Last modified: 26 April 2024


CIAO "Watch Out" Page

This page lists noteworthy items and issues about the CIAO release. For the full list of known issues please review the:

ciao-install setup changes LD_LIBRARY_PATH

[New] (15 Dec 2023) The setup scripts in the new CIAO 4.16 ciao-install installations: ciao.csh and, are inadvertently setting the LD_LIBRARY_PATH environment variable. This may cause other, non-CIAO applications to fail; this includes things like Emacs, gnome-terminal, and any number of other applications. CIAO does not need to have this environment variable set. Important things to know:

  1. Users must not directly source the CIAO setup scripts in their startup scripts (ie .bashrc, .cshrc, .zshrc, etc). Doing so could cause startup applications to fail; thereby preventing users from logging in. Users should create and use the ciao alias as recommended in the Starting CIAO thread.
  2. This issues affects all Linux user who have installed CIAO with the ciao-install script; it does not affect most macOS users. Only macOS users that used ciao-install who have disabled Apple's "System Integrity Protection" (SIP) will be affected by this. macOS users can check the SIP status using the command "csrutil status" (no quotes). If it reports "disabled" then users will be affected by this change and should follow the same recommendations as for Linux users replacing "LD_LIBRARY_PATH" with "DYLD_LIBRARY_PATH".
  3. This issue does not exist when CIAO is installed using conda create. Users affected by this may wish to install CIAO using that method.
  4. After sourcing the CIAO setup script, user can simply unset the LD_LIBRARY_PATH environment variable if it was not already set before CIAO was setup.
    bash$ unset LD_LIBRARY_PATH    
    tcsh% unsetenv LD_LIBRARY_PATH
    This could even be included in the CIAO alias:
    bash$ alias ciao="source /soft/ciao-4.16/bin/ ; unset LD_LIBRARY_PATH"
    tcsh% alias ciao "source /soft/ciao-4.16/bin/ciao.csh ; unsetenv LD_LIBRARY_PATH"
    However, if LD_LIBRARY_PATH is already set before starting CIAO then the original value should be preserved:
    bash$ alias ciao="keep=${LD_LIBRARY_PATH}; source /soft/ciao-4.16/bin/ ; LD_LIBRARY_PATH=${keep}"
    tcsh% alias ciao="set keep=${LD_LIBRARY_PATH}; source /soft/ciao-4.16/bin/ciao.csh ; setenv LD_LIBRARY_PATH ${keep}"

Problems with Xquartz 2.8.5

Some users have reported problems related to disappearing menus using ds9 with Xquartz version 2.8.5 which was released on January 26, 2023. This appears to be a bug in that version of Xquartz; users are advised to downgrade to version 2.8.4 to mitigate the problem.

Files and directories/folders with spaces or other special characters

Users are reminded that CIAO does not work with file names or directories/folders with spaces, " ", or other certain special characters.

SAOImage DS9

Help, I am unable to create regions in ds9!

By default, ds9 will no longer create regions when it starts; that is, clicking in the ds9 window will not create a region. This is because the ds9 interface has changed in version 7.3.2 (released in October 2014), as noted above, so that it no longer starts in region editing mode.

To create or edit regions, users must now manually switch to Region mode by selecting

Edit → Region

from the menu bar or the button bar.

Users can make this the default by editing their preferences:

Edit → Preferences ...
Menus and Buttons                  (left panel)
Edit → Menu → Region               (right panel)
Preserve During Load preferences

CIAO users should not enable any of the following options

Menus and Buttons → File → Menu → Preserve During Load → Pan
Menus and Buttons → File → Menu → Preserve During Load → Region

preferences. Due to the way CIAO starts ds9, having these preferences enabled leads to a half-pixel shift in regions. This shift accumulates if the region file is saved and re-loaded.

Installing & Starting CIAO

Using ciao-install

Items that are relevant for people who install CIAO with ciao-install:

bash, ksh, and zsh use

The obsolete CIAO setup scripts for specific shell variants: bash (ciao.bash) and ksh (ciao.ksh) shells have been removed. All users who installed CIAO with ciao-install that use any of the Bourne shell derivatives including bash, zsh (for macOS Catalina and later), and ksh, must source the script to setup for CIAO.

$ alias ciao="source /soft/ciao-4.16/bin/"
$ ciao

Users who have installed CIAO with conda will continue to activate the environment as described on the download page.

Python 3.11 support only

In CIAO 4.16 installed using ciao-install only Python 3.11 is provided.

The Python 3 for Scientists website provides guidance on updating code written for Python 2, and the CXC Helpdesk can provide support.

Users of the conda installation can select python 3.11, 3.10, or 3.9.

Other issues

CIAO on Mac needs recent XQuartz and XCode

OSX users, particularly those that have upgraded from an earlier OSX version, should ensure that compatible versions of XQuartz (at least version 2.7.11) and XCode (also comes as part of Apple Developer Tools) are installed on the system before proceeding with the CIAO installation.

macOSls: Operation not permitted

Since macOS Catalina, Apple has restricted access to various folders in the user's home directory including Documents, Desktop, and Downloads. By default the Terminal application and Xquart's xterm application do not have access to these folders. Attempting to list the contents from the command line yeilds the following error message:

$ cd Desktop
$ ls
ls: Operation not permitted

This restriction may impede CIAO users who commonly use these folders.

Users can still navigate and display the contents of these folders using the Finder application. CIAO users who want to use these restricted folders need to grant the Terminal and|or xterm applications "Full Disk Access". The setting can be found in the "Security" settings application.

No support for 32-bit Linux, nor OSX 10.15 (Catalina) and earlier.

CIAO is no longer available for 32-bit Linux, nor is it available for OSX 10.15 (Catalina) or earlier versions of OSX. CIAO is also not available for Windows; using CIAO with Windows Subsystem for Linux (WSL) is unsupported. The platform support page describes the operating systems that can be used with CIAO.

Fontconfig error: Cannot load default config file

During the smoke tests some users will see the following message during the obsvis test

Fontconfig error: Cannot load default config file

This error is not critical. As long as the test reports a PASS, then users can ignore that message.

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"
  • The following parameter:
    has the following error(s):
      o Mode field "l" is invalid.
  • The following parameter:
    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 conflicts; 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.".

Certain CIAO tools (e.g. axbary, dmgti, evalpos, detect, wavdetect) are actually shell scripts. If FTOOLS is set to launch automatically in the startup script, these tools may reinitialize it and cause a parameter file conflict. Commenting the FTOOLS startup out of your .cshrc/.bashrc/.zshrc file and starting FTOOLS manually before starting CIAO should resolve this issue.

Conflicts with Other Software Packages

There are some known conflicts between CIAO and other software or system libraries and tools. Issues not covered in this "Watch Out" page are listed on the "Other Software Packages" bug page.


Incorrect GTIs when time-filtering grating data with dmcopy opt=all

When a time filter is applied to a level=1.5 (evt1a.fits) or level=2 (evt2.fits) grating file and the dmcopy opt=all option is used, the GTI block in the output file is not updated to reflect the correct time range. Time-related header keyword values - such as ontime, livetime, and exposure - will be incorrect because they are calculated from the time ranges in the GTI block.

This bug affects all ACIS and HRC grating data analysis. Read the bug report for details and a workaround.


Installing 3rd party modules with pip3

Users must be careful when using pip3 to install 3rd party modules such as Astropy and Scipy into CIAO. The latest version of these packages MAY require updated versions of packages that CIAO needs; numpy being the most likely conflict.

pip3 installing source code packages

Many of the python packages available via pip are either pure python or are precompiled binary distributions. However, some packages are provided as source code and will need to compile against the libraries on the users system. Users may experience problems building these packages due to some remaining hard-coded paths in some configuration files.