[chimerax-users] ChimeraX/1.3 could not start in CentOS 7
Greg Couch
gregc at cgl.ucsf.edu
Fri Jul 15 16:57:37 PDT 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 at utsouthwestern.edu
> Tel: (214)-645-1561
>
>
> ------------------------------------------------------------------------
>
> UTSouthwestern
>
> Medical Center
>
>
> The future of medicine, today.
>
>
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