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.,

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-CentOS8-7.1.1-1.x86_64.rpm

- 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"

} ]

} ]

}

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