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Washington-University / workbench

Connectome Workbench
http://www.humanconnectome.org/software/get-connectome-workbench.html
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HCP workbench v1.5.0 wb_view segmentation fault #49

Closed ShaoshiZ closed 3 years ago

ShaoshiZ commented 3 years ago

Hi,

I am using CentOS7 and have installed workbench v.1.5.0. I receive a libGL error when I try to open wb_view

Info: Resources loaded:
   :/About   :/BalsaUploadDialog   :/Cursor   :/Fonts   :/general_resources.qrc   :/help_resources.qrc   :/HelpFiles   :/LayersPanel   :/OLD_help_resources.qrc   :/PaletteEditorDialog   :/PaletteSettings   :/qt-project.org   :/RecentFilesDialog   :/SceneFileDialog   :/SpecFileDialog   :/Splash   :/ToolBar   :/update_resources.sh

libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast

The user interface can still be loaded but it exits when I click 'Open Other...' and shows this error

bin_rh_linux64/wb_view: line 17: 38300 Segmentation fault      "$directory"/../exe_rh_linux64/wb_view "$@"

Any suggestions about how to fix this problem? Thank you.

Regards, Shaoshi

glasserm commented 3 years ago

Is this on a physical display or via some kind of remote access?

ShaoshiZ commented 3 years ago

Is this on a physical display or via some kind of remote access?

I am accessing it via VNC.

glasserm commented 3 years ago

You may need to install the virtualGL package and launch with vglrun wb_view ...

ShaoshiZ commented 3 years ago

You may need to install the virtualGL package and launch with vglrun wb_view ...

Thanks for the suggestion. But is this specifically required by workbench v.1.5.0? I'm asking this because I can open workbench v.1.4.2 by directly running wb_view without virtualGL.

johnvelab commented 3 years ago

Does running “glxgears” work (may not be installed on your computer)?

Also, what is the output of “glxinfo”?

Try running “LIBGL_DEBUG=verbose wb_view”. What output does it produce?

John

From: "Shaoshi.Z" @.> Reply-To: Washington-University/workbench @.> Date: Thursday, April 22, 2021 at 4:46 AM To: Washington-University/workbench @.> Cc: Subscribed @.> Subject: Re: [Washington-University/workbench] HCP workbench v1.5.0 wb_view segmentation fault (#49)

You may need to install the virtualGL package and launch with vglrun wb_view ...

Thanks for the suggestion. But is this specifically required by workbench v.1.5.0? I'm asking this because I can open workbench v.1.4.2 by directly running wb_view without virtualGL.

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ShaoshiZ commented 3 years ago

Thanks for the reply!

Shaoshi

johnvelab commented 3 years ago

You appear to have multiple versions of wb_view installed on your computer.

What is the command you use to run wb_view 1.5.0?

Try “LIBGL_DEBUG=verbose” followed by the command you use to run wb_view 1.5.0.

From: "Shaoshi.Z" @.> Reply-To: Washington-University/workbench @.> Date: Thursday, April 22, 2021 at 11:21 AM To: Washington-University/workbench @.> Cc: johnvelab @.>, Comment @.***> Subject: Re: [Washington-University/workbench] HCP workbench v1.5.0 wb_view segmentation fault (#49)

Thanks for the reply!

QGtkStyle was unable to detect the current GTK+ theme.

libGL: OpenDriver: trying /usr/lib64/dri/tls/swrast_dri.so

libGL: OpenDriver: trying /usr/lib64/dri/swrast_dri.so

libGL: Can't open configuration file /etc/drirc: No such file or directory.

libGL: Can't open configuration file /home/shaoshi.z/.drirc: No such file or directory.

libGL: Can't open configuration file /etc/drirc: No such file or directory.

libGL: Can't open configuration file /home/shaoshi.z/.drirc: No such file or directory.

but the version shown in GUI is 1.1.1, not 1.5.0. Everything else seems to be working fine.

Shaoshi

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ShaoshiZ commented 3 years ago

Sorry, my bad. I forgot I've set the default workbench version to 1.1.1. Now I receive the following warnings and errors when I open workbench 1.5.0

Info: Resources loaded:
   :/About   :/BalsaUploadDialog   :/Cursor   :/Fonts   :/general_resources.qrc   :/help_resources.qrc   :/HelpFiles   :/LayersPanel   :/OLD_help_resources.qrc   :/PaletteEditorDialog   :/PaletteSettings   :/qt-project.org   :/RecentFilesDialog   :/SceneFileDialog   :/SpecFileDialog   :/Splash   :/ToolBar   :/update_resources.sh

libGL: OpenDriver: trying /usr/lib64/dri/tls/swrast_dri.so
libGL: OpenDriver: trying /usr/lib64/dri/swrast_dri.so
libGL: dlopen /usr/lib64/dri/swrast_dri.so failed (/apps/HCP/workbench-1.5.0/bin_rh_linux64/../libs_rh_linux64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /usr/lib64/libLLVM-7-rhel.so))
libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
/apps/HCP/workbench-1.5.0//bin_rh_linux64/wb_view: line 17: 74193 Segmentation fault      "$directory"/../exe_rh_linux64/wb_view "$@"

It still has the same issue as before.

johnvelab commented 3 years ago

The message

(/apps/HCP/workbench-1.5.0/bin_rh_linux64/../libs_rh_linux64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /usr/lib64/libLLVM-7-rhel.so))

indicates it might be a libstdc++ problem. We include libstdc++ in our distribution and it might be incompatible with your operating system. Go into the workbench distribution’s “libs_rh_linux64” directory and rename libstdc++.so.6 to save_libstdc++.so.6 so that wb_view will not try to load it. After that, try running wb_view. If wb_view still fails, send us the output and then rename the library back to its original name.

From: "Shaoshi.Z" @.> Reply-To: Washington-University/workbench @.> Date: Thursday, April 22, 2021 at 12:51 PM To: Washington-University/workbench @.> Cc: johnvelab @.>, Comment @.***> Subject: Re: [Washington-University/workbench] HCP workbench v1.5.0 wb_view segmentation fault (#49)

Sorry, my bad. I forgot I've set the default workbench version to 1.1.1. Now I receive the following warnings and errors when I open workbench 1.5.0

Info: Resources loaded:

:/About :/BalsaUploadDialog :/Cursor :/Fonts :/general_resources.qrc :/help_resources.qrc :/HelpFiles :/LayersPanel :/OLD_help_resources.qrc :/PaletteEditorDialog :/PaletteSettings :/qt-project.org :/RecentFilesDialog :/SceneFileDialog :/SpecFileDialog :/Splash :/ToolBar :/update_resources.sh

libGL: OpenDriver: trying /usr/lib64/dri/tls/swrast_dri.so

libGL: OpenDriver: trying /usr/lib64/dri/swrast_dri.so

libGL: dlopen /usr/lib64/dri/swrast_dri.so failed (/apps/HCP/workbench-1.5.0/bin_rh_linux64/../libs_rh_linux64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /usr/lib64/libLLVM-7-rhel.so))

libGL error: unable to load driver: swrast_dri.so

libGL error: failed to load driver: swrast

/apps/HCP/workbench-1.5.0//bin_rh_linux64/wb_view: line 17: 74193 Segmentation fault "$directory"/../exe_rh_linux64/wb_view "$@"

It still has the same issue as before.

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ShaoshiZ commented 3 years ago

Thanks for the suggestion. I think I have fixed the problem. I copied libstdc++.so.6.0.19 from /usr/lib64 to /workbench-1.5.0/libs_rh_linux64 and renamed it to libstdc++.so.6. Now everything is working.

BTW, I noticed that, at the top of the GUI, it actually shows 'Connectome Workbench 1.4.2' instead of '1.5.0'.

Shaoshi

coalsont commented 3 years ago

Thanks for mentioning the version, looks like the zip downloads on humanconnectome didn't get the right versions, there was a minor mishap that didn't get corrected properly - it is literally only one commit behind, the commit that changed the version number (and nothing else).

coalsont commented 3 years ago

The versions on humanconnectome should report the correct version now.