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

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Hello,

Thank you for the reply.

1. Regarding the Nvidia drivers, we don’t have GPUs in most of our nodes (which is where I’m running freeview from). The CPUs should be doing all the rendering in this case. 2. I am the administrator of this cluster, so that isn’t an issue on my end. 3. I pulled one of our CentOS 8.1.1911 nodes out of the cluster and installed freesurfer-CentOS8-7.1.0-1.x86_64.rpm locally using rpm. 4. When I run /usr/local/freesurfer/7.1.0-1/bin/freeview, I get :

r1pl-hpcf-n09: ~$ /usr/local/freesurfer/7.1.0-1/bin/freeview

QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-aps003'

MESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)

libGL error: failed to load driver: swrast

Aborted (core dumped)

And the /var/spool/abrt/ccpp-2020-11-10-08:26:55-23032/core_backtrace is attached. If you can’t view it, I can paste it into an email. It looks very similar to the original backtrace that I pasted before. Even with the rpm installed as intended (i.e. in /usr/), it seems that not be functioning correctly. It still seems to me that it is failing in the vtkXOpenGLRenderWindow::CreateAWindow() function. The top of the trace is glibc, but everything calls glibc in the end. It isn’t clear if this is a glibc, vtk or some other issue.

Thoughts?

Best regards,

Ali

From: fsbuild fsbuild@contbay.com Date: Monday, November 9, 2020 at 6:53 AM 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 {Disarmed}

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:

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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.commailto:fsbuild@contbay.com> Date: Thursday, November 5, 2020 at 11:47 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: "Snedden, Ali" <Ali.Snedden@nationwidechildrens.orgmailto: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.,

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- R.

On Nov 5, 2020, at 22:39, Snedden, Ali Ali.Snedden@nationwidechildrens.org wrote:

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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(QFlagsQEventLoop::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(QFlagsQEventLoop::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" } ] } ] }

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