External Email - Use Caution 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 <fsbu...@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.sned...@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.sned...@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 <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>
Date: Thursday, November 5, 2020 at 11:47 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: "Snedden, Ali"
<ali.sned...@nationwidechildrens.org<mailto:ali.sned...@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
behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-CentOS8-7.1.1-1.x86_64.rpm<https://secure-web.cisco.com/1QZIJ88lwtFx6VmuYRB6Ek0p0z5DJpVCiwpX_sqG4Q-_PgIBGSFVMmvHa5PX_tSYQlikEfAHpvTBdpaDBDMxKd7xqde5eOIi14LoCIa6GDfRVekWdEbt5EefvXL_jrNXCgBDQldBt7U98ySNVsJ6c-V0_LCqzfti2BqXABqvShl6VyJ0JILlXwIajPzj8no4L2R8x-e7QXPDDTIG0e3xFgg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1E-Qe_Hvm6g6wD56NVkmthi1iJUOJPPQNl-9fXS_yGUIaPZKUjoLeqT0DxZXufB9ux0361tqfw3z_QZljk8mJ2F9FVJDeawytoJz8fFbwAWjWobKVOYIFhEvdLtFwRrVLMmJpmfkb1DryiMLGYcfS3YusRGuqYexYmvpx2pTBSeg1uZg_77bdll8HgzJzf4IPzElgdbAJeyI8kmHYncZ4ig%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Fpub%2A2Fdist%2A2Ffreesurfer%2A2F7.1.1%2A2Ffreesurfer-CentOS8-7.1.1-1.x86_64.rpm__%2A3B%2A21%2A21ODYTt7Uqo6LDP14%2A213gVX_lnwYFFaG14x_OHkTpZNYG2P2SQX9wOWa4wzlgJBswRFuxi5kShvbt0507gBtCWPQyw4BbU%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSU%21%21ODYTt7Uqo6LDP14%21xp98o3I-_PscE1IQL-C0zRf0clHsGYOk2rITPle_2Sw4_vZ_e2G_Wm0jKRxVQA4axedIgnpDwIw%24>
- R.
On Nov 5, 2020, at 22:39, Snedden, Ali <ali.sned...@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<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1p3e-wzCLyaqljBygktYD0fI17wqRD8NsdtGPBvAsp6OxLjSbfoDhtrAIgWhaNo4PgEvsu_GoeyFmSqqwC8L9WHTgXOcbXC3QsWpmZD1-Cd37Ns9JdIgBBXBuyvJKcuwZQLWONfraLGMv5JcyjCNrA3PUXqtdruWObBXbXelQlM-AUdhaV_M_ALWPZ5N7yQ89_TvyaU_O_AtLpvvIRp-Nig/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1c_iDvoEJ4EiHSV0ohWpryIIDN1QImUKajxhPaWy0GK7OxZQsHayAhXM0sojFZxLIkZr1OO6stVd0ZgImVB4utQpSiXawsRJaexXLeyKpfNWfa5gfBdUaYSh73894i-bGsGsuGE3Gw4z7lUKAdmrO-jn9BuVQ68ttZeK0SJixLM-d6yEduUbhANBqerywcgo3-ohm6JstUgj21J8s7hPuXw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fmail.nmr.mgh.harvard.edu%2A2Fmailman%2A2Flistinfo%2A2Ffreesurfer__%2A3B%2A21%2A21ODYTt7Uqo6LDP14%2A213gVX_lnwYFFaG14x_OHkTpZNYG2P2SQX9wOWa4wzlgJBswRFuxi5kShvbt0507gBtCWPFSsp80g%2A24__%3BJSUlJSUlJSUlJSUlJSUl%21%21ODYTt7Uqo6LDP14%21xp98o3I-_PscE1IQL-C0zRf0clHsGYOk2rITPle_2Sw4_vZ_e2G_Wm0jKRxVQA4axedIvBgdJ2I%24>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1YaOhaE67AidZZlMio-m7YycpahZVH9xmNA_ohwvBkxEASnPuDFuzU778UQyz5WaX0Dk3rL3Zu54cm0mH_cQ6xed_mgHq6uKcXr4dYTKjthaLi9uAR6Q8fJ3IeDraudvx3Bptr8WU3CUxe4_ozpqWZbidt4f7xQubpZiWxu8CKlvZqP7ofwBdmcatH65a1Du3ksdBhdOeq1ai7ajlH78csw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1EzQNc1ZWlSaaxeCJC7XFzRjWXcwN7wLKdlBAOIzPtU-TQ8BAyCPfdyaaVLC2Ij6Ydg-XPbs2YftkybLtI5_dQC65tjq9VZYEPI653LUsQJTkXX3Dby7fccJVRIXPnkEIorT7YsLcmtA1aUCMp8xnBLZtnE_2ifHXeu2Zx9dsLZV2qHr4NxPDzvfWrgzSzaA4pEOWXaW-fzxRJLVs0kB2sA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21ODYTt7Uqo6LDP14%21xp98o3I-_PscE1IQL-C0zRf0clHsGYOk2rITPle_2Sw4_vZ_e2G_Wm0jKRxVQA4axedIzOMyBAA%24>
freeview_corebacktrace
Description: freeview_corebacktrace
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
