Spitzer Documentation & Tools
Downloading the GeRT

Getting Started

Follow the instructions below for downloading and installing the GeRT. When testing the GeRT after installation, be sure to check the output directory to make sure that the new BCDs have been created, even if no warning messages were seen.

Download the GeRT tarballs

We have 5 versions of the GeRT. The online system uses the Solaris--Forte version and all cababilities should work for this version. GNU-compiled versions of the GeRT for Solaris, Linux, and the Mac have also been created. The current GNU versions of the GeRT can carry out science BCD processing, but the calibration IC pipelines do not work on these versions yet. See the Gert System Requirements for more information.

Solaris SunOS 5.8 compiled with FORTE: Download the gzipped tarball

Solaris SunOS 5.8 compiled with GNU 3.4.5: Download the gzipped tarball

Linux Red Hat Enterprise 3 compiled with GNU 3.4.5: Download the gzipped tarball

Mac OSX PowerPC (10.3/10.4) compiled with GNU 3.4.5: Download the gzipped tarball

Mac OSX Intel (up to and including 10.8) compiled with GNU 3.4.5: Download the gzipped tarball

Installation Instructions

Follow the steps below to install and test the GeRT, using the appropriate gzipped tarball for your operating system.

  1. Unpack the downloaded tarball in the directory in which you want to install the GeRT:
    unix% gunzip gert_gnuSOL_060415.tar.gz 
    unix% tar -xvf gert_gnuSOL_060415.tar
  2. Edit the SOS_GeRT environment parameter in the gert_setup.csh file to match your GeRT installation path. The GeRT setup and scripts are designed for tcsh/csh.
    cd GeRT_gnuSOL_060415
    unix% emacs gert_setup.csh
    Edit the line:
    setenv SOS_GeRT  /your/gert/installation/path/GeRT/GeRT_gnuSOL_060415
  3. [optional] If you have perl threads (Thread.pm), then set GERT_THREAD in gert_setup.csh, otherwise leave GERT_THREAD set to zero (no threads).

    Use perl Thread.pm for increased speed (if available)

    GERT_THREAD =~ num_cpu + 1 --> 2xnum_cpu for optimal performance
    GERT_THREAD 0 = no threads (e.g., Can't locate Thread.pm in @INC )

  4. Source gert_setup.csh to set environment
    unix% source gert_setup.csh
    Environment parameters used by scripts:

    SOS_LOCAL = location of the cal and cdf directories = SOS_GeRT
    SIRTF_BIN = location of the binaries = SOS_GeRT/bin
    WRAPDIR = location of the scripts = SOS_GeRT/scripts

    SIRTF_BIN is added to your PATH. The LD_LIBRARY_PATH is set to SOS_GERT/lib for the Solaris versions but is not used for LINUX and Mac versions. The setup script checks for perl and sets PERL_PATH if needed. You need PERL to run the GeRT.

  5. Test the GeRT on your system.
    unix% cd testme
    unix% $WRAPDIR/gert.pl INtest.lis OUTdir 
    --> Runs the GeRT on input list of files given by INtest.lis and puts the products in OUTdir. Confirm that the *.bcd.fits files are successfully made in the OUTdir/bcd directory.

    To run with perl threads, then
    unix% $WRAPDIR/gert_thread.pl INtest.lis OUTdir 
    If you try to use gert_thread.pl and get errors with a message like "Can't locate Thread.pm in @INC", then you do not have perl threads on your system, and you need to set GERT_THREAD=0 and run gert.pl.

    For default processing, the GeRT reads the header of the first file to determine the data type and picks the appropriate pipeline. The important keywords which control the pipeline processing are CHNLNUM, EXPTYPE, and FOVID.

    CHNLNUM = 2 for 70um
    CHNLNUM = 3 for 160um
    EXPTYPE = scn ==> Scan data, normal science pipeline is run.
    EXPTYPE = pht ==> Photometry data, normal science pipeline is run.
    If EXPTYPE=pht and FOVID>117, then the data are 70um
    FINE-scale observations and the appropriate calibration files are chosen.
    EXPTYPE = sed ==> 70um SED data, SED pipeline is run.EXPTYPE = tpm ==> Total power mode data, TPM pipeline is run.
    EXPTYPE = d2a ==> DARK data, DARK pipeline is run.
    EXPTYPE = sfl ==> IC data from scanning, IC pipeline is run.
    EXPTYPE = pfl ==> IC data from photometry, IC pipeline is run.
    EXPTYPE = ffl ==> IC data from FINE-scale photometry, IC pipeline is run.
    EXPTYPE = dfl ==> SED IC data, IC pipeline is run.
    EXPTYPE = tfl ==> Total power IC data, IC pipeline is run.

    Users can force the GeRT to run a specfic pipeline by providing the EXPTYPE on the command line (3rd input argument). For example, if you would like to make your own IC calibration file from your science data you could try the following, e.g.:
    unix% $WRAPDIR/gert.pl IN70.lis OUTdir sfl
    where "sfl" causes the GeRT to run the IC pipeline.

    The output BCD products from the GeRT have the same suffixes as those from the SSC archive and are put in the OUTdir/bcd directory. The BCDs and/or fBCDs can be coadded using mopex. The gert.pl script also makes numerous intermediate products which can be useful for diagnostic purposes.


There is no automatic update system for the GeRT. When a new version is released, it will be advertised on the Data Analysis and Tools page.