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Last modified: 2 May 2025

URL: https://cxc.cfa.harvard.edu/ciao/watchout.html
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CIAO "Watch Out" Page

WHAT'S NEW | WATCH OUT

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

macOS Sequoia 15.4 incompatible with ciao-install | matplotlib on MacOS | SAOImage ds9 | Installing & Starting CIAO | Analysis | Python

macOS Sequoia 15.4 incompatible with ciao-install

A change to macOS Sequoia version 15.4 and newer has introduced an incompatibility with CIAO installed using the ciao-install script. Users who installed CIAO with ciao-install and upgrade their macOS from an earlier version to 15.4 (or later version) will find that certain applications will begin to fail when previously they worked. Users may see an error message which contains something similar to this: 

Traceback (most recent call last):
  File "/Users/ciao_user/miniforge3/envs/ciao-4.17/lib/python3.11/site-packages/numpy/core/__init__.py", line 24, in <module>
    from . import multiarray
  File "/Users/ciao_user/miniforge3/envs/ciao-4.17/lib/python3.11/site-packages/numpy/core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/Users/ciao_user/miniforge3/envs/ciao-4.17/lib/python3.11/site-packages/numpy/core/overrides.py", line 8, in <module>
    from numpy.core._multiarray_umath import (
ImportError: dlopen(/Users/ciao_user/miniforge3/envs/ciao-4.17/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <CAA510D4-816A-34E5-9021-485EF5D56159> /Users/ciao_user/miniforge3/envs/ciao-4.17/lib/libopenblas.0.dylib
  Reason: tried: '/Users/ciao_user/miniforge3/envs/ciao-4.17/lib/libgfortran.5.dylib' 
  (duplicate LC_RPATH '@loader_path'), '/Users/ciao_user/miniforge3/envs/ciao-4.17/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'),  
  '/Users/ciao_user/miniforge3/envs/ciao-4.17/lib/python3.11/site-packages/numpy/core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'),
  '/Users/ciao_user/miniforge3/envs/ciao-4.17/lib/python3.11/site-packages/numpy/core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'),
  '/Users/ciao_user/miniforge3/envs/ciao-4.17/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'),
  '/Users/ciao_user/miniforge3/envs/ciao-4.17/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file),
  '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

Users will need to re-install CIAO using the conda create method. Also first time CIAO installers using macOS Sequoia 15.4 must use the conda create method.

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)
Save
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 ciao.sh

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 ciao.sh script to setup for CIAO. 

$ alias ciao="source /soft/ciao-4.17/bin/ciao.sh"
$ 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

CIAO 4.17 only supports Python 3.11.

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.

macOS ls: 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:
    "foo,b,l,no,,,"Keyword""
has the following error(s):
  o Mode field "l" is invalid.

  • 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".

  • Parameter xoffset: invalid range (INDEF, INDEF).
Parameter yoffset: invalid range (INDEF, INDEF).
pset: unable to initialize tool/parameter file "tgdetect".

  • ....
pquery: unable to prompt for parameter "-".
pquery: unable to prompt for parameter "-".
/Users/will_i_am/.conda/envs/ciao/bin/wavdetect: line 66: test: -ge: unary operator expected
ERROR: Input background file or a default normalized background filename must be specified as input for wrecon.

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.

Python

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.

NumPy 2 warnings [New] (17 dec 2024)

CIAO does not support version 2.0 or higher of NumPy, which means that if NumPy gets updated then users will see an error like 

ImportError: numpy.core.multiarray failed to import

along with the screen message 

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.0 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

If this happens then re-install version 1 of NumPy with the following command: 

% pip install 'numpy < 2'
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.

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