Chandra X-Ray Observatory
	(CXC)
Skip to the navigation links
Last modified: 12 June 2015

URL: http://cxc.harvard.edu/ciao/bugs/smoke.html

Bugs: Installation & Smoke Tests

The following is a list of known issues that may be seen when installing CIAO 4.7. If you encounter a problem that is not listed here, contact CXC Helpdesk for assistance.


Table of Contents

ciao-install

ObsVis

Running Remotely

Upgrading?

ChIPS

Sherpa

Prism

ds9


Bugs

ciao-install

    OSX : Sherpa or Chips failures due to easy-install numpy conflicts. [New]

    OSX users who have used python's easy-install utility to install packages into their system version of Python can experience problems if those packages installed an incompatible version of numpy. This is due to CIAO's python picking up the path to the incompatible library via the OSX Frameworks directories.

    The exact error users may see depends on the versions installed. Users have reported seeing the following error message in the sherpa smoke tests:

    ...
    ciao-4.7/lib/python2.7/site-packages/sherpa/data.py:396: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
      elif None in total_staterror:
    ...    
    

    or the following message in all the python tests (chips, sherpa, crates)

    RuntimeError: module compiled against API version 9 but this version of numpy is 4
    

    Users can check that they are getting the correct version of numpy by doing the following:

    $ python -c "import numpy;print numpy.__file__"
    /Library/Python/2.7/site-packages/numpy-1.9.2-py2.7-macosx-10.9-intel.egg/numpy/__init__.pyc
    

    The above output is wrong. The location of the numpy.__file__ should be .../ciao-4.7/ots/lib/python2.7/site-packages/numpy/__init__.pyc.

    Workaround:

    To avoid this problem users need to disable OSX Frameworks from their CIAO installation of python. This requires modifying the file

    .../ciao-4.7/ots/lib/python2.7/_sysconfigdata.py
    

    At/around line number 433, users need to change:

    'PYTHONFRAMEWORK': 'Python',

    to

    'PYTHONFRAMEWORK': '', 

    After the file has been changed, the python command above should point to the CIAO location.

    ./ciao-install: line 291: cd: ${DOWNLOAD_DIR}: No such file or directory
    ./ciao-install: line 268: cd: ${DOWNLOAD_DIR}: No such file or directory
    
    [New]

     (22 Jan 2015) ciao-install requires the full, absolute directory name for the download directory. If users specify a relative path ciao-install may fail with the error message above (where ${DOWNLOAD_DIR} is the directory name).

    Problem downloading ciao-install with Chrome browser.

    Users have reported problems downloading the ciao-install script using the lastest version of the Chrome web browser on OSX 10.6.8 and some Linux systems. Those users should try with Safari or another browser.

    Running ciao-install fails with:

    ERROR: Unable to retrieve ftp://cxc.harvard.edu/pub/ciao/all/ciao-control
    ERROR: Unable to download ciao-control
    ERROR: Bad Download. Please try again. If the problem continues Please
    contact the CfA helpdesk.

    or

    Resolving cxc.harvard.edu... 131.142.185.90
    Connecting to cxc.harvard.edu|131.142.185.90|:21... connected.
    Logging in as guest ...
    Error in server response, closing control connection.

    These messages indicate a conflict in FTP configurations between the user's machine and the CXC. (This is often seen with home internet providers such as a cable company.) If you have access to another computer and/or IP address, e.g. in a university office, you can run ciao-install with the --download-only flag to get the tarfiles. Then transfer them, if necessary, to the home machine.

    If you do not have access to another machine or IP address, contact CXC Helpdesk for help with the download.

    When running 32bit smoke tests on 64bit machine, obsvis or sherpa smoke tests fail.

    This occurs when switching from a 32 to 64bit build (or vice versa), leaving incompatible .fontconfig files cached on the user's system.

    Workaround:

    Remove the .fontconfig cache:

    unix% rm ~/.fontconfig/*
    

    and the GUIs should run.

ObsVis

    Fontconfig error: Cannot load default config file 

    As long as the test reports PASS this error can be ignored. Users may want to clear out their fontconfig cache (especially if switching between 32bit and 64bit applications)

    unix% rm $HOME/.fontconfig/*
    

    Users should log out and back in again after doing this.

    OBSVIS Error: Retrieving calibration updates from server produced the following error: 'Network timeout'

    Occasionally the connection to the server times out during the smoke test before ObsVis can get the data it needs. Try running the GUI from the command line:

    unix% obsvis

    If the problem persists, contact CXC Helpdesk.

Running Remotely

    If the DISPLAY environment variable is not set, the smoke test may appear to hang at prism-smoke001

    CIAO has several graphical applications that require the user have an active DISPLAY. If no X11 display is available then the applications will re-try for several minutes until their timeout has exceeded.

    Problems running ChIPS when using remote desktop viewers: for example VNC or NX.

    ChIPS requires a display device that support OpenGL. When the display is being viewed remotely through for example VNC or NX, both the host machine and the software rendering the display must support OpenGL.

    Useres may see one of the following messages

    error: xp_attach_gl_context returned: 2
    
      - or -
      
    X Error of failed request: 0
    Major opcode of failed request: 148 (GLX)
    Minor opcode of failed request: 26 (X_GLXMakeContextCurrent)
    Serial number of failed request: 26
    Current serial number in output stream: 26
    
    
    

    Users should verify that they can run the OpenGL utility

    unix% glxgears 
    

    The result will be a new window with 3 rotating gears and the number of frames per seconds (fps) will be displayed in the terminal. If glxgears is not working then users can try to set:

    bash:   export LIBGL_ALWAYS_INDIRECT=1
    tcsh:   setenv LIBGL_ALWAYS_INDIRECT 1
    

    If that does not solve the problems users will need to contact their systems group for additional help.

Upgrading?

    Customized resource, $HOME/.*.rc, may cause conflicts

    Several CIAO applications make use of resource files in the users home directory. These typically contain global application preferences. The list of resource files, or .rc files, is shown below.

    • .chips.rc
    • .ciaoinstall.rc
    • .ciaorc
    • .obsvisrc
    • .pegrc
    • .prismrc
    • .sherpa.rc

    If users have made customizations to these file it may cause the CIAO smoke tests to fail. This has been seen several times with sherpa users who have setup to use pyfits and/or matplotlib and are upgrading to the lastest version of CIAO.

    Users should move their customized version of these files to another directory and re-try the smoke tests. The files will get re-created and the customizations can be re-introduced in the new version of these files.

    Customized $HOME/.ipython-ciao4.5 settings

    Users upgrading from CIAO 4.5 may experience problems during the sherpa and/or chips smoke tests if they have made customizations to their $HOME/.ipython-ciao4.5, IPython settings.

    The type of error will depend on the exact customization made by the user.

    If any customizations have previously been made to these files then users should rename the directory before running the CIAO smoke tests. After the tests successfully complete users will need to re-introduce their customizations back into the directory that will get recreated.

    ds9 asking to update preferences

    If the user has ds9 and saved any preferences, it will stop during the smoke tests asking to upgrade the preference file. Usually this occurs during the obsvis tests if the all CIAO packages were installed.

    Users should simply select "Yes" when asked. If users select "No", they will be prompted with the same message every time ds9 starts -- it is run several times during the CIAO smoke tests.

ChIPS

    OSX X11 libfontconfig compatibility problems [New]

    Some OSX users may see the following error during the smoke tests or when running CIAO:

    dyld: Library not loaded: /opt/X11/lib/libfreetype.6.dylib
    Referenced from: /Applications/ciao/ciao-4.7/binexe/chipsServer
    Reason: Incompatible library version: chipsServer requires version 18.0.0 or later, but libfreetype.6.dylib provides version 17.0.0
    

    Workaround:

    To work around the issue, users need to remove the libfreetype and libfontconfig libraries that CIAO provides and link them to the system libraries.

    % sudo ln -s /opt/X11 /usr/X11
    % rm $ASCDS_INSTALL/ots/lib/libfreetype.6.dylib
    % rm $ASCDS_INSTALL/ots/lib/libfontconfig.1.dylib
    % ln -s /opt/X11/lib/libfreetype.6.dylib $ASCDS_INSTALL/ots/lib/libfreetype.6.dylib
    % ln -s /opt/X11/lib/libfontconfig.1.dylib $ASCDS_INSTALL/ots/lib/libfontconfig.1.dylib
    

    $ASCDS_INSTALL is set by the CIAO setup scripts.

    (ChipsServer:8980): Gtk-CRITICAL **: IA__gtk_text_buffer_insert_pixbuf: assertion `GDK_IS_PIXBUF (pixbuf)' failed
    ChipsServer:8980): GLib-GObject-CRITICAL **: g_object_unref: assertion `G_IS_OBJECT (object)' failed
    (ChipsServer:9481): Gtk-CRITICAL **: IA__gtk_text_buffer_insert_pixbuf: assertion `GDK_IS_PIXBUF (pixbuf)' failed
    (ChipsServer:9481): GdkPixbuf-CRITICAL **: gdk_pixbuf_new_from_file: assertion `error == NULL || *error == NULL' failed
    ChipsServer:9481): GLib-GObject-CRITICAL **: g_object_unref: assertion `G_IS_OBJECT (object)' failed
    ChipsServer:9980): Gtk-CRITICAL **: IA__gtk_text_buffer_insert_pixbuf: assertion `GDK_IS_PIXBUF (pixbuf)' failed 
    

    Workaround:

    While the above warnings and errors do not cause a problem with CIAO, users can suppress them by clearing out the mime.cache file.

    /bin/rm $HOME/.local/share/mime/mime.cache 
    

    ChIPS freezes

    A few Linux users have reported a problem where the smoke tests freeze at the first chips test. The plot window may remain and have to be killed by the window manager and/or the chipsServer process may run-away and start to consume 100% of a CPU.

    If this happens, you should first check that you have the latest version of the display driver available for your distribution and hardware.

    Runtime Error: Chips Error: Unable to connect to server

    If the X server takes too long to initialize, the ChIPS smoke tests will fail with this message. Run the smoke tests a second time and the errors should go away.

    Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so:
    cannot open shared object file: No such file or directory
    OR
    Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so:
    cannot open shared object file: no such file or directory
    OR
    Gtk-WARNING **: Unable to locate theme engine in module_path: "clearlooks"

    The warning is cosmetic and doesn't impact how ChIPS works.

       [6/42] Running test chips-smoke001 .Gtk-Message: Failed to load module "canberra-gtk-module"
    .. PASS
    

    As long at the test reports PASS, the warning can be ignored. If the test fails, users need to examine the log file to diagnose the problem.

    Workaround:

    The gnome session sets GTK_MODULES to load some debugging tools. If the user simply unsets the GTK_MODULES environment variable, then the warning messages will disappear:

    unsetenv GTK_MODULES
    

    *** Cannot find the double-buffered visual.
    *** Trying single-buffered visual.
    *** No appropriate OpenGL-capable visual found.

    The messages may be accompanied by a traceback error:

    Traceback (most recent call last):
      File "/tmp/smoke.al/chips-smoke001/chips-smoke001.py", line 2, in <module>
        strip_chart(3)
      File "/usr/ciao-4.4/lib/python2.7/site-packages/pychips/extensions.py", line 3436, in strip_chart
        __pychips_base__.grid_objects(1, entries,0, gaps,1)
      File "/usr/ciao-4.4/lib/python2.7/site-packages/pychips/pychips_base.py", line 935, in grid_objects
        return _pychips.ChipsRemoteMod_grid_objects(*args)
    RuntimeError: chips ERROR: No current window to perform operation on
    

    Workaround:

    • This error may indicate that the necessary graphics drivers are not installed on the machine running CIAO. For example, if you have a Nvidia graphics card and are running the 32-bit version of CIAO, you must have the 32-bit Nvidia drivers installed.

    • If you have SSH-ed into another machine to run CIAO, be sure that the -X or -Y (or both: "ssh -XY") options were used to enable X11 forwarding. If that doesn't resolve the issue, set

      setenv LIBGL_ALWAYS_INDIRECT 1
      

      This should happen by default when logging into a remote machine, but occasionally the system needs it set explicitly.

    If this information does not resolve the problem, contact CXC Helpdesk for additional diagnostic help.

    libGL warning: 3D driver claims to not support visual 0x4b

    All chips smoke tests may fail due to this warning produced by some ATI graphics cards. The warning is benign and can be ignored.

    Xlib: extension "RANDR" missing on display /tmp/...

    The chips smoke tests may report this warning. The warning is benign and can be ignored.

    CIAO is installed as root and the Chips/GUI smoke tests fail

    The ChIPS and the GUI applications, such as prism and obsvis, open windows as part of running the smoke tests. Often the root account is not allowed to open a window on the machine, which causes these tests to fail.

    The path to diff.log indicates this test was run as the root user:

    /tmp/smoke.root/prism-smoke001/diff.log 
    

    It is is strongly suggested that CIAO be installed as a non-privileged user and not as the root user. If CIAO must be installed in a directory owned by root and you are following the manual process, then

    1. unpack CIAO as root (so creating the ciao-<ver>/ directory);
    2. use the chown utility to change ownership of this directory to the installer's username.

    ChIPS smoke test comparison fails due to comma in place of decimal point

    Some system languages (e.g. Italian) use a comma in place of decimal point by default. This will cause the ChIPS smoke test comparison to fail, because the file packaged with CIAO uses decimal points:

    unix% cat /tmp/smoke.user/chips-smoke001/diff.log
    5c5
    <     Plot [plot1]   (0,15,0,65)  .. (0,90,0,90)
    ---
    >     Plot [plot1]   (0.15,0.65)  .. (0.90,0.90)
    11c11
    <     Plot [plot2]   (0,15,0,40)  .. (0,90,0,65)
    ---
    >     Plot [plot2]   (0.15,0.40)  .. (0.90,0.65)
    20c20
    <     Plot [plot3]   (0,15,0,15)  .. (0,90,0,40)
    ---
    >     Plot [plot3]   (0.15,0.15)  .. (0.90,0.40)
    

    If the decimal point/comma difference is the only thing recorded in the log file, ChIPS is fine to use.

Sherpa

    Sherpa: "ERROR: test_image (sherpa.image.tests.test_image.test_image)"

    The Sherpa smoke test fails and the log contains these errors:

    ERROR: test_image (sherpa.image.tests.test_image.test_image)
    ----------------------------------------------------------------------
    Traceback (most recent call last):
    ValueError: total size of new array must be unchanged
    

    This is an intermittent error in the code that Sherpa uses to talk with DS9 via XPA. Run the smoke tests a second time and the errors should go away. If they do not, contact CXC Helpdesk for further assistance.

    sherpa-smoke001 fails with in test_xspec_models
    (Linux 64-bit, OSX 10.9)

    .........................................ERROR: XSXSabsori model evaluation failed
    F.................................................................................
    .........................................................
    ======================================================================
    FAIL: test_xspec_models (sherpa.astro.tests.test_xspec.test_xspec)
    ----------------------------------------------------------------------
    Traceback (most recent call last):
      File "/astro/ciao-4.4/lib/python2.7/site-packages/sherpa/astro/xspec/tests/test_xspec.py", line 80, in test_xspec_models
        not numpy.isinf(vals).any() )
    AssertionError
    
    ----------------------------------------------------------------------
    Ran 180 tests in 24.795s
    
    FAILED (failures=1)
    

    Running the smoke tests again often reports a success for this test; the instructions for running smoke tests are in the Installing CIAO thread.

    This failure has been seen with different XSPEC models including XSXSsirf and possibly others.

Prism

    (prism:2236): Gtk-WARNING **: GModule (/usr/lib64/gtk-2.0/2.10.0/engines/libclearlooks.so)
    initialization check failed: Gtk+ version too old (micro mismatch)

    This warning messages may be generated when prism is run during smoke testing or run from the command line. The warnings are harmless, but annoying.

    Workaround:

    Remove or rename the $HOME/.gtkrc-2.0 and/or $HOME/.gtkrc-2.0-kde4 file to eliminate the warnings.

    Segmentation fault

    The prism smoke tests will segmentation fault if there are incompatible .fontconfig files cached on the user's system. Remove the .fontconfig cache:

    unix% rm ~/.fontconfig/*
    

    If this does not fix the prism problem, contact CXC Helpdesk.

    CIAO is installed as root and the Chips/GUI smoke tests fail

    The ChIPS and the GUI applications, such as prism and obsvis, open windows as part of running the smoke tests. Often the root account is not allowed to open a window on the machine, which causes these tests to fail.

    The path to diff.log indicates this test was run as the root user:

    /tmp/smoke.root/prism-smoke001/diff.log 
    

    It is is strongly suggested that CIAO be installed as a non-privileged user and not as the root user. If CIAO must be installed in a directory owned by root and you are following the manual process, then

    1. unpack CIAO as root (so creating the ciao-<ver>/ directory);
    2. use the chown utility to change ownership of this directory to the installer's username.

ds9

    The ds9 smoke test results may differ in the least significant figure.

    A sample diff log from test ds9-smoke001:

    13c13
    <  1.73363528e+02 2.58432381e+01 
    ---
    >  1.73363528e+02 2.58432382e+01 
    22c22
    <  1.73357457e+02 2.58464050e+01 
    ---
    >  1.73357457e+02 2.58464051e+01 
    75c75
    <  1.73322543e+02 2.58736917e+01 
    ---
    >  1.73322543e+02 2.58736916e+01 
    99c99
    <  1.73310395e+02 2.58821467e+01 
    ---
    >  1.73310395e+02 2.58821466e+01 
    

Last modified: 12 June 2015
Smithsonian Institute Smithsonian Institute

The Chandra X-Ray Center (CXC) is operated for NASA by the Smithsonian Astrophysical Observatory. 60 Garden Street, Cambridge, MA 02138 USA.   Email:   cxchelp@head.cfa.harvard.edu Smithsonian Institution, Copyright © 1998-2017. All rights reserved.