Spitzer Documentation & Tools
Downloading, Installing, and Updating MOPEX

NOTE (Apr 10, 2016) A memory leak in "mosaic_rmask" affecting large-coverage mosaics has been fixed. Download the new binary available for your system and place it in your Mopex "bin" directory, as "mosaic_rmask":

  • mosaic_rmask_mac64_patch2016
  • mosaic_rmask_linux64_patch2016
  • As always, command-line users should "source mopex-script-env.csh". This does not change the output of this program - it is just a change in memory allocation.

    A "feature" noted by a user: don't use ".tbl" as a suffix for an image list input to the Mosaic task.

    NOTE (Jan 10, 2016) There have been a few reports of problems with mosaic_coadd failing on some Linux and Mac OSX systems (e.g. Yosemite) when large numbers of input images are used. New binaries are available here. If you have encountered a problem, first try downloading the new binary available for your system and placing it in your Mopex "bin" directory, as "mosaic_coadd":

  • mosaic_coadd_mac64_patch2016
  • mosaic_coadd_linux64_patch2016
  • As always, command-line users should "source mopex-script-env.csh". This does not change the output of this program - it is just a change in memory allocation.

    NOTE (Apr 20, 2015) Mac OSX 10.10 (Yosemite) or later users: You may not be able to start the Mopex GUI by clicking on "mopex.app" or after an auto-update. The OS will issue a message that "PowerPC applications are no longer supported." The workaround is that you can start the GUI from the command line:

    prompt% (your Mopex dir)/mopex.app/Contents/MacOS/JavaApplicationStub &

    We hope to address the issue in a future release.

    NOTE (Dec 18, 2014) Linux and Mac OSX 10.9 (Mavericks) or later users: New Mopex binaries are available here to fix a known issue. If you have not already updated, please do so by downloading the new binary available for your system and placing them in your Mopex "bin" directory, as "mosaic_coadd" or "fiducial_image_frame":

  • mosaic_coadd_mac64_patch2014
  • fiducial_image_frame_linux64bit_patch2014
  • As always, command-line users should "source mopex-script-env.csh". These bugs do not change the output of these programs - they are just minor memory overwrite issues. These changes will be in the next Mopex update.

    The current version of the MOPEX installers is 18.5.0; auto-updates to the latest versions of all files are available through the GUI. If you have an old version of MOPEX already installed, you can skip to the last step ("Updating the GUI"). The exception is if you have upgraded to Mac OSX 10.7 (Lion) or above. In that case, you should install the appropriate version of MOPEX below rather than attempting an update. Supported platforms and system requirements are described on the MOPEX System Requirements page.

    With the 18.5.0 version, there are two versions of Mac and Linux installers, a 64-bit version (the default) and a 32-bit version. Most users should be able to use the 64-bit versions (and Mac Lion+ users must use it).

    Changes since the previous version are described in the MOPEX Change Log. Remaining bugs are listed in the MOPEX Bug List.

    Note: Install scripts require a cshell (csh, tcsh, or equivalent).

    Download and Installation

    A MOPEX installer contains both the GUI and command-line versions (except that there is no command-line version for Windows). A second tar file of sample data is also available. Example namelists are provided in the cdf directory for use with the sample data.

    Linux

    1. Download the installation file: mopex18_5_0-linux64.sh (188 MB)
    2. Download the sample data file (optional): mopex16_sample_data.tar.gz (171 MB zipped / 257 MB unzipped).
    3. Make the installation file executable:
      prompt> chmod +x ./mopex18_5_0-linux.sh
    4. Run the installation file:
      prompt> ./mopex18_5_0-linux.sh
    5. Follow the instructions below to set up and start MOPEX

    Mac OSX 10.4+

    1. Download the installation file: mopex18_5_0-mac64.dmg (201 MB)
    2. Download the sample data file (optional):mopex16_sample_data.tar.gz (171 MB zipped / 257 MB unzipped).
    3. Double click on the file
    4. Drag the mopex folder to wherever you want MOPEX to be kept
    5. Follow the instructions below to set up and start MOPEX

    32-bit Versions

    1. mopex18_5_0-linux32.sh
    2. mopex18_5_0-mac32.dmg
    Installation steps are the same as above

    Solaris 10+

    1. Download the installation file: mopex18_5_0-solaris.sh (187 MB)
    2. Download the sample data file (optional): mopex16_sample_data.tar.gz (171 MB zipped / 257 MB unzipped).
    3. Make the installation file executable:
      prompt> chmod +x ./mopex18_5_0-solaris.sh
    4. Run the installation file:
      prompt> ./mopex18_5_0-solaris.sh
    5. Follow the instructions below to set up and start MOPEX

    Windows

    1. Download the installation file: mopex18_5_0-windows.exe (173 MB)
    2. Download the sample data file (optional):mopex16_sample_data.tar.gz (171 MB zipped / 257 MB unzipped).
    3. Double click on the file to install
    4. Install a copy of Cygwin (default setup is fine) for your system at http://www.cygwin.com.
    5. Make a copy of the cygwin1.dll file for MOPEX. The original is in C:\cygwin\bin\cygwin1.dll. The copy goes in your Mopex bin directory, by default, C:\Program Files\Mopex\platform\windows\bin.
    6. Add a Cygwin Environment Variable for your account. From Start:
      Control Panel - User Accounts(twice) - Change my Environment Variables
      Select a New Variable: CYGWIN
      Value: nodosfilewarning
      (In XP, use Control Panel - System - Advanced - Environment Variables)
    7. If editing a new namelist (*.nl) file to be read in, you would give the full paths to files this way, for example:
      IMAGE_STACK_FILE_NAME = C:/cygwin/home/me/mydata/ImageList.txt
      If you put MOPEX in the default directory (with the space), it is easiest just to copy what you need from the default "cdf" and "cal" directories to your own directories. A cal file might then look like this in your namelist file:
      PMASK_FILE_NAME = C:/cygwin/home/me/mydata/cal/mips24_pmask.fits
    8. Follow the instructions below to set up and start MOPEX


    Starting the GUI

    After completing the installation, the MOPEX GUI can be launched from the executable file (the command "mopex" in Unix-like environments, or double-clicking on the mopex.app icon in Mac or mopex in Windows).

    For Mac versions starting with Lion, security blocks may be on ("Gatekeeper"). Double-clicking may lead to a message like:

    "mopex" is damaged and can't be opened. You should move it to the
    Trash.

    Click "Cancel". You will need to temporarily disable Gatekeeper, launch MOPEX, then re-enable Gatekeeper again (if you wish). You only need to do this once.

    To temporarily disable Gatekeeper, open "System Preferences". Under "Personal", click "Security & Privacy". If necessary, click the lock and enter your password. Under "Allow applications downloaded from", select "Anywhere". You may leave this window open.

    Go back and double-click on mopex.app. You may receive the following message:

    "mopex" is an application downloaded from the Internet. Are you sure
    you want to open it?

    Click "Open".

    Now you can go back to the "Security & Privacy" window and set "Allow applications downloaded from..." to whatever value you are comfortable with. You should be able to run MOPEX with just a double click without altering Gatekeeper.

    Please ensure that you are connected to the internet when you launch MOPEX for the first time - it will automatically check for any available updates. When the software first starts, you will be presented with a blank window. Go to the Help menu to get introductory material by selecting Overview. To begin using the program, go to the File menu and open either a new pipeline or read in your existing MOPEX namelist.

    Starting the command-line MOPEX

    After completing the installation instructions, the MOPEX environment variables must be set up as follows:

    1. Edit mopex-script-env.csh to set the installation path MOPEX_INSTALLATION to the current directory (pwd) e.g. if MOPEX is in /home/joe/mopex, then you should set the following in mopex-script-env.csh:
    setenv MOPEX_INSTALLATION /home/joe/mopex

    2. Ensure that PERL_PATH is set to your perl installation path

    3. Running cshell (not bash), source mopex-script-env.csh:
    prompt> source mopex-script-env.csh

    4. The MOPEX perl scripts can now be called from the command line, e.g.:
    prompt> mosaic.pl -n mosaic_I1.nl

    Updating the GUI

    All updates to MOPEX are distributed via the auto-update function of the GUI. To use the auto-update, MOPEX needs to be able to connect to the internet. The net status is displayed at the bottom of the GUI. If you do not see Net Up, you may need to address the problem.

    MOPEX will automatically download any available updates whenever it is restarted. To check for updates without re-starting MOPEX, go to the Options menu on the task bar and toggle Use Automatic Mopex Version Update off and back on again.

    Updates will provide new functionality and cal files as they are developed. Existing files may be replaced if new versions are distributed with the same name, but other files will not be deleted. So, if you modify namelists or calfiles, we recommend changing their name to protect them from being overwritten. Even in you do not plan to use the GUI to run the scripts, we recommend using the update function rather than reinstalling all of MOPEX when updates become available. Note that updating MOPEX overwrites the mopex-script-env.csh setup file. You will need to modify this file after each update if you wish to run MOPEX on the command line. The GUI is unaffected by this file.