[chimerax-users] ChimeraX/1.3 could not start in CentOS 7
Long Gui
Long.Gui at UTSouthwestern.edu
Thu Jul 14 14:55:06 PDT 2022
Dear ChimeraX developers,
I am installing the ChimeraX/1.3 in one of our GPU workstation (CentOS Linux 7). The installation processed well but after I tried to start the chimerax program, it showed:
QFactoryLoader::QFactoryLoader() checking directory path "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms" ...
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqeglfs.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqeglfs.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"eglfs"
]
},
"archreq": 0,
"className": "QEglFSIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("eglfs")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqlinuxfb.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqlinuxfb.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"linuxfb"
]
},
"archreq": 0,
"className": "QLinuxFbIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("linuxfb")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimal.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimal.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"minimal"
]
},
"archreq": 0,
"className": "QMinimalIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("minimal")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimalegl.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimalegl.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"minimalegl"
]
},
"archreq": 0,
"className": "QMinimalEglIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("minimalegl")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqoffscreen.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqoffscreen.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"offscreen"
]
},
"archreq": 0,
"className": "QOffscreenIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("offscreen")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqvnc.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqvnc.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"vnc"
]
},
"archreq": 0,
"className": "QVncIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("vnc")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-egl.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-egl.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"wayland-egl"
]
},
"archreq": 0,
"className": "QWaylandEglPlatformIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("wayland-egl")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-generic.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-generic.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"wayland"
]
},
"archreq": 0,
"className": "QWaylandIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("wayland")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-egl.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-egl.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"wayland-xcomposite-egl"
]
},
"archreq": 0,
"className": "QWaylandXCompositeEglPlatformIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("wayland-xcomposite-egl")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-glx.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-glx.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"wayland-xcomposite-glx"
]
},
"archreq": 0,
"className": "QWaylandXCompositeGlxPlatformIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("wayland-xcomposite-glx")
QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so"
Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"xcb"
]
},
"archreq": 0,
"className": "QXcbIntegrationPlugin",
"debug": false,
"version": 331520
}
Got keys from plugin meta data ("xcb")
QFactoryLoader::QFactoryLoader() checking directory path "/usr/libexec/UCSF-ChimeraX/bin/platforms" ...
Cannot load library /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxcb-icccm.so.4: cannot open shared object file: No such file or directory)
QLibraryPrivate::loadPlugin failed on "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so" : "Cannot load library /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxcb-icccm.so.4: cannot open shared object file: No such file or directory)"
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb.
Fatal Python error: Aborted
Current thread 0x00007f107e0f8740 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 159 in __init__
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 577 in init
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in <module>
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Aborted (core dumped)
I have also typed: ldd /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so
linux-vdso.so.1 => (0x00007ffc9f19e000)
libQt5XcbQpa.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5XcbQpa.so.5 (0x00007f760e4a4000)
libfontconfig.so.1 => /lib64/libfontconfig.so.1 (0x00007f760e245000)
libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f760df86000)
libz.so.1 => /lib64/libz.so.1 (0x00007f760dd70000)
libQt5Gui.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5Gui.so.5 (0x00007f760d43e000)
libQt5DBus.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5DBus.so.5 (0x00007f760d1b2000)
libQt5Core.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5Core.so.5 (0x00007f760c9bc000)
libGL.so.1 => /lib64/libGL.so.1 (0x00007f760c712000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f760c4f6000)
libX11-xcb.so.1 => /lib64/libX11-xcb.so.1 (0x00007f760c2f4000)
libxcb-icccm.so.4 => not found
libxcb-image.so.0 => not found
libxcb-shm.so.0 => /lib64/libxcb-shm.so.0 (0x00007f760c0ef000)
libxcb-util.so.1 => /lib64/libxcb-util.so.1 (0x00007f760bee8000)
libxcb-keysyms.so.1 => /lib64/libxcb-keysyms.so.1 (0x00007f760bce5000)
libxcb-randr.so.0 => /lib64/libxcb-randr.so.0 (0x00007f760bad5000)
libxcb-render-util.so.0 => not found
libxcb-render.so.0 => /lib64/libxcb-render.so.0 (0x00007f760b8c6000)
libxcb-shape.so.0 => /lib64/libxcb-shape.so.0 (0x00007f760b6c2000)
libxcb-sync.so.1 => /lib64/libxcb-sync.so.1 (0x00007f760b4ba000)
libxcb-xfixes.so.0 => /lib64/libxcb-xfixes.so.0 (0x00007f760b2b2000)
libxcb-xinerama.so.0 => /lib64/libxcb-xinerama.so.0 (0x00007f760b0af000)
libxcb-xkb.so.1 => /lib64/libxcb-xkb.so.1 (0x00007f760ae92000)
libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f760ac6a000)
libXext.so.6 => /lib64/libXext.so.6 (0x00007f760aa58000)
libX11.so.6 => /lib64/libX11.so.6 (0x00007f760a719000)
libxkbcommon-x11.so.0 => /lib64/libxkbcommon-x11.so.0 (0x00007f760a511000)
libxkbcommon.so.0 => /lib64/libxkbcommon.so.0 (0x00007f760a2d1000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f760a0cc000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f7609dc4000)
libm.so.6 => /lib64/libm.so.6 (0x00007f7609ac2000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f76098ab000)
libc.so.6 => /lib64/libc.so.6 (0x00007f76094dd000)
libxcb-icccm.so.4 => not found
libxcb-image.so.0 => not found
libxcb-render-util.so.0 => not found
libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00007f76092da000)
libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f7608fc3000)
libexpat.so.1 => /lib64/libexpat.so.1 (0x00007f7608d99000)
libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f7608b93000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f7608983000)
libpng15.so.15 => /lib64/libpng15.so.15 (0x00007f7608758000)
libdbus-1.so.3 => /lib64/libdbus-1.so.3 (0x00007f7608507000)
libicui18n.so.56 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libicui18n.so.56 (0x00007f760806e000)
libicuuc.so.56 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libicuuc.so.56 (0x00007f7607cb5000)
libicudata.so.56 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libicudata.so.56 (0x00007f76062d2000)
/lib64/ld-linux-x86-64.so.2 (0x00007f760ea02000)
libGLX.so.0 => /lib64/libGLX.so.0 (0x00007f76060a2000)
libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x00007f7605dce000)
libXau.so.6 => /lib64/libXau.so.6 (0x00007f7605bca000)
libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f7605967000)
libsystemd.so.0 => /lib64/libsystemd.so.0 (0x00007f7605736000)
libcap.so.2 => /lib64/libcap.so.2 (0x00007f7605530000)
librt.so.1 => /lib64/librt.so.1 (0x00007f7605328000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f7605101000)
liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f7604eda000)
liblz4.so.1 => /lib64/liblz4.so.1 (0x00007f7604ccb000)
libgcrypt.so.11 => /lib64/libgcrypt.so.11 (0x00007f7604a4a000)
libgpg-error.so.0 => /lib64/libgpg-error.so.0 (0x00007f7604844000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f760462a000)
libdw.so.1 => /lib64/libdw.so.1 (0x00007f76043d9000)
libattr.so.1 => /lib64/libattr.so.1 (0x00007f76041d3000)
libelf.so.1 => /lib64/libelf.so.1 (0x00007f7603fbb000)
I have searched the ChimeraX mail list and found several previous email talking about this issue but I have tried all of them
For instance, I have re-install the libxcb library: sudo yum reinstall libxcb
but none of it could work.
Would you like to check this and let me know how to solve this problem?
Thanks a lot!
Long Gui, Ph.D.
Postdoc Researcher, Nicastro Lab
University of Texas Southwestern Medical Center
Long.Gui at utsouthwestern.edu
Tel: (214)-645-1561
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
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