Re: [chimerax-users] ChimeraX/1.3 could not start in CentOS 7

15 Jul 2022


      So it looks like the relevant error is:
...
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)
But the ldd output is even more helpful because there are other missing 
libraries.  The missing packages are xcb-util-wm, xcb-util-image, 
xcb-util-renderutil for libxcb-icccm.so.4, libxcb-image.so.0, and 
libxcb-render-util.so.0 respectively.  So you should "sudo yum install 
xcb-util-wm xcb-util-image xcb-util-renderutil" to fix this particular 
problem.
Since you don't have those libraries already installed, it seems like 
you have installed Chimerax on a remote server instead of a desktop 
system.  That is officially not supported unless you are running 
ChimeraX in nogui mode (which doesn't need those libraries).   That 
said, using VirtualGL on the server can work around remote display problems.


     HTH,


     Greg


On 7/14/2022 2:55 PM, Long Gui via ChimeraX-users wrote:
...
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@utsouthwestern.edu
Tel: (214)-645-1561
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Re: [chimerax-users] ChimeraX/1.3 could not start in CentOS 7

Greg Couch