thread": true
,   "stacktrace":
      [ {   "crash_thread": true
        ,   "frames":
              [ {   "address": 140352624871839
                ,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"
                ,   "build_id_offset": 227743
                ,   "function_name": "raise"
                ,   "file_name": "/usr/lib64/libc-2.28.so"
                }
              , {   "address": 140352624782581
                ,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"
                ,   "build_id_offset": 138485
                ,   "function_name": "abort"
                ,   "file_name": "/usr/lib64/libc-2.28.so"
                }
              , {   "address": 140352824105729
                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
                ,   "build_id_offset": 1358593
                ,   "function_name": "vtkXOpenGLRenderWindow::CreateAWindow()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
                }
              , {   "address": 140352824102018
                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
                ,   "build_id_offset": 1354882
                ,   "function_name": "vtkXOpenGLRenderWindow::WindowInitialize()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1..0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
                }
              , {   "address": 140352824096013
                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
                ,   "build_id_offset": 1348877
                ,   "function_name": "vtkXOpenGLRenderWindow::Start()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
                }
              , {   "address": 140352717995302
                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
                ,   "build_id_offset": 1154342
                ,   "function_name": "vtkRenderWindow::DoStereoRender()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
                }
              , {   "address": 140352717996715
                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
                ,   "build_id_offset": 1155755
                ,   "function_name": "vtkRenderWindow::DoFDRender()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
                }
              , {   "address": 140352718000997
                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
                ,   "build_id_offset": 1160037
                ,   "function_name": "vtkRenderWindow::DoAARender()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
                }
              , {   "address": 140352717997021
                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
                ,   "build_id_offset": 1156061
                ,   "function_name": "vtkRenderWindow::Render()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7..1.so.1"
                }
              , {   "address": 140352824097713
                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
                ,   "build_id_offset": 1350577
                ,   "function_name": "vtkXOpenGLRenderWindow::Render()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
                }
              , {   "address": 5878611
                ,   "build_id": "0de18d9e888c309c18e5e9450078f0fa6f19efa3"
                ,   "build_id_offset": 1684307
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"
                }
              , {   "address": 140352637235160
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2695128
                ,   "function_name": "QMetaObject::activate(QObject*, int, int, void**)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352637290759
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2750727
                ,   "function_name": "QTimer::timeout(QTimer::QPrivateSignal)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352637291576
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2751544
                ,   "function_name": "QTimer::timerEvent(QTimerEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352637241259
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2701227
                ,   "function_name": "QObject::event(QEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352873383932
                ,   "build_id": "ea0a04e7776bc525b6915e5ad0c369c06d3bcc24"
                ,   "build_id_offset": 1447932
                ,   "function_name": "QApplicationPrivate::notify_helper(QObject*, QEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Widgets.so.5"
                }
              , {   "address": 140352873412800
                ,   "build_id": "ea0a04e7776bc525b6915e5ad0c369c06d3bcc24"
                ,   "build_id_offset": 1476800
                ,   "function_name": "QApplication::notify(QObject*, QEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Widgets.so.5"
                }
              , {   "address": 140352637064112
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2524080
                ,   "function_name": "QCoreApplication::notifyInternal2(QObject*, QEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352637396158
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2856126
                ,   "function_name": "QTimerInfoList::activateTimers()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352637398113
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2858081
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1..0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352610068093
                ,   "build_id": "2fa0454e76ccf97da64b0e34042c5e7470ed5328"
                ,   "build_id_offset": 317053
                ,   "function_name": "g_main_context_dispatch"
                ,   "file_name": "/usr/lib64/libglib-2.0.so.0.5600.4"
                }
              , {   "address": 140352610069064
                ,   "build_id": "2fa0454e76ccf97da64b0e34042c5e7470ed5328"
                ,   "build_id_offset": 318024
                ,   "function_name": "g_main_context_iterate.isra.21"
                ,   "file_name": "/usr/lib64/libglib-2...0.so.0.5600.4"
                }
              , {   "address": 140352610069216
                ,   "build_id": "2fa0454e76ccf97da64b0e34042c5e7470ed5328"
                ,   "build_id_offset": 318176
                ,   "function_name": "g_main_context_iteration"
                ,   "file_name": "/usr/lib64/libglib-2.0.so.0.5600.4"
                }
              , {   "address": 140352637398919
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2858887
                ,   "function_name": "QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352570720945
                ,   "build_id": "ef1892fde946d169edac88b08f41832db8acd8d7"
                ,   "build_id_offset": 910001
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5XcbQpa.so..5"
                }
              , {   "address": 140352637057578
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2517546
                ,   "function_name": "QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352637092336
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2552304
                ,   "function_name": "QCoreApplication::exec()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1..0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 4615883
                ,   "build_id": "0de18d9e888c309c18e5e9450078f0fa6f19efa3"
                ,   "build_id_offset": 421579
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"
                } ]
        } ]
}
 

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer