Urania

It’s been such a busy month that I missed the fact that Nor Pirzkal has released a new version of SciSoft OSX. Released on February 4, 2008, this version, dubbed 2008.2.1 is only for Intel-based Macs. ^[1] This new version contains the following improvements:

• Certain links to libraries that I have previously noted had to be manually fixed have been fixed.
• The IRAF within SciSoft OSX has been updated to the latest release, version 2.14. However, as noted in his February 25 post, Nor notes if mkiraf fails to create a proper login.cl, you should do the following:

  edit /scisoft/all/packages/iraf/iraf/unix/hlib/mkiraf.csh
  and replace the first two uncommented lines with
  
  set iraf = "/scisoft/all/packages/iraf/iraf/"
  set imdir = "/scisoft//all/packages/iraf/imdirs"

I’ll update this blog post as I experiment with the new release. But just from looking at the release notes:

• SAO Image DS9 is still at version 4.13 and not the current version 5.1. This is an issue mostly for Leopard users, since the older version of DS9 doesn’t run under Leopard without some tweaks. This is an easy enough upgrade.
• fv (an interactive FITS file viewer) is still at version 4.4 instead of the current version 5.1. You can download the current version and replace the one in the /scisoft/i386/Applications directory in case you view this as necessary.
• It installs /scisoft with permissions set such that the owner is the second user account created on most Macs (User 502). Previously it installed as owned by the first user account (user 501). This is not a huge issue if you have “sudo” privileges on the Mac (any “Administrative” user does, its the default on the first account created), just type the following on the command line:

  sudo chown -R root:admin /scisoft

  and enter your password when prompted. This will set the root account to own the files, which is appropriate in a multiuser situation. If you are the only user, you could set yourself up as owner by replacing ‘root’ above with your username (you can determine your username by typing “whoami” on the command line).

I have placed a mirror of this new version on my Unofficial Scisoft OSX Mirror page as well

The folks behind SAOImage DS9 have now released version 5.1. The big change I’ve noticed since the last version is that version 5.1 works without issues under Leopard’s new X11 implementation. Of course, the disadvantage is you now must download a version compatible with your OS version as well as your CPU.

• If you want the Aqua (MacOS X native version, download the appropriate one of the following files. If you want to use the Aqua-native version from IRAF, you will need to access the command-line binary within the SAOImage DS9.app application bundle as “SAOImage\ DS9.app/Contents/MacOS/ds9“.
  • MacOSX 10.4 Tiger Aqua Interface, Universal (PPC and Intel)
  • MacOSX 10.5 Leopard Aqua Interface, Universal (PPC and Intel)
• If you want the X11-based command line driven version
  • Darwin PPC 10.4 Tiger version
  • Darwin Intel 10.4 Tiger version
  • Darwin PPC 10.5 Leopard version
  • Darwin Intel 10.5 Leopard version

More detailed release notes are available here. See my previous post on SAOImage DS9 5.0 to see how it is possible to upgrade the binaries included with SciSoft OSX.

Because a reader of this blog contacted me to inform me that the official Scisoft OSX download links appear to be down (scisoftosx.dyndns.org is not resolving), I have placed a mirror of the latest versions for both PPC and MacIntel online here. I will take down this mirror if the maintainers of Scisoft OSX ask, but at least for now, it is online.

No… the new Scisoft OSX isn’t out quite yet, but I got the following note from Nor Pirzkal responding to my post regarding the various broken symbolic links in SciSoft OSX 2007.11.1.

Just to let you know that I just implemented your changes in 2007.11.2b. Thanks again.

So it looks like these bugs will be fixed when Scisoft OSX 2007.11.2b is released soon. I have to hand it to them, Nor is pretty quick to respond to these bugs, given he has a full time job which doesn’t involve maintaining SciSoft OSX!

Wow, Nor Pirzkal and Francesco Pierfederici have kept quite busy making small updates to Scisoft OSX for Intel. They released another new version today (available for download here). Here’s the entire description of the changes in this version of Scisoft OSX from the release notes:

This version updated Python to version 2.5.1 and correct some minor issue with the bash version of the irafuser.bash script when running under OSX 10.5 Leopard. Missing GCC runtime fortran libraries are also now included. This version was test under OSX 10.5 and seems to run fine. Note that 10.5 does deal with X11 applications slightly differently. Once the Setup.bash script has been source[d], you should add the following line to your .bash_profile: export DISPLAY=127.0.0.1:0.0 This will enable all Scisoft X11 applications to start from Terminal.app

I am not running Leopard (and probably will not switch until the winter break, when I have time to deal with all the X11 issues it creates), so I can’t confirm the ability to run under Leopard, but its great to know they are keeping SciSoft OS X up to date.

Issues with this Release of Scisoft OSX

• I did notice this new version of Scisoft OSX doesn’t appear to link its IRAF install with the rvsao IRAF package (used for radial velocity computations). Doesn’t matter to me to much since I compiled the newer version and linked to it, but it is funny they include the rvsao package at /scisoft/all/packages/iraf/extern/rvsao but don’t link to it in the $hlib/extern.pkg file, which I do believe they did in the older versions.
• I may not have noticed this earlier, but in the libraries directory /scisoft/i386/lib, some of the symbolic links are broken. Specifically:
  • All the items in this directory linking to the OpenMotif library items are not linked, it appears /scisoft/i386/Packages/OpenMotif-2.3.0/lib doesn’t exist. However, /scisoft/i386/Packages/OpenMotif-2.3.0/lib.org does. So I symbolically linked lib to lib.org via:

    cd /scisoft/i386/Packages/OpenMotif-2.3.0/
    ln -s lib.org/ lib

    And now all the links to the OpenMotif libraries within /scisoft/i386/lib work.
  • The CFITSIO library is mis-linked to an older version which no longer is installed. So I needed to:

    cd /scisoft/i386/lib/
    rm libcfitsio.a
    ln -s ../Packages/cfitsio-3.040/lib/libcfitsio.a libcfitsio.a

    and the CFITSIO library was properly linked again.
  • libpng.so was apparently not compiled within /scisoft/i386/Packages/libpng-1.2.10/lib, so there is no quick fix for that broken link.
  • I removed a link to python2.4 in /scisoft/i386/lib and replaced it with a link to python 2.5:

    cd /scisoft/i386/lib/
    rm python2.4
    ln -s ../Packages/pygtk-2.8.6/lib/python2.5/ python2.5

• All the CFITSIO headers in /scisoft/i386/include/ are linking to an older version (3.006) instead of the current installed version (3.040). Fixed via:
• There are symbolic links in the /scisoft/i386/bin directory to a variety of executables from the sm plotting package which doesn’t appear to have been installed as part of the Scisoft OSX distribution.
• Not really a bug, but the version of SAOImage DS9 is version 4.1.3 and not the current version 5.0.0. Of course, given the long history of dangerous version X.0.0 software, this maybe safer that way.

On October 15, the folks behind SAOImage released SAOImage DS9 version 5.0. The big change I noticed is they now have a completely MacOS X native (read “Aqua”) version of ds9 (but only if you use the application package version of ds9, the command line versions remain X11)! I downloaded the following three versions:

• MacOSX 10.4.x (Universal)
• Darwin PPC 10.4.x
• Darwin Intel

The new features lists page tells us that this release includes:

• MacOSX Aqua Support: DS9 has been ported to MacOSX Aqua and is an universal application which no longer requires X11.
• Compressed FITS Support: DS9 supports compressed FITS images using RICE compression.
• Mask Support: DS9 supports overlay masks. A mask is defined as a valid FITS image, in which a non zero value indicates that the selected mask color is to be displayed instead of the data value color.
• SkyView Support: DS9 provides support for HEASARC’s image cutout service, SkyView. This site provides image cutout service for a number of image surveys, including SDSS.
• Multi-Language Support: DS9 provides multi-language support. By default, the language used for menus and dialog boxes is based on the value of the operating system locale variable. The user may override the default value by selecting the desired language in the preferences or by the -language command line option.
• Preferences: Preferences are automatically saved when a user changes an option. Selecting the saving preferences menu item is no longer needed.

More detailed release notes are available here. I was able to get this version of ds9 integrated with SciSoft OSX by doing the following:

1. Decompress the command line version of ds9 via the terminal using tar xzvf ds9.darwinppc.5.0.tar.gz (PPC version) or tar xzvf ds9.darwinintel.5.0.tar.gz (Intel version). When the decompression is done, all you have is an executable called ds9.
2. Next, from the terminal, go to the /scisoft/bin directory (on PPC) or /scisoft/i386/bin/ directory (on Intel) and rename the old ds9 executable to something like ds9_old (using something like mv ds9 ds9_old).
3. Copy your newly decompressed ds9 executable into the SciSoft OSX binary directory. I should note the command line version of ds9 still requires X11.

Another new version of Scisoft OSX for Intel has been released and is available for download here. Here’s the entire description of the changes in this version of Scisoft OSX from the release notes:

This version contains an updated [ESO-]MIDAS package.         

I checked the list of packages included and sure enough, the only change was in the ESO-MIDAS package (whose current version is actually 07SEPpl1.0).

• MIDAS 07FEBpl1.1 (previously MIDAS 06FEBpl1.0)

I don’t use ESO-MIDAS, which is an image reduction package aimed as users of ESO’s La Silla facilities and the VLT at Paranal, so I can’t really comment as to the usefulness of this update. As with previous versions of Scisoft, the release notes warn if you use Aquaterm devices for PGPLOT, GNUPLOT, or any other packages that you “must manually run /scisoft/i386/Applications/Aquaterm.app once first to enable the aquaterm devices.”

I have also confirmed that this release also fixes the IRAF problem with symbolic linking to mkpkg and xc in /scisoft/i386/bin/ I referred to earlier in my blog.   Thanks for the fix guys!

Finally, as I noted with the last release of Scisoft, my standard method for updating Scisoft OSX is to move my existing /scisoft directory to /scisoft_old and then I unpack the new version. That way, in case anything goes wrong, I can always switch back.

Update: I have updated this blog entry to reflect some updated information from Nor Pirzkal regarding the best way to fix this glitch.  This problem has been fixed in Scisoft OSX MacIntel version (2007.9.1).

During my adventures compiling the hectospec-related IRAF packages, I was using Scisoft OSX and discovered there were a couple of issues with the symbolic links for the mkpkg command necessary for compiling new IRAF packages.

• In the Scisoft OSX PPC Beta (2006.11.1b) mkpkg appears to be mis-linked, so it can’t be executed. So I did the following in the terminal:

  cd /scisoft/binsudo rm mkpkgsudo ln -s ../iraf/iraf/unix/bin.macosx/mkpkg.e mkpkg

• In the Scisoft OSX MacIntel version (2007.1.1) and Scisoft OSX MacIntel version (2007.7.1), there are some missing symbolic links to mkpkg and xc in the directory for MacIntel binaries.  As a result, both mkpkg and xc were instead pointing to PowerPC binaries. I fixed this as follows (again, from the command line):

  cd /scisoft/i386/bin/sudo ln -s /scisoft/all/packages/iraf/iraf/unix/bin.macintel/mkpkg.e mkpkgsudo ln -s /scisoft/all/packages/iraf/iraf/unix/bin.macintel/xc.e xc

  This mis-linking certainly didn’t help getting things to compile under MacIntel, since IRAF was attempting to compile MacIntel code using PowerPC versions of mkpkg and xc.

Thanks for Nor Pirzkal for giving me some feedback on fixing this problem.  He tells me he has made the appropriate changes so that the next version of Scisoft OSX will not have this  issue.By the way, my complaint here should in no way be construed as a critique of the efforts of Francesco Pierfedericki and Nor Pirzkal in putting together Scisoft OSX. They have done a great deal of work to put together an awesome package. For two people to track over 2 GB of software and not expect some glitches is unrealistic. And I for one am extremely grateful that his efforts have saved me a lot of time.

Maple is a nice symbolic mathematics pages from the Canadians at Maplesoft. Our school as a site license which is an awesome deal as students can buy personal copies for much less than the price of a typical textbook. As such, our students can be expected to use the software for their classes. One of the really slick bits on the Mac is you can run Maple from the command line (useful when I need to compute an integral quickly).

I am running Maple 11, so I just placed the following alias in my ~/.tcshrc file (I run tcsh by default because I am old school and dislike bash):

alias maple "/Library/Frameworks/Maple.framework/Versions/11/bin/maple"

If you are running the PPC version of SciSoft, it messes around with some environmental variables, breaking this trick, you can instead use

alias maple "unsetenv DYLD_FALLBACK_LIBRARY_PATH; /Library/Frameworks/Maple.framework/Versions/11/bin/maple; setenv DYLD_FALLBACK_LIBRARY_PATH /scisoft/lib"

If you are using Maple 10, substitute a “10″ where you see an “11″ above.