This document contains information about the IPAC Science Applications (SciApps) software, which is a collection of third party software for scientific analysis that is maintained as a service to IPAC scientists to facilitate their research work.
SciApps is normally supported during regular business hours (i.e., no support on weekends and Caltech holidays), at a level of 50% of a full-time IPAC (research scientist) employee. Temporary reductions to this level of support are sometimes necessitated; for example, due to the travel schedule of the SciApps Administrator. Upcoming periods of reduced support availability are listed here:
| Dates | SciApps Support |
Notes |
| 28 Sep 2012 | No Support | LAST DAY OF SciApps SUPPORT! |
• 17 Sep 2012: New SciApps distribution for macintel (6, 7) and linux, released on the networked /SciApps partition and as tarballs for stand-alone installation. Beta release in Aug 2012. This is the final SciApps update.
• 18 Apr 2012: Applied workaround to IDL v8.1 to restore idlde GUI functionality under OS X 7.3 (Lion).
• 18 Jan 2012: New SciApps distribution for macintel (5, 6, 7), released on the networked /SciApps partition and as tarballs for stand-alone installation. Updated APT to v20 in the macintel and linux distributions to support HST Cycle 20 proposals; new tarballs available for linux. Bash shell initialization files now available.
• 24 Oct 2011: Interim update for macintel, confirming operational status of SciApps routines for OS X 10.7 (Lion). Minor s/w update to macintel and linux (added Eclipse subroutine library). Updated tarballs for macintel (5, 6, 7) and linux available.
• 29 Aug 2011: New SciApps distribution for solaris (Corbomite Maneuver) released on the networked /SciApps partition.
• 13 July 2011: Interim update to fix library links for ImageMagick tasks in macintel6 distribution.
• 6 July 2011: Interim update to provide APT v19.2 for all supported operating systems (macintel, linux, solaris).
• 31 May 2011: New SciApps distribution for linux (Tholian Web) released on the networked /SciApps partition and as tarballs for stand-alone installation. IDL updated to v8.1 on all platforms (except macosx = PowerPC Macs). Simplified FAQ organization on the SciApps web page.
• 25 April 2011: Interim update of stsdas and tables external packages to v3.13 in IRAF v2.14.1 for macintel distributions (networked and stand-alone).
• 8 April 2011: Interim update of IRAF to v2.15.1a for macintel distributions (networked and stand-alone).
• 25 March 2011: Interim update of IDL to v8.0.1 for all distributions (except macosx).
• 4 March 2011: Interim update to macintel5 and macintel6 distributions (networked and stand-alone) to fix path definition issue that prevented some python tasks from working. Networked SciApps users do not need to take any action. Users who have already installed the basic and, optionally, pyraf patch tarballs should download and install the new python patch tarball and, optionally, updated pyraf patch tarball. All stand-alone SciApps users will need the basic (python) patch, but only users who want to use pyraf or IRAF 2.14.1 will need the pyraf patch. Users who have not yet installed the basic tarball can simply download and install the updated basic tarball, which includes the necessary patches.
• 3 March 2011: All tarballs for stand-alone installation of SciApps restored to the IPAC ftp site following resolution of disk space issues.
• 28 February 2011: New SciApps distribution for macintel (Doomsday Machine) released on the networked /SciApps partition and as tarballs for stand-alone installation. IDL libraries updated for all operating systems.
• 19 January 2011: Interim update to upgrade IDL to v8.0 on all platforms following deployment of new IPAC license manager (except macosx - as of v8.0, ITT VIS Exelis Visual Information Solutions no longer supports IDL for PowerPC Macs. Affected users can still use IDL v7.1.1 and previous versions; the “idl” command will default to v7.1.1 on macosx computers). Also updated APT to version 19.0, required for HST Cycle 19 proposal preparation.
• 9 December 2010: Postponed start of next round of updates (mainly motivated by ongoing work on new IDL license server, evaluation of future support for macosx, volume of SciApps support requests, and confluence of non-SciApps constraints on available resources).
• 8 September 2010: New SciApps distribution for solaris (The Alchemist) released on the networked /SciApps partition. Interim update to macintel6, macintel6, macosx, and linux to roll back default version of SExtractor to v2.5.0. Version 2.8.6 is still available but should be considered unstable – see SExtractor entry in the Table of Available Software for more information.
• 8 July 2010: Added Support Schedule section at top of SciApps web page.
• 15 June 2010: Interim update to provide APT version 18.2, required for HST Cycle 18 Phase II preparation and submission (network and stand-alone).
• 2 June 2010: New SciApps distribution for linux (Jefferson Twilight) released on the networked /SciApps partition and as tarballs. Updated mac distribution (Doctor Orpheus) on network and stand-alone to reflect new IRAF and library directory structure (which were updated to facilitate further Snow Leopard integration), but no changes were made to the software versions. There is no need to reinstall the mac tarballs if your current mac installation is working; any problems with the mac networked SciApps can be resolved by logging out/in. Added instructions in the FAQ for using your own IDL license file with the SciApps IDL installation.
• 12 May 2010: SciApps moved from redshift to ipacsci0. Updated references to redshift in documentation.
• 4 May 2010: Interim update to provide missing SuperMongo initialization links in macintel6, macintel5, and macosx (network and stand-alone).
• 1 April 2010: Interim update to provide missing SExtractor libraries in macintel6, macintel5, and macosx (network and stand-alone).
• 31 March 2010: New SciApps distribution for macintel and macosx (Doctor Orpheus) released on the networked /SciApps partition and as tarballs. Updated procedure for obtaining and installing stand-alone SciApps tarballs.
• 22 January 2010: New SciApps distribution for solaris (Your Little Dog) released on the networked /SciApps partition. There will be no stand-alone (tarball) release for solaris.
• 11 January 2010: Interim update to upgrade APT to v18.0 in macintel, macosx, and linux distributions.
• 11 December 2009: Interim update to upgrade IDL to v7.1.1 in macintel, macosx, and linux distributions.
• 5 October 2009: New SciApps distribution for linux (Cowardly Lion) released, both on networked /SciApps partition and as stand-alone tarballs. Revised SciApps initialization procedure for macintel and macosx (same as the procedure for linux) released; this revision fixes the problem with logging in when the automounter has unmounted /SciApps. Patch for macintel version of pgplot released in tarball form; already deployed for networked SciApps. IDL has been moved into /SciApps (from /COTS); should be transparent to users.
• 22 September 2009: Interim update to SciApps (Flying Monkey) for macintel and macosx (networked and stand-alone): updated CALDB (CIAO) to version 4.1.4.
• 15 September 2009: Interim update to SciApps (Flying Monkey) for macintel and macosx (networked and stand-alone): updated APT to version 17.4.3 to provide support for HST proposal preparation using post-servicing mission parameters.
• 25 August 2009: Released SciApps (Flying Monkey) stand-alone tarballs for macintel and macosx.
• 22 July 2009: New SciApps distribution for macintel and macosx (Flying Monkey) released. Old SciApps for macintel and macosx will cease functioning on 31 August 2009.
• 8 May 2009: DS9 upgrade appears to have worked; only problems resulted from some users who had aliased old versions of the DS9 binary (which moved). Resolved these with individual users. Proceeding with inventory and clean-up of existing SciApps s/w, setting up for shift to new initialization scripts, followed by updating process. Now have access to macintel, macosx, and solaris operating systems, still waiting for SciApps linux machine to be brought online. SciApps User Survey closed.
• 24 April 2009: DS9 for Solaris and Mac upgraded to latest version (5.6.2; sorry Linux users, you have to wait a little longer). Some user-transparent changes made to /SciApps directory structure to prepare for new initialization and updating plans. Everything should still work for users with old (i.e., pre-July 2009) SciApps initialization files, but they should now receive the new version of DS9.
• 13 April 2009: SciApps User Survey released to IPAC. ISG completes sciapps account creation and transferal of ownership of the /SciApps partition, paving the way for updates to commence (eventually – some logistical work and clean-up of the /SciApps partition must be accomplished first).
• 30 March 2009: A new SciApps Administrator takes office. Expect many updates, changes, and improvements to SciApps soon.
The following operating systems receive active SciApps support. Previous versions of these operating systems will be supported on a best-effort basis. If necessary, please contact the ISG to upgrade the operating system of your computer.
| OS X 10.8 Mountain Lion (macintel8) – NOT SUPPORTED! |
| Mac OS X 10.7 Lion (macintel7) – FROZEN! |
| Mac OS X 10.6 Snow Leopard (macintel6) – FROZEN! |
| Mac OS X 10.5 Leopard (macintel5) – FROZEN! |
| Mac OS X 10.5 Leopard for PowerPC (macosx) – FROZEN! |
| Red Hat Enterprise Linux 5.3 (linux) – FROZEN! |
| Solaris 10 (solaris) – FROZEN! |
The following table lists the dates of the last and planned next updates of the SciApps distributions for each supported operating system. A reminder email for all updates will be circulated with at least 1 week of advance warning. SciApps may not be available for up to one day (but typically less) when updates occur. Planned updates will be postponed if no changes to the current SciApps distribution are required one month before the scheduled date.
| OS | Current SciApps Version Name |
Release Date (Interim Updates) |
Next Planned Release |
| macintel7 macintel6 |
Eyafjallajokull | 17 Sep 2012 | FROZEN! |
| macintel5 | Frumious Bandersnatch | 18 Jan 2012 (18 Apr 2012) |
FROZEN! |
| macosx | Doctor Orpheus | 31 Mar 2010 (19 Jan 2011) (8 Sep 2010) (15 Jun 2010) (2 Jun 2010) (1 Apr 2010) |
FROZEN! |
| linux | Theistareykjarbunga | 17 Sep 2012 | FROZEN! |
| solaris | Corbomite Maneuver | 29 Aug 2011 | FROZEN! |
The following table contains the historical record of release dates of previous SciApps distributions (starting in July 2009).
| OS | Previous SciApps Version Name |
Release Date (Interim Updates) |
| macintel7 macintel6 macintel5 |
Frumious Bandersnatch | 18 Jan 2012 (18 Apr 2012) |
| Doomsday Machine (Lion Compatible) |
28 Feb 2011 (24 Oct 2011) (13 Jul 2011) (6 Jul 2011) (8 Apr 2011) (25 Mar 2011) (4 Mar 2011) |
|
| macintel6 macintel5 |
Doctor Orpheus | 31 Mar 2010 (19 Jan 2011) (8 Sep 2010) (15 Jun 2010) (2 Jun 2010) (1 Apr 2010) |
| Flying Monkey | 22 Jul 2009 (15 Sep 2009) (22 Sep 2009) (11 Dec 2009) (11 Jan 2010) |
|
| macosx | Flying Monkey | 22 Jul 2009 (15 Sep 2009) (22 Sep 2009) (11 Dec 2009) (11 Jan 2010) |
| linux | Jefferson Twilight | 2 Jun 2010 (25 Mar 2011) (28 Feb 2011) (19 Jan 2011) (8 Sep 2010) (15 Jun 2010) |
Cowardly Lion | 5 Oct 2009 (11 Dec 2009) (11 Jan 2010) |
| solaris | The Alchemist | 8 Sep 2010 (6 Jul 2011) (25 Mar 2011) (28 Feb 2011) (19 Jan 2011) |
| Your Little Dog | 22 Jan 2010 (15 Jun 2010) |
The following table lists the software packages and versions that are currently available in SciApps. Current version release dates are listed in parentheses in the format YYMMDD (MMDD = ---- or DD = -- indicates no precision on release date below year or month, respectively). Available older versions of software titles are listed in italics. See the FAQ for instructions to access old versions of IDL; old versions of other software (except IRAF) are generally not easily accessible without exploring the SciApps installation tree. Columns shaded in grey are frozen distributions that have not been updated for one or more SciApps update cycles.
| Software | macintel7 OS X 10.7 Lion | macintel6 OS X 10.6 Snow Leopard | macintel5 OS X 10.5 Leopard | macosx OS X 10.5 Leopard | linux | solaris | Notes |
| AIPS | user install (see FAQ) |
user install (see FAQ) |
user install (see FAQ) |
user install (see FAQ) |
user install (see FAQ) |
user install (see FAQ) |
Astronomical Image Processing System for radio data. |
| APT (runapt) | 20.2.2 [64!] (120718) 20.0, 19.4 |
20.2.2 [64!] (120718) 20.0, 19.4, 19.2, 19.0 |
20.0F [64!] (120111) 19.4, 19.2, 19.0, 18.2 (see Notes) |
none (see Notes) |
20.2.2 [64] (120718) 20.0, 19.2, 19.0, 18.2 |
none (see Notes) |
The Astronomer's Proposal Tools package is used to submit Phases I/DD and II proposals for the Hubble Space Telescope. The SciApps version of APT is optimized for computers with 2 GB or more of RAM. As of v19, APT is no longer supported by STScI for non-Intel Macs. Starting with v20, running APT under Mac OS X 10.5 (Leopard) requires a 64-bit computer; consequently, while this version has been installed in SciApps, local hardware limitations have prevented testing it for even basic aliveness. As of v20, APT is no longer supported by STScI for solaris computers. See the FAQ for additional information.
Lion Notes: Running this software for the first time may require installing Java. Follow the on-screen instructions provided by Lion at runtime. |
| cfitsio library | 3.310 (120718) 3.280 |
3.310 (120718) 3.280 |
3.280F (110512) 3.260, 3.240, 3.140 |
3.240F@ (100126) 3.140@ |
3.310 (120718) 3.270, 3.240, 3.200 |
3.280F (110512) 3.240, 3.210 |
Library of C and Fortran subroutines for reading and writing data files in FITS format. To compile programs linked to libcfitsio, specify the library path -L$SciAppsLib to the compiler. |
| CIAO (ciao) | 4.4% [64!] (111215) |
4.4 [64!] (111215) 4.3.0, 4.2.0 |
4.3.0F (101215) 4.2.0, 4.1.2 |
none (see Notes) |
4.3.1 (110426) 4.2.0, 4.1.2 |
4.3.1F (110426) 4.2.0 (see FAQ) |
Chandra Interactive Analysis of Observations. Version for macosx (PowerPC) running OS X 10.5 (Leopard) is not available. Starting with v4.4, CIAO no longer runs on Mac OS X 10.5 (Leopard). |
| CIAO: CALDB | 4.4.7 (111215) |
4.4.7 (111215) 4.4.1, 4.2.0 |
4.4.1F (101215) 4.2.0, 4.1.4, 4.1.3 |
none | 4.4.3 (110426) 4.2.2, 4.2.0, 4.1.4, 4.1.3 |
4.4.5F (110630) 4.2.2, 4.2.0, 4.1.4, 4.1.3 |
Calibration Database for CIAO. Note: for a given CALDB version number, installations of CIAO for all operating system use the same CALDB installation. |
| DS9 [SAOimage] (ds9) | 7.0.2 (120703) 6.2 |
7.0.2 (120703) 6.2, 6.0 |
6.2F (101015) 6.0, 5.6.2 |
6.0F@ (100115) 5.6.2@ |
7.0.2 [64] (120703) 6.2, 6.1, 5.6.3 |
6.1.2F (100515) 6.0, 5.7, 5.6.2, 4.0b7, 3.0b6, 2.0 |
Astronomical imaging and data visualization application. |
| Eclipse (e.g., dfits, fitsort, etc) | 5.0.0F% (050923) |
5.0.0F% (050923) |
5.0.0F (050923) |
none | 5.0.0F (050923) |
none | An ESO ANSI C library, focused mainly on image and 1d signal processing, with emphasis on infrared and visible images and spectra. Only the eclipse-main package is installed in SciApps. To avoid a name conflict with a WCStools routine, the eclipse routine setpix is called esetpix in SciApps. |
| Firefox | none | none | none | none | none | 6.0F (110816) 5.0, 4.0.1 |
This version of Firefox and its plugins are out of date, vulnerable to malicious actions, and should not be used. Includes flash and java plugins. Earlier versions are available via the commands firefox5 and firefox4. |
| fpack (fpack, funpack) | 1.6.0% (1102--) |
1.6.0 (1102--) 1.5.1 |
1.6.0F (1102--) 1.5.1 |
none | 1.6.0 [64] (1102--) |
1.6.0F (1102--) |
Optimal compression of images in the FITS data format. Starting with v2.3, the ATV fits image viewer in IDL can read fpacked FITS images.
IMPORTANT NOTE: for FITS files with real pixel values, the fpack algorithm is lossy and results in a small degradation of precision in the restored files – see the fpack web page for more information. |
| Fv (fv) | 5.3% (0907--) |
5.3% (0907--) |
5.3F (0907--) 5.2.1 |
5.2.1F@ (0807--) (see Notes) |
5.3 (0907--) |
5.3F (0907--) |
Graphical program for viewing and editing any FITS format image or table. Also provides the interface to HEASOFT through Hera (see FAQ). |
| g77 | 3.4.0F% (0610--) |
3.4.0F% (0610--) |
3.4.0F (0610--) |
3.4.0F (0610--) |
none (see Notes) |
3.4.3F (0610--) (see Notes) |
Open source FORTRAN compiler. Available in /usr/bin/ for linux. Copied from /opt/TWWfsw/ for solaris. Development halted in 2006 in favor of gfortran (see below); no further updates to g77 are anticipated. |
| g95 | 0.92F% (090624) |
0.92F% (090624) |
0.92F (090624) |
0.91F (0803--) |
0.92 [64] (090624) 0.91 (see Notes) |
0.92F (090624) |
Open source FORTRAN compiler. Starting with v0.92 for linux, the compiler is 64-bit capable, but defaults to 32-bit integers for compatibility with older code. |
| gfortran | 4.6.2 [64] (111020) |
4.6.2 [64] (111021) 4.5.0 |
4.6.2F (111021) 4.4.1, 4.4.0 |
4.4.1F (0907--) 4.4.0 |
none (see Notes) |
none (see Notes) |
Open source FORTRAN compiler. Available in /usr/bin/ for linux; not available for solaris. In order to use gfortran on macintel computers, you must issue the following one-time command in a terminal window:
sudo ln -s $SciApps_longpath/gfortran /usr/local/ |
| Ghostscript (gs) | 9.02 (110330) |
9.05 (120208) 9.02 |
9.02F (110330) 9.00, 8.64 |
8.64F (090203) |
none (see Notes) |
7.07F (030517) (See Notes) |
An interpreter for the PostScript language. Available in /usr/bin/ for linux. Copied from /opt/TWWfsw/ for solaris - will not be updated. |
| Ghostview (gv) | 3.6.5% (0807--) |
3.6.5 (0807--) |
3.6.2F (0609--) |
3.6.2F (0609--) |
3.5.8 (9706--) |
3.6.1F (041219) (see Notes) |
Postscript previewer. Copied from /opt/TWWfsw/ for solaris - will not be updated.
Lion Notes: gv v3.6.5 displays three warnings on the command line related to the translation table when running under Lion, but this does not appear to affect its functionality. |
| Grace (xmgrace) | none (see Notes) |
5.1.16F% (040704) |
5.1.16F (040704) |
5.1.16F@ (040704) |
5.1.22F (080521) |
5.1.22F (080521) |
GUI-enabled scientific plotting package (like Supermongo, but with a GUI). Development of Grace appears to have greatly slowed, or stopped altogether, with a promised v6 release stalled for several years. Future updates are not expected.
Lion Notes: Grace runs as PowerPC software even on macintel computers, so is no longer supported under Lion. |
| HEASOFT | none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
A unified release of the FTOOLS and XANADU software packages for X-ray data. |
| IDL (idl) | 8.2 [64] (120629) 8.1 |
8.2 [64] (120629) 8.1, 8.0.1, 8.0, 7.1.1, 7.0.6 |
8.1F [64] (110314) 8.0.1, 8.0, 7.1.1, 7.0.6, 7.0 |
7.1.1F (090928) 7.0.6, 7.0 |
8.2 [64] (120629) 8.1, 8.0.1, 8.0, 7.1.1, 7.0.6, 7.0, 6.0 |
8.1F [64] (110314) 8.0.1, 8.0, 7.1.1, 6.0, 5.6, 5.5, 5.4, 5.2 |
Interactive Data Language. It does everything. As of v8.0, Lion Notes: Upon starting IDL in Lion, some users report a problem in which the following message is displayed several times, and repeated frequently thereafter: “This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.” This issue can be resolved as follows: (1) Issue the command sudo -s and enter your password. This will place you in root user mode - be careful what you do! (2) Start IDL by issuing the idl command. (3) After it starts, immediately exit from IDL. (4) Issue the exit command to leave root user mode. This should resolve the issue with IDL, and you should be able to start it normally now. Note that this process requires that your user account has sudo (i.e., Administrator) privileges. |
| IDL: astro library | 21Jul12 11Jan12, 26Nov11, 07Oct11, 24Jan11, 21Jan10, 15May09 |
21Jul12 11Jan12, 26Nov11, 07Oct11, 24Jan11, 21Jan10, 15May09 |
11Jan12F 26Nov11, 07Oct11, 24Jan11, 21Jan10, 15May09 |
24Jan11F 21Jan10, 15May09 |
21Jul12 24Jan11, 17May10, 15May09 |
24Jan11F 17May10, 15May09 |
Useful astronomy-related routines for IDL. Requires using IDL v6.1 or higher. |
| IDL: ATV (atv) | 3.0b2 (111121) 2.3 |
3.0b2 (111121) 2.3, 2.1, 1.5.2 |
3.0b2F (111121) 2.3, 2.1, 1.5.2 |
2.3F (101018) 2.1, 1.5.2 |
3.0b2 (111121) 2.3, 2.2, 2.1, 1.5.2 |
2.3F (101018) 2.2, 2.1, 1.5.2 |
DS9-like FITS image viewer for IDL.
NOTE: starting with v3, ATV works only with IDL v8+, and requires the Coyote Graphics Library (which is now provided by SciApps). For earlier versions of IDL, use ATV v2.3, which can be called as atv23 in IDL v6 or v7. For best results with v2.3 (not required for v3+), include the following line in your ~/.idl_startup file: device, true_color=24, decomposed=0, retain=2 |
| IDL: buie library | 8.0 (110914) |
8.0 (110914) 7.1, 7.0 |
8.0F (110914) 7.1, 7.0 |
7.1F (100204) 7.0 |
8.0 (110914) 7.1, 7.0, 6.0 |
8.0F (110914) 7.1, 6.0, 5.6, 5.5, 5.4, 5.2 |
More astronomy-related IDL routines. The version number for the buie library is tied to the IDL version number. More recent versions of the buie library might not work with older versions of IDL, so SciApps automatically serves the correct version of the buie library depending on the version of IDL being used. |
| IDL: Coyote Graphics library | Dec2011 (111205) |
Dec2011 (111205) |
Dec2011F (111205) |
none | Dec2011 (111205) |
none | Library of IDL graphics routines, required by ATV v3+. |
| IDL: Transit Analysis Package: TAP (tap) | 2.1 (110130) |
2.1 (110130) |
2.1F (110130) |
2.1F (110130) |
2.1 (110130) |
2.1F (110130) |
IDL package designed for the analysis of extrasolar planet transit light curves, utilizing Markov Chain Monte Carlo fitting techniques. |
| IDL: Transit Analysis Package: autoKep (autokep) | 1.0 (110130) |
1.0 (110130) |
1.0F (110130) |
1.0F (110130) |
1.0 (110130) |
1.0F (110130) |
IDL package designed to provide streamlined transit light curves from MAST Kepler archive fits files. |
| IDL: IDLwave macros | 6.0F (060217) |
6.0F (060217) |
6.0F (060217) |
6.0F (060217) |
6.0F (060217) |
6.0F (060217) |
Macros for writing IDL programs in Emacs. IDLwave v6.1+ is incorporated into Emacs v22.0+; consequently, no further updates to the SciApps installation of IDLwave will be made. See the FAQ for initialization instructions. |
| ImageMagick | 6.7.8 (120702) 6.7.3 |
6.6.7F (110129) 6.5.9 |
none | none | none (see Notes) |
none | A software suite to create, edit, and compose bitmap images. Available in /usr/bin/ for linux. |
| IRAF (cl) | 2.16 [64] (120322) 2.15.1a, 2.14.1 |
2.16 [64] (120322) 2.15.1a, 2.14.1 |
2.15.1aF [64] (110125) 2.14.1 |
2.14.1F (080916) |
2.16 [64] (120322) 2.15.1a, 2.14.1 |
2.14.1F (080916) (see Notes) |
Image Reduction and Analysis Facility, built and distributed by NOAO. Starting with v2.15, IRAF is 64-bit capable; in order to run IRAF in 64-bit mode, your computer must be running a 64-bit kernel - see the FAQ for more info. NOAO currently does not support a solaris version of IRAF beyond v2.14.1. Not all external packages have been carried forward into the 2.15 release of IRAF; consequently, the 2.14 version is still available in SciApps - see the FAQ for instructions for starting IRAF v2.14.1. Note that using the stsdas/tables external packages on a 64-bit OS (linux, macintel6, macintel7) requires forcing IRAF to run in 32-bit mode - see the FAQ. See the FAQ for an important notice about SciApps support for IRAF external packages. |
| Iris (iris, sedimporter) | 1.1 (120720) 1.0 |
1.1 (120720) 1.0 |
1.0F (111007) |
none | 1.1 (120720) 1.0 |
none | Virtual Astronomical Observatory (VAO) application for analysis of 1-D astronomical spectral energy distributions. SciApps automatically provides either the 32-bit or 64-bit version of Iris, depending on which kernel is running. |
| JSkyCalc (jskycalc) | 1.2.1 (0807--) |
1.2.1 (0807--) |
1.2.1F (0807--) |
none | 1.2.1 (0807--) |
none | Astronomical almanac and sky viewing calculator. The original text-based skycal package written in C has now been deprecated and replaced by this Java-based, GUI-enabled version. |
| MacVim (vi, vim, gvim, mvim) | 7.3 (110918) |
7.3 (110918) |
none | none | none | none | GUI-enabled version of the venerable vi editor for the Mac. |
| pgplot | 5.3.1% (------) |
5.3.1% (------) |
5.3.1F (------) |
5.3.1F (------) |
5.2.2 (010226) |
5.2.2F (010226) |
Fortran- or C-callable, device-independent graphics subroutine library for making simple scientific graphs. The web documentation lists v5.2.2 as most recent, but is still valid for more recent versions. To compile programs linked to libcpgplot, specify the library path -L$SciAppsLib to the compiler. |
| PIA (pia) | none (see Notes) |
none (see Notes) |
none (see Notes) |
none (see Notes) |
none (see Notes) |
10.0F (020507) (see Notes) |
ISOPHOT Interactive Analysis. User Survey returned zero users, and development halted in 2002; no further updates are anticipated, but the old SciApps installation (solaris only) is preserved here. Requires use of IDL v5, so users must first redefine the default version of IDL by issuing the command “idl56”, then exit out of IDL before starting PIA. |
| pigz (pigz, unpigz) | 2.2.4 (120311) 2.2.3, 2.1.6 |
2.2.4 (120311) 2.2.3, 2.1.6 |
2.2.3F (120115) 2.1.6 |
2.1.6F (100117) |
2.2.4 (120311) 2.1.6 |
none | Parallel Implementation of GZip. A fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. For example, for a 1.5 Gb tarball on a 2.8 GHz Intel Core i7 quadcore iMac running OS X 10.6.2, compression (uncompression) with gzip (gunzip) took 89 (22) seconds, whereas with pigz (unpigz) v2.1.6, the compression (uncompression) took 21 (16) seconds. |
| python and associated software | none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
Dynamic object-oriented programming language. |
| python: scientific tools | user install (see FAQ) |
user install (see FAQ) |
user install (see FAQ) |
none (see FAQ) |
user install (see FAQ) |
user install (see FAQ) |
Libraries for python that provide scientific applications. |
| SExtractor (sex) | 2.5.0% (060714) |
2.5.0 (060714) 2.8.6 (see Notes) |
2.5.0F (060714) 2.8.6 (see Notes) |
2.5.0F (060714) 2.8.6 (see Notes) |
2.5.0 [64!] (060714) 2.8.6 [64!] (see Notes) |
2.5.0F (060714) (see Notes) |
Source Extractor. Builds a catalogue (with photometry) of objects from an astronomical image. Version 2.5.0 is the last fully stable version. Version 2.8.6 includes some non-essential improvements (which do not affect the basic source detection and photometry functions) that rely on the external ATLAS library, which is extremely sensitive to hardware and compilation options. This version of SExtractor is available via the command “sex286”, but should be considered unstable and used with caution. External library incompatibilities prevent compilation of v2.8.6 for solaris. |
| skycalc | 6.3 (0501--) (see Notes) |
6.3 (0501--) 5.0 |
5.0F (0102--) |
5.0F@ (0102--) |
6.3 (0501--) 5.0 |
5.0F (0102--) |
Astronomical almanac calculator. Part of the skycal package. The original text-based skycal package written in C has now been deprecated in favor of a Java-based, GUI-enabled version of skycal, which is available in SciApps as jskycalc. |
| skycalendar | 6.3 (0501--) (see Notes) |
6.3 (0501--) 5.0 |
5.0F (0102--) |
5.0F@ (0102--) |
6.3 (0501--) 5.0 |
5.0F (0102--) |
Astronomical calendar. Part of the skycal package. The original text-based skycal package written in C has now been deprecated in favor of a Java-based, GUI-enabled version of skycal, which is available in SciApps as jskycalc. |
| skyview | 3.6% (061130) |
3.6% (061130) |
3.6F (061130) |
3.6F@ (061130) |
3.6 (061130) |
3.6F (061130) |
Image display and analysis program for the interactive analysis of astronomical data. Skyview v3.8 exists, but has only been compiled for Ubuntu linux. |
| SuperMongo (sm) | 2.4.36% (090908) |
2.4.36 (090908) |
2.4.36F (090908) 2.4.26@ |
2.4.36F (090908) 2.4.26 |
2.4.36 (090908) 2.4.26 |
2.4.36F (090908) 2.4.26 |
Interactive scientific plotting package. See the FAQ for initialization instructions. |
| SWarp (swarp) | 2.19.1 (100904) |
2.19.1 (100904) 2.17.6 |
2.19.1F (100904) 2.17.6 |
2.17.6F (090409) |
2.19.1 (100904) 2.17.6 |
none | Resamples and co-adds FITS images using any arbitrary astrometric projection defined in the WCS standard. |
| TeX (latex) | 2011 (110730) 2010, 2009, 2008 |
2011 (110730) 2010, 2009, 2008 |
2011F (110730) 2010, 2009, 2008 |
2009F@ (091107) 2008@ |
none (see Notes) |
tetex 3.0F (see Notes) |
Typesetting package often used to prepare journal articles. Available in /usr/bin/ for linux. The tetex 3.0 package is copied from /opt/TWWfsw/ for solaris - it will not be updated. See the FAQ for more information. |
| TeX: aastex macros | 5.2 (050617) |
5.2 (050617) |
5.2F (050617) |
5.2F@ 050617) |
5.2 (050617) (see FAQ) |
5.2F (050617) (see FAQ) |
Latex macros for preparing manuscripts for AAS journals. |
| TeX: emulateapj macros | 16Dec11 2May11, 13Aug10, 16Feb10, 20Apr08 (see FAQ) |
16Dec11 2May11, 13Aug10, 16Feb10, 20Apr08 (see FAQ) |
2May11F 13Aug10, 16Feb10, 20Apr08 (see FAQ) |
16Feb10F 20Apr08 (see FAQ) |
16Dec11 13Aug10, 16Feb10, 20Apr08 (see FAQ) |
13Aug10F 16Feb10, 20Apr08 (see FAQ) |
Latex macros for formatting manuscripts to look like printed ApJ articles. See the FAQ for more information. |
| WCSTools | 3.8.5 (120312) 3.8.4 |
3.8.5 (120312) 3.8.4, 3.8.1 |
3.8.4F (110901) 3.8.1, 3.7.2 |
3.8.1F@ (091110) 3.7.2@ |
3.8.5 (120312) 3.8.1, 3.6.2 |
3.8.1F (091110) 3.6.2 |
World Coordinate System Tools for astronomical images. Type “man wcstools” for a list and short description of the WCSTools tasks. |
| WIP (wip) | none (see Notes) |
none (see Notes) |
none (see Notes) |
2.3F (980122) |
2.3F (980122) |
2.3F (980122) |
Interactive graphics package. See the FAQ for initialization instructions. Development halted in 1998; no further updates are anticipated, but the old SciApps installation is preserved here. A version for macintel is not available. |
| xgterm | 2.0beta (081117) |
1.3.2F% (03----) |
1.3.2F (03----) |
1.3.2F@ (03----) |
2.0beta (081117) |
1.3.1F (02----) |
Graphics-enabled xterm window for use with IRAF. Part of x11iraf.
Lion Notes: The current distributed stable version of xgterm (1.3.2) will not run under Lion because it was compiled as PowerPC software. Thus, SciApps for Lion uses the 2.0beta version of xgterm. Linux also uses 2.0beta to provide 64-bit functionality. |
| XPA | 2.1.14 (120301) |
2.1.14 (120301) 2.11.13, 2.1.11 |
2.1.13F (101015) 2.1.11, 2.1.9 |
2.1.13F@ (101015) 2.1.11@, 2.1.9@ |
2.1.14 (120301) 2.1.13, 2.1.12, 2.1.9 |
2.1.12F (100515) 2.1.10 |
X Public Access. Web data retrieval tasks used by DS9. |
TABLE NOTES
| |||||||
The current SciApps distributions for macintel7 (Lion), macintel6 (Snow Leopard), and linux are available as tarballs for stand-alone installation on laptops and off-site computers that cannot mount the IPAC /SciApps partition.
If you have a desktop computer that is on the IPAC network, then you do NOT need to install SciApps from the tarballs. Please see the initialization instructions for SciApps on networked computers.
The licenses for the various software titles included in SciApps generally fall into four categories:
Typically, use of properly licensed software by multiple employees at the same institution/company does not incur any additional burden. The networked version of SciApps, which is only available to employees on the IPAC computer network, falls into this category. However, the stand-alone (tarball) version of SciApps could potentially by used by IPAC employees for personal use, or even by non-IPAC employees. This qualifies as distribution (or conveyance, in the terms of the GNU Public License) and some licenses make specific consequential requirements. These typically include the provision that a copy of the license must be included with the distributed software and, in the case of the GNU Public License, if software is distributed as a binary, then the user must also be given the opportunity to obtain the source code. Commercial licensed software, of course, cannot be distributed outside the bounds of the purchased license; hence, IDL (for which IPAC owns an institutional site license for use with the networked SciApps) is not provided as part of the stand-alone SciApps installation. In all cases, the software titles included in SciApps (both networked and stand-alone) are in compliance with their corresponding licensing requirements. In particular, for both the networked and stand-alone SciApps distributions, an easily identifiable copy of the license for each software title is either available in the corresponding installation sub-directory for that title, or can be accessed from within the software itself (typically as part of the "About" or "Help" menu). In addition, a separate tarball is available for download below that provides the source code for all software titles requiring distribution of source code with binaries.
| Package | OS | Version Name | Release Date (Original Release) | Link |
| SciApps (source code) | n/a | n/a | 17 Sep 2012 | Download |
| SciApps (basic distribution) | macintel7 | Eyafjallajokull | 17 Sep 2012 | Download |
| SciApps (basic distribution) | macintel6 | Eyafjallajokull | 17 Sep 2012 | Download |
| SciApps (basic distribution) | linux | Theistareykjarbunga | 17 Sep 2012 | Download |
| CIAO v4.4, CALDB v4.4.7 (patch) | macintel7 | Eyafjallajokull | 17 Sep 2012 | Download |
| CIAO v4.4, CALDB v4.4.7 (patch) | macintel6 | Eyafjallajokull | 17 Sep 2012 | Download |
The “patch” tarballs upgrade an existing stand-alone basic distribution of SciApps to include additional or updated software. With the exception of the CIAO/CALDB patch (which is never included in any of the basic SciApps tarballs), a patch tarball should only be applied to stand-alone full versions of SciApps that were installed before the release date of the patch. The tarballs for the full SciApps distributions created on or after any patch tarball release date will already include the patch. After downloading a “patch” tarball, follow steps 3 and 4 below.
The “only” tarballs install stripped down versions of SciApps containing only the indicated software. After downloading an “only” tarball, follow steps 3–6 below. Note that multiple SciApps “only” tarballs can not be installed into the same ~/SciApps directory. However, one could create multiple SciApps directories (e.g., ~/SciApps1, ~/SciApps2, etc.) to store separate SciApps “only” distributions. Each “only” distribution will have its own individualized initialization file (e.g., ~/SciApps/setup/sciapps_irafonly.(c)sh for the IRAF-only installation) and will have to be sourced separately in the ~/.*shrc file (as in step 5 below). Note that using this method of creating separate SciApps directories requires making a slight modification to the “dmod” environment variable setting located near the top of the initialization file. For example, if I stored the IRAF-only distribution of SciApps in a directory called ~/SciApps1, then I would modify the dmod setting in ~/SciApps1/setup/sciapps_irafonly.csh from its default value of
setenv SciApps_irafonly_dmod ''
to a new value of
setenv SciApps_irafonly_dmod '1'
to reflect the change in the default SciApps directory name. The value of the dmod environment variable is appended to the default SciApps directory name.
The SciApps User Survey closed on 1 May 2009 – thanks for your input! The results from this survey (tabulated below) will help to maximize the efficiency of available SciApps administration resources by identifying the specific needs and desires of SciApps users. This will allow targeted development of SciApps to make it as useful as possible for IPAC scientists.
Many thanks for the large number of survey responses. The final survey results are summarized below.
| Software | Frequently | Sometimes | Rarely | Never | Software | Frequently | Sometimes | Rarely | Never | |
| AIPS | 3 | 3 | 3 | 23 | Lickmongo | 1 | 2 | 2 | 27 | |
| APT | 1 | 5 | 3 | 23 | pgplot | 5 | 4 | 5 | 18 | |
| cfitsio library | 5 | 6 | 5 | 16 | pia | 0 | 0 | 0 | 32 | |
| CIAO | 2 | 0 | 3 | 27 | python | 4 | 5 | 4 | 19 | |
| DAOphot | 5 | 8 | 6 | 13 | SAOimage DS9 | 27 | 3 | 1 | 1 | |
| FV | 3 | 4 | 4 | 21 | SExtractor | 7 | 7 | 4 | 14 | |
| GSL | 0 | 0 | 1 | 31 | skycalc | 3 | 4 | 3 | 22 | |
| IDL | 23 | 2 | 3 | 4 | skycalendar | 1 | 1 | 3 | 27 | |
| IDL astro library | 23 | 1 | 1 | 7 | skyview | 8 | 4 | 4 | 16 | |
| IDL atv | 6 | 4 | 2 | 20 | SuperMongo | 3 | 5 | 3 | 21 | |
| IDL buie library | 2 | 1 | 1 | 28 | swig | 1 | 0 | 0 | 31 | |
| IDLwave | 2 | 1 | 4 | 25 | wcstools | 6 | 9 | 3 | 14 | |
| IRAF | 14 | 10 | 4 | 4 | wip | 1 | 5 | 1 | 25 | |
| LHEAsoft | 3 | 0 | 0 | 29 | xgterm | 13 | 6 | 1 | 12 |
| ctio = 10 | color = 3 | crutil = 5 | fitsutil = 11 | focas = 1 | gemini = 4 |
| gmisc = 1 | guiapps = 3 | ifocas = 0 | mtools = 7 | mscred = 11 | mxtools = 1 |
| nmisc = 2 | rvsao = 3 | stsdas = 16 | tables = 14 | xray = 1 |
Q: How do I set up my computer to use SciApps?
A: Check on your computer for the presence of a root-level symbolic link that defines a permanent path to /SciApps. To do this, issue the following command in a Terminal or xterm window:
ls -l /SciApps
There are three possible outcomes:
Once you have the correct /SciApps symbolic link on your computer, simply include the correct SciApps initialization command in your shell configuration file (see which shell can I use?). For bash users,
and for tcsh users,
The flag force_idl controls whether or not SciApps will override the set-up for a local installation of IDL and force usage of the SciApps installation of IDL. If you want to use your own installation of IDL, then remove force_idl from the command string. SciApps looks for local installations of IDL in /Applications/rsi or /Applications/itt (macintel, macosx), and /usr/local/rsi or /usr/local/itt (linux, solaris).
The flag verbose can be added to the SciApps initialization command, and controls whether or not SciApps will display an initialization confirmation message, as well as a number of possible warning messages. This is mostly useful when diagnosing problems with the SciApps initialization on your computer, and is not recommended as the default usage.
SciApps will be globally initialized the next time you log out and back in. It will be locally initialized for any new terminal window (e.g., an xterm) that you open, or by typing . ~/.bashrc or source ~/.cshrc or source ~/.tcshrc (as appropriate for your particular shell) in any existing window.
In the old (pre-July 2009) implementation of SciApps, a set of nested files were created in your home directory by the initialization script, and these were used to set up the software distribution. In the new version of SciApps, the initialization settings, definitions, etc., are all moved into the script itself, so all you have to do is source the set-up script. This also gives you freedom to structure your shell configuration file(s) as you desire, and the ability to insert the SciApps initialization command at any desired point in the shell configuration (e.g., in order to preferentially place the SciApps directories in your PATH at a desired priority level).
Q: What do I do with the shell configuration files created by the old (pre-July 2009) SciApps?
A: The old (pre-July 2009) SciApps initialization created or modified an assortment of nested shell configuration files in your home directory (~/). For example, a typical initialization on a solaris computer would create or modify ~/.tcshrc, ~/.tcshrc.solaris, and ~/.user.post.csh and/or ~/.user.post.solaris.csh. The file ~/.tcshrc is sourced every time X11 starts or a new X window starts. The files ~/.tcshrc.solaris and ~/.user.post.csh are sourced (in that order) by ~/.tcshrc. The file(s) ~/.user.post.csh and/or ~/.user.post.solaris.csh are sourced by ~/.tcshrc.solaris. The file ~/.user.post.csh is intended to contain your personal command aliases and/or environment variable definitions. All of the other files contain old SciApps initialization commands, aliases, and definitions.
The new SciApps initialization requires only one command in your ~/.*shrc file, as noted above. So, at a bare minimum, all you would need to have a functional computer account with SciApps initialized is a ~/.*shrc file that contains only the SciApps initialization command. Additional command aliases and/or environment variables can be added directly to ~/.*shrc, or may still be sourced from a separate file (e.g., ~/.user.post.csh) by including the line
source ~/.user.post.csh
at the bottom of your ~/.tcshrc file.
So, the recommended procedure for transitioning from the old SciApps to the new SciApps is to first move the existing configuration files to harmless names; for example,
(substitute the appropriate OS name for “solaris” in this example). These files can (optionally) eventually be deleted once you are comfortable that your current SciApps and overall shell configurations are stable and conform to your desires.
Next, create a new ~/.tcshrc file that contains the new SciApps initialization command discussed above, followed (and/or preceded, as desired) by your personal command aliases or environment variable definitions, if any.
The old SciApps initialization also created a file called ~/.local_iraf. This file is no longer used and should be deleted or renamed; e.g.,
Q: Which shell can I use?
A: The SciApps initialization scripts will currently function under the C shell (csh), TENEX C shell (tcsh), and Bourne shell (bash). Of the two C shells, tcsh is preferred, since some software (notably IRAF) occasionally has problems running under csh due to long variable names.
For instruction for changing your default shell on Mac laptops and self-administered Mac computers, see
http://mactips.dwhoard.com/mactips/system/change-default-shell
For all other ISG-administered computers, contact the ISG.
Q: I get an error message that looks like this:
and SciApps will not initialize. What is wrong?
A: It is likely that you do not have the /SciApps partition mounted on your computer, or you have an incorrect mount point or root-level symbolic link to /SciApps (also see “How do I set up my computer to use SciApps?”).
Issue the command
(substitute your current operating system for “linux”), then you have an incorrect mount point that must be changed to the correct version noted above – contact ISG. Note that changing the mount point, although necessary for the new SciApps initialization, will disable access to the old (pre-July 2009) SciApps (this is OK, as the old SciApps will be phased out anyway).
In the Connect to Server pop-up window, enter
for the Server Address and press the Connect button. This is a temporary mounting and will be unmounted if you reboot your computer.
Q: How can I use SciApps on my laptop or home computer?
A: The /SciApps partition can only be mounted on a computer that is permanently connected to the IPAC network, which typically excludes laptops and off-site computers. You can run most of the SciApps tasks remotely by logging in to your IPAC computer from your laptop or home computer. Stand-alone tarball installations of the current distributions of SciApps for macintel and linux are also available – see “Stand-alone Installation” for additional information.
Q: How do I request additional help with SciApps?
A: Submit a ticket to the ISG Helpdesk. However, note that as of 28 Sep 2012, there is no dedicated support for SciApps at IPAC.
Q: I'm new to using a Mac computer – help!
A: A number of useful tips for configuring your Mac in astronomer-friendly ways are compiled at D. W. Hoard's Mac OS X Configuration Tips web page.
Q: How do I initialize SuperMongo (sm) before running it for the first time?
A: This is accomplished by creating a .sm file in your home directory that defines the correct paths to a number of SuperMongo configuration files. This can be accomplished by running the SciApps SuperMongo setup script using the SciApps command alias sm_setup. This alias actually runs the following command:
This process only needs to be done once, before the first time you run SuperMongo. An existing .sm file in your home directory will be renamed to .sm{timestamp} before the script writes the new file.
Q: How do I initialize the WIP interactive graphics package (wip) before running it for the first time?
A: This is accomplished by creating a .wipinit file in your home directory that defines a number of environment variables used by wip, and can be used to add your own customizations. This can be accomplished by running the SciApps WIP setup script using the SciApps command alias wip_setup. This alias actually runs the following command:
This process only needs to be done once, before the first time you run WIP. An existing .wipinit file in your home directory will be renamed to .wipinit{timestamp} before the script writes the new file.
Q: How can I use an older version of IRAF?
A: The default version of IRAF in SciApps is 2.16+ on all platforms for which it is available. In order to use older versions of IRAF (2.14.1 or 2.15.1a) instead, you must append the flag iraf214 or iraf215 to the SciApps initialization command in your ~/.*shrc file; for example, for tcsh users,
source /SciApps/setup/sciapps.csh iraf214
See “How do I set up my computer to use SciApps?” for additional information about setting up SciApps on your computer.
Q: How can I use IRAF v2.15+ in 64-bit mode on my Intel Mac?
A: IRAF uses the result of the uname -m command to determine if your Intel Mac is running a 64-bit kernel: i386 = 32-bit, while x86_64 = 64-bit. It then sets the value of the system variable IRAFARCH to either macosx (32-bit) or macintel (64-bit), and delivers the appropriate IRAF binaries. (Note that these labels differ somewhat from their use in the rest of SciApps, where macintel indicates any 64-bit capable Mac containing an Intel processor, regardless of whether it is running in 32-bit or 64-bit mode, whereas macosx indicates any Mac using a PowerPC processor.)
Only Mac OS X v10.6+ is capable of running in 64-bit mode. If you are not running the 64-bit kernel (check the output of the uname -m command) but want to start IRAF in 64-bit mode anyway, then you can manually set the value of the system environment variable IRAFARCH, as follows:
setenv IRAFARCH macintel
Alternatively, you can append the flag iraf64bit to the SciApps initialization command in your ~/.*shrc file; for example, for tcsh users
source /SciApps/setup/sciapps.csh iraf64bit
See “How do I set up my computer to use SciApps?” for additional information about setting up SciApps on your computer.
Another option is to boot your Mac into the 64-bit kernel, in which case IRAF will deliver the 64-bit binaries by default. Click here for instructions on how to, first, determine whether your Mac is capable of booting the 64-bit kernel and, second, selecting the desired kernel.
Note that starting in mid-2010, Apple began shipping Mac Pros (and, subsequently, other models) with Snow Leopard set to boot into the 64-bit kernel by default (prior to that, Snow Leopard would boot into the 32-bit kernel by default). While this presents no problem to IRAF 2.15+ (which will happily serve you the 64-bit version of IRAF), it can cause problems if you are running some external IRAF packages. Notably, these include the STScI packages stsdas and tables, which are only supported by STScI as 32-bit software. In this case, you would have to reboot your computer into the 32-bit kernel (hold down the 3 and 2 keys while rebooting), run the 32-bit version of IRAF 2.15+ (ensure that you have not followed any of the steps outlined above for forcing IRAF to run in 64-bit mode), and run the installed 32-bit versions of stsdas and tables. Click here for instructions to determine whether your Mac is running the 64-bit kernel or the 32-bit kernel.
Similarly, some IRAF v2.16 tasks (e.g., geomap) crash when attempted to run in 64-bit mode, even if your Mac is running in 64-bit mode. In this case, you can force IRAF to run in 32-bit mode by appending the flag iraf32bit to the SciApps initialization command; for example, for tcsh users
source /SciApps/setup/sciapps.csh iraf32bit
Q: Which external packages are supported in the SciApps installation of IRAF?
A: Prior to the IRAF 2.15 release, external packages in SciApps were maintained (and documented) on a case-by-case basis. However, starting with IRAF 2.15, the new dynamic package loading feature allows for package directories created in the iraf$extern directory to be automatically defined at runtime when IRAF is started. This greatly simplifies the installation and maintenance of IRAF external packages, since (for example) the IRAF configuration files no longer have to be updated manually following installation or update of external packages. Consequently, in order to simplify the corresponding documentation of IRAF external packages, individual documentation of the installed versions of packages will no longer be maintained on the SciApps web page. The SciApps Administrator will endeavour to keep an up-to-date suite of widely used external packages available within IRAF. The available packages are listed upon first starting IRAF, and (starting with v2.15.1a) the version number and/or date for each package is listed upon loading that package in IRAF. If you require an IRAF package that is not currently installed, or have reason to believe that an installed package is out of date, then please contact the ISG. Note that external packages in IRAF v2.14 will generally not be updated in the future, since that version of IRAF is only being maintained temporarily as a transitional option until more external packages become compatible with IRAF v2.15+.
Note for Linux users: The STScI external packages stsdas and tables for IRAF are only supported by STScI as 32-bit software. Thus, they will not run under the 64-bit version of IRAF (and, in fact, are not even installed with the SciApps distribution of IRAF v2.15.1a). If you want to use these packages, then you will have to use the 32-bit version of IRAF (2.14.1).
Q: How can I use the gemini package in IRAF?
A: The gemini package has a number of constraints depending on the version of IRAF being used and the versions of two supporting external packages (fitsutil and gmisc). Options for using the gemini package are as follows:
Q: Why is there no mxtools package for solaris IRAF?
A: Although source code and pre-compiled binaries for the mxtools package are available (e.g., on the NOAO IRAF FTP site), these date from 2001. These files will neither compile from source nor run as pre-compiled executables on current solaris computers. This behavior is likely related to backwards compatibility issues in the solaris operating system. If you absolutely need the mxtools package to run on a solaris computer, then please contact the SciApps Administrator; otherwise, it is no longer going to be supported in SciApps for solaris.
Q: How can I use an old version of IDL?
A: To start an old version of IDL (see the Table of Available Software for the list of old versions of IDL available for each supported operating system), use the command idlNN, where NN is the version number with the decimal point removed. For example, to start IDL version 5.6, you would use the command idl56. This command also redefines the generic idl command to point at the selected version number in subsequent usage (in the current X11 or Terminal window only). In order to go back to the most recent version of IDL (or a different old version), the command idlNN must be run again, with the desired version number specified.
Q: How can I add my own paths to the IDL search path?
A: An IDL search path is normally added to the IDL_PATH environment variable using a command placed in the ~/.*shrc file with the format (for tcsh users)
setenv IDL_PATH +/path/to/idl/files/1
for the first instance, and
setenv IDL_PATH ${IDL_PATH}:+/path/to/idl/files/2
for subsequent entries. (Incidentally, the + symbol in these paths ensures that IDL will search all sub-directories at the end of the path, as well as the directory specified by the path.)
In order to add your own IDL search paths to the path defined by SciApps, simply ensure that all of your setenv IDL_PATH ... commands are placed before the SciApps initialization command line in your ~/.*shrc file. Your IDL search path definitions will be appended to the SciApps IDL search path.
Q: All of the IPAC IDL licenses are in use. If I have my own license, how can I use the SciApps installation of IDL?
A: Follow these instructions:
Q: How do I enable the idlwave macros in Emacs?
A: If you do not already have a .emacs file in your home directory, then copy the minimal file from the SciApps distribution using the SciApps command alias idlwave_setup. This alias actually runs the following command:
If you do already have a ~/.emacs file, then just add the following lines to it:
If any of these lines are already present in your .emacs file, then comment out the old versions of the lines before adding the new versions to your .emacs file. Running the idlwave_setup command will rename any pre-existing .emacs file in your home directory to .emacs{timestamp} before writing the new file.
Q: Why isn't APT available for my computer?
A: As of APT v19 (released in January 2011), STScI supports APT on Linux, Solaris 10, and 64-bit Intel Macs running OS X 10.5 (Leopard) and OS X 10.6 (Snow Leopard). For 32-bit Intel Macs only OS X 10.6 (Snow Leopard) is supported. Non-Intel (i.e., PowerPC) Macs are not supported. (This is due to APT's upgrade to Java 6 which is only supported on the Intel platforms.) APT requires a minimum of 512 Mb of RAM, but at least 1 Gb of RAM is recommended.
Starting with APT v20 (released in January 2012), solaris is no longer supported by STScI, and Leopard (OS X 10.5) is only supported on 64-bit Intel Macs.
Additional Mac OS X System Configuration Issues:
Q: APT crashes on my Mac – how can I fix this?
A: The most likely culprit is an incorrect version of Java. APT will only run using Java 6 (version 1.6), which was updated in Mac OS X in mid-June of 2009. In addition, APT requires Java 6 to be the first Java version in the Java search path. In order to correct this, run
Under the General tab, rearrange the available Java versions so that Java 6 is at the top of the priority list. Quit Java Preferences and run APT. You can either restore the original order in Java Preferences after finishing with APT, or leave it – having Java 6 at the top of the priority list should not have an adverse effect on other applications.
Note that Java 6 is intended for 64-bit Intel Macs. It will not run – nor will it be available as an option in Java Preferences – on a PowerPC Mac (even if it is a 64-bit PowerPC Mac) nor on a 32-bit Intel Mac. As of v19, APT is no longer supported on non-Intel Macs, and will only run on a 64-bit Intel Mac that is using either Leopard (OS X 10.5) or Snow Leopard (OS X 10.6), or on a 32-bit Intel Mac that is using Snow Leopard (OS X 10.6).
Q: Where's my favorite software package? Why isn't it supported in SciApps (anymore)?
A: The limited SciApps administrative resources preclude supporting many software packages that do essentially the same thing, or complex software packages that are utilized by very few people. In the interests of providing useful software for IPAC scientists, while at the same time streamlining the SciApps maintenance and updating tasks to facilitate a frequent and regular update schedule, some duplicate and under-utilized software packages were eliminated.
For example, SciApps now supports one command line plotting package (SuperMongo) and one (new) GUI-enabled plotting package (Grace). Software packages such as WIP and Lickmongo, which provide essentially the same services (i.e., producing scientific plots) are no longer supported in SciApps. (Actually, both IDL and pgplot – which are supported in SciApps – can also be used to construct publication-quality scientific plots, so really there are already four plotting packages supported in SciApps.)
Q: Why isn't python available in SciApps?
A: Limited SciApps support for python and associated software for the macintel operating systems was initially provided starting with the Doomsday Machine (Feb 2011) release. However, in the final supported SciApps release (Eyafjallajokull – Sep 2012), support for python and associated software has been removed.
While I recognize that this might be inconvenient for some SciApps users, please understand that this decision was made after careful consideration of the best interests of providing a final, robust software package as SciApps transitions to an unsupported state. To date, SciApps support for python and associated software was not yet mature, and was undergoing a constant evolution toward stability. I appreciate the feedback and testing assistance from IPAC python users, which have contributed to improvements in SciApps python support during the past 18 months. However, it became clear over the past several months, as I have been working on this final SciApps update, that achieving a robust python implementation, that could stand on its own without ongoing dedicated support, would not be possible. In the long run, it will be better for IPAC python users to start their own python-related software installations from the ground-up, rather than adapting mid-course to a partial, and unsupported, SciApps installation.
Here are some additional details that contributed to the decision to remove python support from the final SciApps update:
A few additional notes about the Enthought Python Distribution (EPD):
Q: Why isn't AIPS available in SciApps?
A: A straightforward installation of AIPS with access for multiple users requires a generic computer user group name and permission for all users to have write access to parts of the AIPS installation directory. However, there is no common “generic” group id that covers everyone at IPAC and, more importantly, users do not have write access to the /SciApps partition. Past SciApps installations of AIPS have been hacked to get around these requirements, but this has not been conducive to keeping AIPS up to date since the whole thing has to be torn down and remade each time it is updated. Fortunately, a self-updating, single-user, binary installation of the current (and future) version of AIPS is now easy and painless on all platforms, using the installer script provided by NRAO.
Given the relatively small number of regular AIPS users at IPAC (as per the SciApps User Survey), it was decided to no longer support a system-wide distribution of AIPS. Instead, installation of AIPS will be done on a case-by-case basis. If you want to install AIPS yourself, then please follow the instructions for a binary installation on the AIPS web page; otherwise, you may contact the SciApps Administrator for assistance.
Q: Why isn't HEASOFT available in SciApps?
A: All HEASOFT tasks can now be run remotely using the Hera data analysis service at HEASARC. Hera provides all of the HEASARC software packages, local disk space, and computing resources needed to do general processing of FITS format data files residing on the user's local computer, and to do advanced research using the publicly available data from High Energy Astrophysics missions. Because of the small number of HEASOFT users at IPAC, a local installation of HEASFOT will not be maintained as part of SciApps. Please utilize the Hera service instead.
To use HEASOFT through Hera, start the Fv image viewer (which is maintained as part of SciApps), select Connect to Hera... from the main menu window, then follow the on-screen instructions to establish a Hera user account. See “Getting Started with Hera” and “Frequently Asked Questions about Hera” for additional information.
Q: What else do I need to know about using TeX/laTeX in SciApps?
A (macintel/macosx): SciApps for macintel and macosx contains the BasicTeX version of MacTeX, which is accessed from the command line only. BasicTeX is utilitarian but perfectly functional; the SciApps version has been supplemented to include the aastex and emulateapj class files, and the apjfonts and txfonts packages.
Apply the emulateapj class using the following command in the .tex file preamble:
\documentclass[iop]{emulateapj}
For best results, also use the ApJ fonts package:
\usepackage{apjfonts}
and then compile the postscript output using:
dvips -Papjfonts -o filename.ps filename
Versions of the emulateapj style file starting with 16Feb10 are not backwards compatible with versions of BasicTeX prior to 2009.
A (linux/solaris): TeX is installed by default in /usr/bin/ on linux computers and in /opt/TWWfsw/bin/ for solaris computers. In order to make the aastex or emulateapj macros available, SciApps defines the TEXMFHOME environment variable on linux and solaris computers to point to the corresponding SciApps installation directory; that is
Q: Why don't any of the fortran compilers for macintel or macosx work?
A: When trying to use any of the SciApps fortran compilers (g77, g95, gfortran) for macintel or macosx, if you receive an error message similar to
gfortran: error trying to exec ‘as’: No such file or directory
or
g77: installation problem, cannot exec ‘as’: No such file or directory
then the problem is that you do not have gcc installed on your computer. Strangely enough, the fortran compilers require you to have a C compiler installed, because they share the same assembler (i.e., the ‘as’ that cannot be found).
Under Mac OS X, gcc is not installed with OS X by default, and must be installed on your computer from the “Xcode Tools” (or, on recent installations, just “Xcode”) package inside the “Optional Installs” folder on the original OS X installation DVDs that came with your computer. This process requires root level access to your computer, so please contact ISG to install the Xcode Tools.
Q: Why doesn't CIAO work (completely) on Solaris computers?
A: The prism task in the solaris installation of CIAO is unusable due to compatibility problems with the IPAC solaris font configuration. Additionally, the chips task in CIAO for solaris will not work in a remote display environment, so this task will not function under the SciApps architecture. This is due to an incompatibility in the Solaris X server, and cannot be repaired. Please note that CIAO is fully functional in the macintel and linux distributions of SciApps.
Q: When I run skyview with the -n24 option, it crashes with an error message that looks like this:
How can I fix this?
A: The -n24 option causes skyview to execute in 24-bit mode with no graphics (i.e., without invoking X11). However, skyview still needs one resource that it usually gets from X11; namely, a table of the colors with RGB values for each color. In the absence of X11, skyview looks for the file rgb.txt in a standard place: /usr/lib/X11. If rgb.txt is not located in that directory, then skyview will crash. The following table gives the standard location for rgb.txt under different operating systems.
| OS | RGBFILE |
| macintel | /usr/X11/share/X11 |
| macosx | /usr/X11/share/X11 |
| linux | /usr/X11R6/lib/X11 |
| solaris | /usr/openwin/lib/X11 |
The SciApps initialization defines these locations for rgb.txt. However, if the file is in a different location on your system, then you will first have to locate it, and then redefine the environment variable RGBFILE; for example, by including a line like
in your ~/.tcshrc file (or bash equivalent in ~/.bashrc) after the command to source the SciApps set-up script.
Q: I upgraded my Mac from Tiger to Leopard, and now the colors are gone from the overlays in skyview – what's going on?
A: The skyview developers have been notified of this bug, but do not currently know its origin. A workaround is to invoke skyview as follows:
Q: How do I run gimp on a solaris computer?
A: For the Your Little Dog (Jan 2010) release of SciApps for solaris, the possibility of installing an up-to-date version of the GNU Image Manipulation Program (gimp) was investigated. Unfortunately, this was found to be impossible, due to its dependence on a large number of libraries and associated applications that are missing or out of date on IPAC solaris computers.
An older version of gimp is currently available in /opt/TWWfsw/bin on IPAC solaris machines; however, to successfully start this version of gimp, you will probably have to use the somewhat clunky command
unset LD_LIBRARY_PATH ; /opt/TWWfsw/bin/gimp & ; . ~/.bashrc
for bash users or, for tcsh users, the following command
unsetenv LD_LIBRARY_PATH ; /opt/TWWfsw/bin/gimp & ; source ~/.tcshrc
to get around a GLIB incompatibility issue. This command could be
aliased to "gimp" in your ~/.*shrc file.