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Last modified: 21 September 2010

URL: http://cxc-newtest.cfa.harvard.edu/ciao4.2/bugs/other.html

Bugs: Other Software Packages


The following is a list of known conflicts between CIAO and other software packages.

A list of bugs fixed in CIAO 4.2 is available.


Caveats

  1. Parameter file conflicts with HEAsoft

  2. IPython Packaged with CIAO OTS (12 Dec 2007)

  3. Linking external software: system environment variables not defined when starting CIAO (04 Jun 2008)

  4. cannot restore segment prot after reloc: Permission denied (04 Jun 2008)

  5. Errors if CIAO 4.2 and XMM SAS are started in the same terminal. (02 Mar 2010)


Caveats

  1. Parameter file conflicts with HEAsoft

    Both CIAO and FTOOLS use parameter files to store parameter values for tools, and provide tools for manipulating these files (e.g. plist, pset, punlearn; they have the same name in both systems). The location of the parameter files is taken from the $PFILES environment variables for CIAO and FTOOLS (or $UPARM if $PFILES does not exist).

    Common errors are:

    pget: could not get parameter "foo"
    
    and
    
    The following parameter:
        "foo,b,l,no,,,"Keyword""
    has the following error(s):
      o Mode field "l" is invalid.
    
    and
    
    The following parameter:
    "foo,i,h,INDEF,INDEF,INDEF,"description""
    has the following error(s):
    o Problem converting minimum field "INDEF" to parameter type "i".
    o Problem converting maximum field "INDEF" to parameter type "i".
    

    We recommend that you start FTOOLS before CIAO to minimize problems.

    More information on this problem is available in the CIAO and FTOOLS section of the Starting CIAO thread. Also refer to the related FAQ "The tool is failing because ")sval" has somehow shown up in the parameter value.".

  2. IPython Packaged with CIAO OTS (12 Dec 2007)

    CIAO includes IPython in the CIAO OTS directory which is used by Sherpa and ChIPS to provide command-line user interfaces. These programs create an IPython profile in the directory $HOME/.ipython-ciao.

    If IPython users want any personal customizations to be available when running CIAO, they will have to copy them from $HOME/.ipython to $HOME/.ipython-ciao.

  3. Linking external software: system environment variables not defined when starting CIAO (04 Jun 2008)

    Any system environment variable - LD_LIBRARY_PATH, DYLD_LIBRARY_PATH, PATH, etc. - is not defined when a user sets up a CIAO environment. Rather, the variable is defined as needed in the wrapper scripts that call individual tools, and then undefined when the wrapper script exits. This is fine for the majority of CIAO users.

    For the advanced user who want to override some of the CIAO defaults when running CIAO tools, there are additional steps needed. To append libraries to the CIAO library search path, set LD_LIBRARY_PATH (or DYLD_LIBRARY_PATH on a Mac). To prepend a library to the search path, should set CIAO_LD_LIBRARY_PATH (or CIAO_DYLD_LIBRARY_PATH). The user cannot prepend a search to PATH.

  4. cannot restore segment prot after reloc: Permission denied (04 Jun 2008)

    This means SE Linux is enabled on the user's system. There are 2 things that will fix this; do either of the following, not both:

    1. On the CIAO libraries and executables in the following directories

      $ASCDS_INSTALL/lib 
      $ASCDS_INSTALL/bin 
      $ASCDS_INSTALL/binexe 
      $ASCDS_INSTALL/ots/lib 
      $ASCDS_INSTALL/ots/bin 
      

      run the commands:

      $ su root
      # cd (to above CIAO directories)
      # chcon -c -v -R -u system_u -r object_r -t lib_t *
      # chcon -t texrel_shlib_t *
      
    2. Disable SE Linux

  5. Errors if CIAO 4.2 and XMM SAS are started in the same terminal. (02 Mar 2010)

    If XMM SAS and CIAO 4.2 are running in the same terminal, neither software will work. This is because SAS was built with an older version of GCC than CIAO.

    unix% plist dmcopy
    plist: /soft/XMM/xmmsas_20090615_1801/libextra/libgcc_s.so.1: version 
    `GCC_4.2.0' not found (required by /usr/lib/libstdc++.so.6)
    

    The error occurs regardless of which software was started first.

    Workaround:

    Copy the file /usr/libgcc_s.so.1 to $ASCDS_INSTALL/lib.

    CIAO will find the correct GCC version when tools are run. XMM SAS will be unaffected because the $ASCDS_INSTALL/lib directory is not in the LD_LIBRARY_PATH.

    The next SAS version is going to use a more modern GCC, which should resolve this issue.


Bugs fixed in CIAO 4.2

The following is a list of bugs that were fixed in the CIAO 4.2 software release.

  1. Running CIAO and XSpec in the same terminal (15 Jun 2009)

    The $HEADAS environment variable is redefined when the CIAO software is started. This is necessary as CIAO packages XSpec models and some libraries for use with Sherpa; those models look in the $HEADAS/spectral/modelData directory for needed files.

    Workaround:

    In order to run both CIAO and XSpec in the same window, it is necessary to reset the $HEADAS variable before running XSpec. The following shell script is one method of doing so:

    unix% cat xspec.sh
    #!/bin/csh
    
    setenv HEADAS <Your Local HEADAS Path>
    source ${HEADAS}/headas-init.csh
    
    ${HEADAS}/bin/xspec $*
    

    Place this script in your $PATH. Then CIAO and XSpec may be run in the same window in this way:

    unix% setenv HEADAS /soft/lheasoft/headas/sparc-sun-solaris2.8; \
          source $HEADAS/headas-init.csh
    
    unix% echo $HEADAS
    /soft/lheasoft/headas/sparc-sun-solaris2.8
    
    unix% ciao
    CIAO configuration is complete...
     CIAO version     :  CIAO 4.2 Friday, December 5, 2008
     Proposal Toolkit version :  Cycle 11 Friday, December 5, 2008
     bin dir          :  /soft/ciao/bin
     Python path      :  CIAO
    
    unix% echo $HEADAS
    /soft/ciao/ots/spectral
    
    unix% xspec.sh
    
                    XSPEC version: 12.4.0ag
            Build Date/Time: Tue Jul 15 22:37:42 2008
    
    XSPEC12>
    

    The shell script has its own environment, within which you can reassign the $HEADAS variable. After running XSpec, the shell script exits and you are back to the parent shell, where HEADAS remains set to point to the CIAO location.

    In the future, the definition of HEADAS will occur when Sherpa is used, instead of when CIAO is started. This workaround will then no longer be necessary.


Last modified: 21 September 2010