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.
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 (on disk and tarballs): updated CALDB (CIAO) to version 4.1.4.
15 September 2009: Interim update to SciApps (Flying Monkey) for macintel and macosx (on disk and tarballs): 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.
| Mac OS X 10.5 (Leopard) for Intel (macintel) and PowerPC (macosx) |
| Red Hat Enterprise Linux 5.3 (linux) |
| Solaris 10 (solaris) |
Note that Mac OS X v10.6 (Snow Leopard) is not currently supported in SciApps. However, some tests with the tarball installation of SciApps for macintel on a laptop running OS X v10.6.0 shows at least basic functionality for cfitsio, DS9 (including XPA), GSL, IDL (including astrolib and atv), IRAF, PGPLOT, SExtractor, and xgterm.
It is expected that active SciApps support for PowerPC Macs (macosx) will be gradually phased out as the relevant hardware is replaced through natural attrition by purchases of new Mac equipment. Similarly, it is expected that SciApps support for the Solaris operating system will also be gradually phased out if the current trend of declining purchases of new Sun/Solaris hardware continues.
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 |
| macintel macosx | Flying Monkey | 22 Jul 2009 (15 Sep 2009) (22 Sep 2009) | Feb 2010 |
| linux | Cowardly Lion | 5 Oct 2009 | Mar 2010 |
| solaris | Your Little Dog | - | Dec 2009 |
The following table contains the historical record of release dates of previous SciApps distributions (starting in July 2009).
| OS | Previous SciApps Version Names | Release Dates (Interim Updates) |
| macintel macosx | Flying Monkey | 22 Jul 2009 (15 Sep 2009) (22 Sep 2009) |
| linux | Cowardly Lion | 5 Oct 2009 |
| solaris | Your Little Dog | - |
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; contact the SciApps Administrator for instructions to access old versions of other software.
Currently, only the macintel, macosx, and linux distributions of the new (post-July 2009) SciApps are active. An updated solaris distribution is not yet available (the table currently shows the progress of assembling the solaris distribution, but this software is not yet supported for use).
| Software | macintel | macosx | linux | solaris | Help? | Notes |
| AIPS | none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
w | Astronomical Image Processing System for radio data. |
| APT (runapt) | 17.4.3 (090730) |
17.4.3 (090730) |
17.4.3 (090730) |
bw | The Astronomer's Proposal Tool is used to submit Phase I/DD proposals and Phase II proposals for the Hubble Space Telescope. The SciApps version of APT is optimized for computers with 1 GB or more of RAM. See the FAQ for additional information. | |
| cfitsio library | 3.140 (090318) |
3.140@ (090318) |
3.200 (090904) |
w | Library of C and Fortran subroutines for reading and writing data files in FITS format. | |
| CIAO (ciao) | 4.1.2 (090420) |
none (see Notes) |
4.1.2 (090420) |
bw | Chandra Interactive Analysis of Observations. Version for macosx (PowerPC) running OS X 10.5 (Leopard) is not available. | |
| CIAO: CALDB | 4.1.4 (090917) |
none | 4.1.4 (090917) |
w | Calibration Database for CIAO. | |
| Fv (fv) | 5.2.1 (0807--) |
5.2.1@ (0807--) |
5.3 (0907--) |
bw | Graphical program for viewing and editing any FITS format image or table. Also provides the interface to HEASOFT through Hera (see FAQ). | |
| g77 | 3.4F (0610--) |
3.4F (0610--) |
none (see Notes) |
bw | Open source FORTRAN compiler. Available in /usr/bin for linux. Development halted in 2006 in favor of gfortran (see below); no further updates to g77 are anticipated. | |
| g95 | 0.91 (0803--) |
0.91 (0803--) |
0.91 (0803--) |
bw | Open source FORTRAN compiler. | |
| gfortran | 4.4.0 (0812--) |
4.4.0 (0812--) |
none (see Notes) |
bw | Open source FORTRAN compiler. Available in /usr/bin for linux. | |
| Grace (xmgrace) | 5.1.16 (040704) |
5.1.16@ (040704) |
5.1.22 (080521) |
bw | GUI-enabled scientific plotting package (like Supermongo, but with a GUI). | |
| HEASOFT | none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
bw | A unified release of the FTOOLS and XANADU software packages for X-ray data. |
| IDL (idl) | 7.0 (080320) |
7.0 (080320) |
7.0 [64] (080320) 6.0 |
bf | Interactive Data Language. It does everything. | |
| IDL: astro library | 15May09 | 15May09 | 15May09 | w | Useful astronomy-related routines for IDL. | |
| IDL: atv | 2.1 (090521) 1.5.2 |
2.1 (090521) 1.5.2 |
2.1 (090521) 1.5.2 |
bw | DS9-like image viewer for IDL. | |
| IDL: buie library | 7.0 (090327) |
7.0 (090327) |
7.0 (090327) |
w | More astronomy-related IDL routines. | |
| IDL: IDLwave macros | 6.0 (060217) |
6.0 (060217) |
6.0 (060217) |
bfiw | Macros for writing IDL programs in emacs. IDLwave is incorporated into emacs v22.0 and above. Use of the stand-alone version of IDLwave is only required for earlier versions of emacs. See the FAQ for initialization instructions. | |
| IRAF (cl) | 2.14.1 (080916) |
2.14.1 (080916) |
2.14.1 (080916) |
bw | Image Reduction and Analysis Facility, built and distributed by NOAO. | |
| IRAF: x11iraf | 1.3.2 (03----) |
1.3.2 (03----) |
1.3.2 (03----) |
imw | Various X11 tools for use with IRAF (see xgterm below). | |
| IRAF external: color | rev4 (960314) |
rev4 (960314) |
rev4 (960314) |
bw | Package for creating color composite images and displays from 3-bandpass IRAF images. This can also be done with DS9. | |
| IRAF external: ctio | 22Feb94 | 22Feb94 | 22Feb94 | bw | The CTIO package for IRAF. | |
| IRAF external: fitsutil | 2005 | 2005 | 2005 | bw | Utilities for single and multiple FITS files. | |
| IRAF external: focas | none (see Notes) |
none (see Notes) |
none (see Notes) |
bw | Faint Object Classification and Analysis System. Versions of this package for macintel, macosx, and linux are not available. | |
| IRAF contrib: gemini | 1.9.1 (061220) |
1.9.1 (061220) |
1.9.1 (061220) |
bw | IRAF tools for working with data from the Gemini telescopes. | |
| IRAF external: gmisc | 14Apr04 | 14Apr04 | 14Apr04 | bw | Miscellaneous Gemini-related tasks. Required for the gemini package. | |
| IRAF external: guiapps | 30May03 | 30May03 | 30May03 | bw | Prototypes of IRAF tasks with graphical user interfaces. | |
| IRAF external: mscdb | 4.3 (040209) |
4.3 (040209) |
4.3 (040209) |
bw | Database directory files for the mscred package. | |
| IRAF external: mscred | 4.8 (060213) |
4.8 (060213) |
4.8 (060213) |
bw | CCD mosaic reduction tools. | |
| IRAF contrib: mtools | 05Mar98 | 05Mar98@ | 05Mar98@ | bw | Various IRAF tasks by Jeff Munn. Typing mtools at the cl prompt loads softools, typing mtools again loads mtools. | |
| IRAF contrib: mxtools | none (see Notes) |
none (see Notes) |
2001Dec27 | bw | Photometry analysis package including QDPHOT from Ken Mighell. Versions of this package for macintel and macosx are not available. | |
| IRAF external: nmisc | 06May03 | 06May03 | 06May03 | bw | Miscellaneous NOAO tasks. Required for the gemini package. | |
| IRAF contrib: rvsao | 2.6.9@ (081118) |
2.6.9 (081118) |
2.6.9 (081118) |
bw | Radial velocity analysis package from Doug Mink at SAO. | |
| IRAF contrib: stsdas | 3.9 (081119) |
3.9 (081119) |
3.9 (081119) |
bw | Space Telescope Science Data Analysis System. Some tasks require PyRAF, which is not currently part of SciApps. | |
| IRAF contrib: tables | 3.9 (081119) |
3.9 (081119) |
3.9 (081119) |
bw | Tools and libraries for working with tabular data. Required by the stsdas package. | |
| IRAF contrib: xray | none (see Notes) |
none (see Notes) |
none (see Notes) |
bw | PROS X-ray data reduction tools. Versions of this package for macintel, macosx, and linux are not available. | |
| IRAF contrib: y4k | 2005 | 2005 | 2005 | none (see Notes) |
w | Scripts for processing data from the Y4K instrument on the SMARTS 1-m telescope at CTIO. Scripts are defined in login.cl by mkiraf. Versions of these scripts for solaris are not available. |
| pgplot | 5.3.1 (------) |
5.3.1 (------) |
5.2.2 (010226) |
w | 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. | |
| PIA (pia) | none (see Notes) |
none (see Notes) |
none (see Notes) |
10.0F (020507) |
w | 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. |
| python | none (see FAQ) |
none (see FAQ) |
none (see FAQ) |
bfimw | Dynamic object-oriented programming language. | |
| SAOimage DS9 (ds9) | 5.6.2 (090415) |
5.6.2@ (090415) |
5.6.3 [64] (090715) |
5.6.2 (090420) 4.07b, 3.0b6, 2.0 |
bfw | Astronomical imaging and data visualization application. |
| SExtractor (sex) | 2.4.4 (051019) |
2.4.4@ (051019) |
2.8.6 [64!] (090409) |
imw | Program that builds a catalogue (with photometry) of objects from an astronomical image. | |
| skycalc | 5.0 (0102--) |
5.0@ (0102--) |
5.0 (0102--) |
bw | Astronomical almanac calculator. Part of the skycal package. | |
| skycalendar | 5.0 (0102--) |
5.0@ (0102--) |
5.0 (0102--) |
bw | Astronomical calendar. Part of the skycal package. | |
| skyview | 3.6 (061130) |
3.6@ (061130) |
3.6 (061130) |
bfw | Image display and analysis program for the interactive analysis of astronomical data. | |
| SuperMongo (sm) | 2.4.26@ (021223) |
2.4.26 (021223) |
2.4.26 (021223) |
bfw | Interactive scientific plotting package. See the FAQ for initialization instructions. | |
| TeX (latex) | 2008 (081229) |
2008@ (081229) |
none (see Notes) |
w | Typesetting package often used to prepare journal articles. Available in /usr/bin for linux. See the FAQ for more information. | |
| TeX: aastex macros | 5.2 (050617) |
5.2@ 050617) |
5.2 (050617) (see FAQ) |
w | Latex macros for preparing manuscripts for AAS journals. | |
| TeX: emulateapj macros | 20Apr08 | 20Apr08 | 20Apr08 (see FAQ) |
w | Latex macros for formatting manuscripts to look like ApJ journal articles. | |
| WCSTools (wcstools) | 3.7.2 (071120) |
3.7.2@ (071120) |
3.6.2 (050721) |
imw | World Coordinate System Tools for astronomical images. | |
| WIP (wip) | none (see Notes) |
2.3F (980122) |
2.3F (980122) |
bfw | 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 | 1.3.1 (03----) |
1.3.1@ (03----) |
1.3 (03----) |
im | Graphics-enabled xterm window for use with IRAF. Part of x11iraf. | |
| XPA | 2.1.9 (071121) |
2.1.9@ (071121) |
2.1.9 (071121) |
w | X Public Access. Web data retrieval tasks used by DS9. | |
TABLE NOTES
| ||||||
The following software packages have been completely “retired” from SciApps and are no longer supported or available for any platform (see the FAQ):
In addition, note in the Table of Available Software that some packages (e.g., AIPS, HEASOFT, python) are not maintained as part of the SciApps distributions, but are available to IPAC users via other avenues (described in the table) and are supported (on a best-effort basis) by the SciApps Administrator.
The current SciApps distributions for macintel (Leopard) and macosx (Leopard) are available as tarballs for stand-alone installation on laptop 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 SciApps User Survey is now closed – 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 |
As part of the transition to a new SciApps Administrator (on 30 March 2009), the state of SciApps is being evaluated with the goal of both improving its usefulness as a tool for IPAC scientists and streamlining the task of maintaining it. To those ends, the following plan – which itself is a work in progress – is being followed:
Q: How do I set up my computer to use SciApps?
A: Please read all the way to the end of this section before proceeding.
The original instructions for setting up your computer to utilize the new SciApps (supplied with the distribution release for macintel and macosx in July 2009) was to include the following line in your shell configuration file:
This command would first automatically detect the path to the network-mounted /SciApps disk on your computer (which can vary from computer to computer), and then use that path to locate and run the SciApps initialization script. However, due to unforeseen issues with the automounter on Mac (and, now, Linux) computers, the /SciApps disk might not always be actively mounted, especially if you have, for example, logged out overnight or for a longer interval. This happens because the /SciApps disk partition is automatically unmounted when not in use and/or after a specified period of inactivity. For example, the Mac OS X automounter has a default timeout limit of 1 hour. What this means is that once an hour, the automounter checks to see if you are, at that very instant, actively using all mounted disks (like the /SciApps partition). If you are not actively using a given mounted disk at that time, then automounter unmounts it. Note that OS X automounter does not care if you were using the mounted disk 1 second ago – it will still unmount it if the disk is not in use right now. The disk is automatically remounted on demand; for example, if you try to cd into a directory on the mounted disk or list its contents. However, the command shown above to source the SciApps initialization script will fail because it cannot locate the path to the script when the /SciApps partition is unmounted.
Consequently, the current preferred SciApps set-up procedure for all computers is as follows:
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 following line in your shell configuration file (typically ~/.cshrc or ~/.tcshrc – see which shell can I use?).
The switch 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. This setting is currently only valid for macintel and macosx; linux and solaris will always use the SciApps installation of IDL.
The switch 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 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 X 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 ~/.tcshrc file, as noted above. So, at a bare minimum, all you would need to have a functional computer account with SciApps initialized is a ~/.tcshrc file that contains only the SciApps initialization command. Additional command aliases and/or environment variables can be added directly to ~/.tcshrc, 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 configuration is stable and confirms 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.,
Please contact the SciApps Administrator if you have any questions about this process or desire assistance in implementing it.
Q: Which shell can I use?
A: The SciApps initialization scripts will currently function under the C shell (csh) and TENEX C shell (tcsh). Of these two, tcsh is preferred, since some software (notably IRAF) occasionally has problems running under csh due to long variable names. In the future, SciApps initialization scripts for the Bourne-again shell (bash) on Mac computers will be made available.
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, macosx, and linux are also available – see above for additional information.
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: 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 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: 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: I'm using a PowerPC Mac with the Tiger (OS X 10.4) operating system. Is there a version of DS9 that I can use?
A: Yes. PowerPC Macs (macosx) running OS X 10.4 (Tiger) require an older and specific version of DS9. With a full SciApps initialization, the command ds9_5.1_ppctiger will run the correct version. If you are not using all of SciApps, but wish to create a command alias just for this version of DS9, then put the following line in your ~/.cshrc or ~/.tcshrc file:
Please consider upgrading to Mac OS X 10.5 (Leopard) if you want to be able to use the full functionality of SciApps.
Q: I'm using an Intel Mac with the Tiger (OS X 10.4) operating system. Is there a version of DS9 that I can use?
A: Yes. With a full SciApps initialization, the command ds9_5.6_inteltiger will run the correct version. If you are not using all of SciApps, but wish to create a command alias just for this version of DS9, then put the following line in your ~/.cshrc or ~/.tcshrc file:
Please consider upgrading to Mac OS X 10.5 (Leopard) if you want to be able to use the full functionality 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 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 request additional help with SciApps?
A: Submit a ticket to the ISG Helpdesk. Active SciApps support (e.g., installing updates, answering Helpdesk tickets, etc) is provided on Tuesdays and Thursdays.
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: 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 5 (version 1.5), whereas Mac OS X was updated to include Java 6 (version 1.6) in mid-June of 2009 (in detail, the “Java for Mac OS X 10.5 Update 4” updated Java SE 6 to version 1.6.0_13, J2SE 5.0 to version 1.5.0_19, and J2SE 1.4.2 to 1.4.2_21 – see http://support.apple.com/kb/HT3581). In order to correct this, run
Under the General tab, rearrange the available Java versions so that J2SE 5.0 is at the top of the priority list. Quit Java Preferences and run APT. You can either restore the default order in Java Preferences after finishing with APT, or leave it – having Java 6 lower in 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, or on a 32-bit Intel Mac.
Q: Why isn't python for mac or linux available in SciApps?
A: The simple answer is that installation of python cannot be conveniently contained in the /SciApps partition, because the software expects to be distributed among a variety of locations (e.g., /Library/Frameworks, /Applications, and /usr/local/ on mac systems). Any hacked installation of python forced to be contained in the /SciApps partition would necessarily lose some functionality, notably the GUI interfaces.
Note that Mac OS X 10.5 (Leopard) comes pre-installed with the command line version of python v2.5.1 (070418), while Redhat Enterprise Linux (v5.3) comes pre-installed with the command line version of python 2.4.3 (080917). In addition, a macintel/macosx universal binary installer for python v3.0.1 (090213) is available in the /SciApps partition, and can be easily installed on a user-by-user basis.
If you want to use the full GUI functionality of python v3.0.1 (090213), then do the following:
(1) Copy the universal binary installer to your user account by issuing the following command in a terminal window:
(2) Double-click the installer in a Finder window, or use this command in a terminal window:
This will mount the installer disk image file and open it in a Finder window.
(3) Double-click the MacPython.mpkg icon and follow the installer's instructions.
If you are not comfortable performing this procedure, then contact the SciApps Administrator for assistance.
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 these instructions for a binary installation; 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. Contact the SciApps Administrator if you are interested in installing the full, GUI-enabled version of MacTex on your computer.
A (linux): TeX is installed by default in /usr/bin on linux computers. In order to make the aastex or emulateapj macros available, SciApps defines the TEXMFHOME environment variable on linux 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.