When I moved to Snow Leopard, I discovered that I could not get PGPLOT.pm compiled against the PGPLOT package that comes with Scisoft OSX and soon realized this was because Perl on my Mac Pro is 64-bit whereas the PGPLOT package included with Scisoft OSX was 32 bit. I decided to compile PGPLOT 64-bit native to try to remedy the problem and on the way discovered a few other issues. Here’s what I did to get both PGPLOT and PGPLOT.pm working under Snow Leopard (on both 32-bit and 64-bit computers).

1. Install GFORTRAN: The first thing I did was install Gnu Fortran (aka gfortran) as configured by Gaurav Hanna at the High Performance Computing for Mac OS X website. It turns out the version he compiled for Snow Leopard (here) is 64-bit Intel ONLY, so for my venerable first generation MacBook Pro, I grabbed the 32-bit Intel Leopard version (here), which worked fine in Snow Leopard. Installing them is a simple matter of issuing the proper tar command to unpack the tarball into /usr/local, where all the binaries are installed.

   • sudo tar -C / -xzvf gfortran-snwleo-intel.bin.gz

     (for the 64-bit Snow Leopard version)

   • sudo tar -C / -xzvf gfortran-leopard-intel.bin.gz

     (for the 32-bit Leopard version)

   Once they are installed, you simply have to make sure /usr/local/bin is in your $PATH.

2. Install PGPLOT: I grabbed the PGPLOT source code from Tim Pearson’s website (here) and untarred the tarball into /usr/local/src/pgplot, the default location the code expects to be in (based on the instructions in the install-unix.txt file included in the source code tarball).
   

   sudo tar -C /usr/local/src/ -xzvf pgplot pgplot5.2.tar.gz

3. Install sys_macosx configuration: The PGPLOT source code has various compiler configurations stored in “configuration directories” but it doesn’t come with one for Mac OS X. The MacPorts folks, when they ported PGPLOT, did create such a configuration. However, that configuration is hard coded to require AquaTerm, a nice MacOS X native display program that has not been made 64-bit compliant yet. Furthermore, their version of the configuration requires g77 to compile. The only g77 I could find was not 6-bit compliant, so I ended up hacking the sys_macosx/ configuration directory to include a new gfortran configuration that didn’t require AquaTerm. I am making a tarball of that configuration directory available in the pgplot5.2_macosx_addition.tgz which you can download and unpack into the PGPLOT source directory using:
   

   sudo tar -C -xzvf /usr/local/src/pgplot5.2_macosx_addition.tgz

   [The above line was edited to fix an error noticed by a commenter. - Juan (Oct. 24, 2009)]
4. Compile the PGPLOT binaries: At this point, if you follow the instructions in the install-unix.txt file in the PGPLOT directory you will be fine, baring in mind the configuration you want to use is the “maxosx gfortran_gcc” configuration. However, I will outline the steps I used below.
   1. Create a PGPLOT library/binary directory:Create a directory to contain the PGPLOT libraries. I created /usr/local/pgplot using the command:
      

      sudo mkdir /usr/local/pgplot

   2. Choose the graphics drivers you want: Copy the drivers.list file from the source directory to this new pgplot directory and edit it to match your needs:
      

      cd /usr/local/pgplot
      sudo cp /usr/local/src/pgplot/drivers.list .
      sudo vi drivers.list

      (You can replace this last step with emacs or whatever text editor you prefer). You make a graphics driver part of the compilation by removing the leading exclamation point from the line. I choose to activate the X-Window drivers, the GIF drivers (to create GIF images), and the PostScript printer drivers (which you can use to create PostScript versions of plots for publication). Be aware PNG support requires libpng be installed.
   3. Create the makefile: We now need to create the makefile using PGPLOT’s makemake script. Within the /usr/local/pgplot directory execute:
      

      sudo /usr/local/src/pgplot/makemake /usr/local/src/pgplot  macosx gfortran_gcc

      which should result in the following output
      

      Reading configuration file: /usr/local/src/pgplot/sys_macosx/gfortran_gcc.conf
      Selecting uncommented drivers from ./drivers.list
      Found drivers GIDRIV NUDRIV PSDRIV XWDRIV
      Creating make file: makefile
      Determining object file dependencies.

   4. Create all the binaries: Now you just have to create all the binaries, which is a simple make command:
      

      sudo make

      Assuming everything proceeds without error, you should then see at the end of the output
      

      *** Finished compilation of PGPLOT ***
      
      Note that if you plan to install PGPLOT in a different
      directory than the current one, the following files will be
      needed.
      
             libpgplot.a
             libpgplot.dylib
             grfont.dat
             rgb.txt
             pgxwin_server
      
      Also note that subsequent usage of PGPLOT programs requires that
      the full path of the chosen installation directory be named in
      an environment variable named PGPLOT_DIR.

      At this point, you should (if you are going to use PGPLOT within perl or C compile the C library as well using
      

      sudo make cpg

      Finally, clean out all the temporary object files, you don’t need them. Do this using the makefile by typing
      

      sudo make clean

      If you want to test if things are working you can run one of the PGPLOT demo programs created in this directory. However, the pgdemo* executables seem hard coded to expect the pgplot libraries in the /usr/local/lib directory, to it might be a good idea to do the following step before trying the demos. [Edited in response to a comment about the demos not working. - Juan (Oct. 24, 2009)]
   5. Copy library and header files: This step is optional, but since most programs (including the pgdemo* executables) don’t look in /usr/local/pgplot for library and header files, I copy them to /usr/local/lib and /usr/local/include respectively using
      

5. Making sure I use these PGPLOT binaries: Since I am using Scisoft OSX, I modified my ~/.tcshrc file to change the PGPLOT related environmental variables after loading Scisoft’s environment
   

   setenv PGPLOT_DIR /usr/local/pgplot/

   . If you are not using Scisoft, you can place these lines anywhere in your ~/.tcshrc file. If you stick to using bash, then the corresponding lines in the ~/.bashrc file that you need to create (after setting up Scisoft, if you are using that) are:
   

   export PGPLOT_DIR=/usr/local/pgplot/

   At this point you have a working PGPLOT set of libraries installed. You can stop here if you just want to use PGPLOT from C or FORTRAN source code. If you want to use PGPLOT from within Perl, you need to go further.
6. Install the ExtUtils:: F77 perl module: In order to install PGPLOT support, you need to install ExtUtils:F77 first. You can download ExtUtils::F77 here and once you untar the tarball,
   

   tar xzvf ExtUtils-F77-1.16.tar.gz

   it can be easily compiled using the following standard perl module compilation steps:
   

   cd ExtUtils-F77-1.16
   perl Makefile.PL
   make
   sudo make install

7. Install the PGPLOT perl module: You can download PGPLOT here. Untar the tarball.
   

   tar xzvf PGPLOT-2.20.tar.gz

   We start as we usually do for Perl modules, creating the makefile using the Makefile.PL script:
   

   cd ExtUtils-F77-1.16

   Unfortunately, the Makefile.PL script will create a makefile this creates doesn’t work because it doesn’t call gfortran so we have to change the Makefile.PL script to know about gfortran. So load Makefile.PL and edit the line that reads
   

   use ExtUtils::F77;

   to read
   

   use ExtUtils::F77 qw{Darwin GFortran};

   Once you have done that, create the makefile using
   

   perl Makefile.PL

   Now you still have a problem because this makefile is designed to create a universal binary. However, depending on which platform you downloaded gfortran for (in step 1), you only have 64-bit intel or 32-bit intel support. So you have to delete all mentions of
   

   -arch ppc

   from the makefile as well as removing
   

   -arch i386

   if you are compiling on a 64-bit system or
   

   -arch x86_64

   if you are compiling on a 32-bit system. Once you have done that, you can finish installing the perl module using:
   

   make
   make test
   sudo make install

   I did have some issues with make test because it couldn’t find my X-windows driver due to a bad environment, but the compile reported no errors and I was able to get the make test to work once I had the proper environmental variable settings for PGPLOT_DIR (see step 5).

So that is it, I now have working PGPLOT installations with perl support on both my 32-bit MacBook Pro and my 64-bit Mac Pro.

A minor revision of Scisoft is available for downloading. Many people are experiencing many problems with the Apple Package Installer and I am distributing this release as a simple tar.gz file.

This version of Scisoft is distributed as a simple tar file that can be un-tarred in /. Scisoft expect to be located in /Applications/scisoft/

I can confirm the CONTENTS file distributed with the install is identical to the file for Scisoft 2009.9.1 so this release may just be a way to avoid some issues with the Apple Package Installer program.

This change to a tarball format is good, but it changes how to install the software. However, there is at least one major glitch in this distribution

• WCSTools is missing from the installation! There are symbolic links to the package, but the /Application/scisoft/i386/Packages/wcstools-3.7.3/ directory is empty! If you are upgrading from a previous version of Scisoft OSX, there is an easy way to recover from this problem. I am outlining my suggested installation routine below.
• As I noted for Scisoft 2009.9.1, “on Snow Leopard, Gordon Richards discovered that if you attempt ‘import pylab’ in python, you get a bus error. I can confirm the same error occurs on my Snow Leopard machine using either this SciSoft OSX release or the previous one. Furthermore, I can confirm the error DOES NOT occur in Leopard. I am not a heavy Python user, so I will leave it to Gordon, Nor, and others to investigate this issue. Gordon notes that this blog posting contains instructions for getting pylab installed under a vanilla Snow Leopard install, in case you need them.”

My suggested routine for upgrading to this version of Scisoft OSX from a previous version is the following:

1. Backup the previous version of Scisoft by renaming the /Application/scisoft/ directory to /Application/scisoft_old/.
2. Download the current gzipped tarball of Scisoft OSX. The current version of Scisoft OSX is available for download from the Scisoft OSX website, but I have made the package available on my Scisoft OSX mirror as well, in case it is faster for people.
3. Using the command line in an administrative account, you can untar the tarball using the command:

   sudo tar -C / -xzvf Scisoft_OSX_macintel_2009.10.1.tar.gz

   You will be asked for your account password to allow ’sudo’ to run the tar command as root.
4. The files are untarred with their ownership intact from when Nor created the tarball, so be sure to change the ownership to match your root account using
   

   sudo chown -R root:admin /Applications/scisoft/

5. Finally, if you want to copy over the WCStools package from the previous Scisoft OSX installation, you can use the command:

   sudo cp -r -p /Applications/scisoft_old/i386/Packages/wcstools-3.7.3/ /Applications/scisoft/i386/Packages/wcstools-3.7.3/

   That should get your back the WCStools.

I have alerted Nor to the missing wcstools directory as well as some other minor issues with this release. Hopefully, if Nor has some time, he will make

This version should fix a few outstanding bugs in version 2009.6.1. People running on case sensitive file system will hopefully stopped having problems. This version otherwise upgrades a few minor packages as described in the NEWS and CONTENTS files.

This version requires OSX Intel 10.5.x or higher. It also works fine with OSX 10.6.0 and OSX 10.6.1.

From reviewing the CONTENTS file distributed with the install, the major changes from the previous version as as he indicated, quite minor. They include:

• The following Python packages were updated:
• • matplotlib 0.99 (upgraded from version 0.98.5.2)
  • pyraf 1.8 (upgraded to the current release version from version 1.7.1)
  • pygsl 0.9.4 (upgraded from version 0.9.3)
  • mxDateTime 3.1.2 was added to the distribution. Adds certain useful date manipulation functions to the python installation.
  • pysao 2.1.8 was added to the distribution. This appears to add direct XPA communication capability between python scripts and SAOImage DS9.

• The gsl library was update from version 1.11 to 1.13.
• [From NEWS file] Changed ds9 [command line] unix version a [symbolic] link from an alias. I noticed the SAOImage DS9 website currently says “Note: the next release of DS9, version 5.7, will be available October 15th.”
• [From NEWS file] Fixed references to “packages” to “Packages” in Setup scripts

The glitches I have noticed in this distribution

• As with previous versions, the installer for Scisoft OSX (due to bugs, apparently in Apple’s installer.app) changes the ownership of /Applications after the install. I would run Disk Utility and Fix the Permissions on your root volume after installing Scisoft OSX.
• [Added Sept. 23] Gordon Richards and I have have been investigating some serious annoyances with the python installation on Snow Leopard in this version of SciSoft OSX.
  1. First of all, the installer apparently doesn’t install /Applications/scisoft/i386/Packages/Python-2.5.4/Python.framework/Versions/2.5/Resources/Python.app/ when running on Snow Leopard. This directory contains the python executable. Therefore, in the new SciSoft OSX on Snow Leopard, you can’t run python from the clean install. If you manually copy this directory from the previous SciSoft OSX installation to this one, then I find you can run python again (or in my case, pyraf). I can confirm this directory is apparently installed under Leopard.
  2. On Snow Leopard, Gordon Richards discovered that if you attempt ‘import pylab’ in python, you get a bus error. I can confirm the same error occurs on my Snow Leopard machine using either this SciSoft OSX release or the previous one. Furthermore, I can confirm the error DOES NOT occur in Leopard. I am not a heavy Python user, so I will leave it to Gordon, Nor, and others to investigate this issue. Gordon notes that this blog posting contains instructions for getting pylab installed under a vanilla Snow Leopard install, in case you need them.

The current version of Scisoft OSX is available for download from the Scisoft OSX website, but I have made the package available on my Scisoft OSX mirror as well, in case it is faster for people.

Scisoft OSX Intel 2009.6.1 Released

This version updates the STSDAS/TABLES packages and a few other packages.
It also fixes the issues pointed out by J. Cabanela

The new version of Scisoft OSX 2009.6.1 differs from Scisoft OSX 2009.5.2 in the following ways:

• Stiff was updated from version 1.10 to version 1.12
• HEASARC fv.app was updated from version 5.1 to version 5.2.1 and properly installed.
• HEASARC hera.app was updated from version 5.1 to version 5.2.1 and properly installed.
• HEASARC StudentHera.app was updated from version 5.1 to version 5.2.1 and properly installed.
• SAOImage DS9 was updated to version 5.6.3 from version 5.3b.
• Interestingly, the STSDAS and TABLES IRAF packages are still version 3.10, so I am not sure what updates Nor refers to above for STSDAS/TABLES.

The only glitch I noticed is that permissions problems persist. Specifically, when the installer installs Scisoft OSX, it appears that a bug in Apple’s Installer program triggers a change in ownership of the /Applications directory to that of the second user on the system. I strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using:

sudo chown username:admin /Applications

(where “username” is the primary administrator’s username, in most cases, your username) to perform the repair. I know Nor spent a bit of time trying to resolve this without success last summer, so its a glitch that will probably persist.

I also have a minor gripe. This is not a bug, so much a feature I prefer. I like having the X11 command-line version of ds9 available, so I manually installed the current ds9 command line binary into /Applications/scisoft/i386/bin/.

The current version of Scisoft OSX is available for download from the Scisoft OSX website (or will be shortly) and I have made the package available on my Scisoft OSX mirror as well.

Two years ago, I wrote a blog entry with hints for setting up X11 for the astronomer. The problem is that while the hints in that writeup are still valid, they don’t work if you are using Xquartz because the preferences are stored in a different location for XQuartz versus the built-in X11. As such, I am reproducing those X11 hints here, but with the edits necessary for use with XQuartz.

Once you have installed XQuartz, the X11.app should automatically launch when a program that needs X11 is executed (If you are an old hand at X11, you probably discovered since moving to Leopard that you should NOT set the DISPLAY variable to :0 to display an Xwindow on your primary display, just leave DISPLAY undefined.):

1. There are many hidden preferences in XQuartz just like in many Mac Applications. You can see a list of the hidden (and not hidden) preferences using the command line tool defaults. To see the available XQuartz preferences, type:defaults read org.X.x11NOTE: If you are still using Apple’s built-in X11 implementation (or if you are using MacOS 10.4), just replace ‘org.x.X11’ with ‘com.apple.x11’ in all the following hints.
2. In addition to “reading” the preferences, you can write to them. From the command line you can type:
   • defaults write org.X.x11 no_quit_alert true
     This allows X11 to quit without an alert box. Useful if you find it irritating like I do that X11 will prevent me from logging out or the computer from restarting due to that dialog box. However, this does mean you can accidentally quit X11.app pretty easily if you hit cmd-Q at the wrong time.
   • defaults write org.X.x11 wm_ffm true
     Allows which X11 window is selected to follow the mouse, which is the way X11 behaves under most *nix systems by default.
   • defaults write org.X.x11 wm_click_through -bool true
     This activates click_thorough events in the Quartz window manager, which allows clicks to pinned windows, another behavior common to *nix X11 installations.
3. You can control which window manager is launched (if you prefer something other than the quartz-wm used by default). If you don’t have a ~/.xinitrc file, copy the default one:
   

   cp /private/etc/X11/xinit/xinitrc ~/.xinitc

   
   and then manipulate it with any text editor.
4. BIG LAPTOP USER HINT: Because XQuartz on the Macintosh uses authentication to prevent connections from unauthorized sources to the X11 client, something interesting happens when you change IP address, you will discover you can’t use X11.app from the MacOS X Terminal until you quite and relaunch X11.app. This happens to me all the time on my laptop when I travel and the IP address changes. I recommend either using the Xterm as your terminal or just get used to restarting X11 if you have problems connecting to the terminal.
5. You can run X11 remotely on your Mac, if you can ssh into your Mac, then just use
   

   ssh -Y youraccount@yourcomputer.com

   
   , the -Y flag should allow you to run X11 remotely as long as X11.app is running on your machine before the connection is made. If your ssh on the remote machine doesn’t support X11 connections and you have admin access, you can edit the file /etc/sshd_config on the remote machine and make sure X11 Forwarding is turned on by looking for the following lines and making sure they are uncommented and that all “no”’s are set to “yes”:
   

   X11Forwarding yes
   X11DisplayOffset 10
   X11UseLocalhost yes

And that is it for the hints for now.

• Eclipse 5.0.0 has been added to the distribution. Eclipse is an Integrated Development Environment (IDE) for programming. I don’t find it to be terribly useful, and in fact find it fairly awful in its implementation for IDL, but I am sure there are many people who disagree (enough to foster development of five major versions of it).
• Gnuplot has been updated to version 4.2.5 from 4.2.3
• Eye 1.4.1 has been added to the distribution. Eye is a program designed to allow you to use an artificial neural network to construct SExtractor filters for “adaptive filtering, feature detection and cosmetic corrections.”
• Swarp was updated to 2.17.6 from 2.17.1
• WeightWatcher was updated to 1.8.10 from 1.8.7
• The Python distribution was updated to version 2.5.4 from 2.5.2 and the following python packages were updated:
  • ipython updated to 0.9.1 from 0.8.4
  • Numpy updated to 1.3 from 1.1.1
  • pyfits updated to 2.1.1 from 1.1 (or this could be a typo in the old CONTENTS)
  • matplotlib updated to 0.98.5.2 from 0.98.3
  • pyraf updated to 1.7.1 from 1.6
  • stsci_python updated to 2.8 from 2.6
  • AstroAsciiData updated to 1.1 from 1.0
  • scipy updated to 0.7.0 from 0.6.0
• The STSDAS and TABLES IRAF packages were updated to version 3.10 from 3.08
• fftw library version 3.2.1 added. This will be useful to me since we have been using fftw in the computational physics class I have been teaching this semester.
• I noticed the Aquaterm.app application (used for graphics display by PGPLOT and Gnuplot) is now pre-installed in /Applications/scisoft/i386/Applications/.

Some minor glitches I have noticed in this distribution

1. Permission Problems Persist: When the installer installs Scisoft OSX, it appears that a bug in Apple’s Installer program triggers a change in ownership of the /Applications directory to that of the second user on the system. I strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using: sudo chown username:admin /Applications (where “username” is the primary administrator’s username, in most cases, your username) to perform the repair. I know Nor spent a bit of time trying to resolve this without success last summer, so its a glitch that will probably persist.
2. Older SAOImage DS9 included: I noticed that the SAOImage DS9 distributed with this version of Scisoft OSX is version 5.3b, whereas the current version is 5.6.1, so I manually installed the current ds9 command line binary into /Applications/scisoft/i386/bin/ and the current Aqua application into /Applications/scisoft/i386/Applications/ and everything is working fine there.
3. HEASARC fv.app not installed: The fv.app application in the /Applications/scisoft/i386/Applications/ is actually a second copy of studenthera.app, misnamed. Not sure how that happened, but I manually installed the current version of HEASARC fv.app there without an issue.

All in all, a bunch of small updates, but it gets the package mostly up-to-date again. The current version of Scisoft OSX is available for download from the Scisoft OSX website, but I have made the package available on my Scisoft OSX mirror as well, in case it is faster for people.

Interestingly, the XQuartz wiki notes that

[MacOS] 10.5.7 updates the X11 server to match what shipped with 2.3.2. Most of the userland, however, only saw security updates. The version reported by X11 in 10.5.7 is 2.1.6 to distinguish it from the 2.3.x series which contains a much newer userland.

I have the feeling that the update to MacOS 10.5.7 will be released very soon now.

[UPDATE: In fact, it took almost two weeks, but MacOS 10.5.7 was released on Tuesday, May 12, 2009.]

Well, I’m way late to the game on this, but our long national nightmare is over – Xquartz for Leopard support full screen!

The Xquartz folks latest edition of Xquartz (version 2.3.2.1) includes full-screen support. Now, personally, I like the way X11 integrates with Aqua, but for those who prefer to use only one windowing system at a time, you can now do it on MacOS X Leopard. You can download it here.

Yesterday Mekentosj released version 1.9 of Papers for the Mac as well as a new iPod Touch/iPhone based version of their software (Apple iTunes store link) I have purchased it and can confirm that the synchronization works as advertised, I am now carrying all the papers I have read in the last 10 years in my shirt pocket. Nice!

Here’s the (slightly edited to reflect stuff of interest to astronomers) press release from Mekentosj

Papers 1.9 for Mac – sync your library of science with your iPhone – Published on 02/19/09

IMMEDIATE RELEASE

Mekentosj BV has announced Papers 1.9, the Apple design award-winning application that helps scientists on the Mac manage their personal library of scientific articles. The free update brings over 60 improvements, including an improved workflow for working with collections, support for French and German library proxies. But most of all, it allows you to synchronize your PDF library with the newly introduced Papers for iPhone and iPod touch.

Aalsmeer, The Netherlands – Mekentosj BV has announced Papers 1.9, the Apple design award-winning application that helps scientists on the Mac manage their personal library of scientific articles. The free update brings over 60 improvements, including a better workflow for working with collections, and support for French and German library proxies. But most of all, it allows you to synchronize your PDF library with the newly introduced Papers for iPhone and iPod touch.

With Papers 1.9 mek and tosj continue to improve the user experience and workflows of their popular PDF organizing tool for researchers. And with the ability to synchronize your library with the newly introduced Papers for iPhone and iPod touch it becomes easier than ever to manage your research literature, and now you have it with you wherever you go.

Papers for Mac and Papers for iPhone work together as a great team. Select which collections you want to keep in sync or make use of the smart auto-fill function to fill up your iPhone or iPod with articles based on the criteria that you choose. And if you make changes, or add ratings and notes, or if you download new articles on the road, the next time you sync with Papers on your Mac all those changes are immediately present in your library. It’s that simple. Visit our web site for a screencast to find out more.

Papers Features:
* organize and manage your entire library of scientific PDF files easily and elegantly
* built-in support for searching online article repositories
* built-in webbrowser for browsing publisher websites
* automatic downloading and archiving of PDF files
* tabbed and fullscreen reading of your PDF files
* razor fast spotlight searching of your entire library
* Syncing with the new Papers for iPhone and iPod touch.
* and much more.

Papers has built-in support for the following online repositories:
* ACM portal – Computer science
* NASA-ADS – Astronomy
* arXiv – Preprint repository
* Citeseer – Computer Science
* Google Books
* Google Scholar
* IEEE Xplore – Engineering
* MathSciNet – Mathematics
* Scopus – All sciences NEW
* Web of Science – All sciences

Minimum Requirements:
* Mac OS X Version 10.4 or higher
* Universal Binary for PowerPC and Intel
* 1.5 Ghz or faster G4, G5 or Intel Processor

Pricing and Availability:
Papers is priced at $42 (USD) for a single-user license. (Under)graduate students can apply for a 40% discount. A 30-day trial is available.

About Papers for iPhone:
Papers for iPhone and iPod touch puts your entire research literature database in your pocket, available at your fingertips wherever you go; whether you’re at a conference, in class, visiting your peers, or on the road. To celebrate the launch of Papers for iPhone and iPod touch you can now buy version 1.0 for the introductory price of $9.99 (USD) in the iTunes app store.

Papers is a program made by Mekentosj BV, a Dutch independent software company that writes innovative software for scientists. After a PhD in Cell Biology founder and CEO Alexander Griekspoor switched fields and initially joined the European Bioinformatics institute as a Marie Curie postdoctoral fellow. Alexander is perhaps most well-known as “Mek” from the duo “Mekentosj”. Together with his friend Tom “Tosj” Groothuis he developed a number of scientific Mac applications, two of which won Apple Design Awards for best Best Student and Best scientific Mac OS X application, respectively. What started in his spare time became his passion and has now also become his work: Mekentosj Inc. He aims to create new and innovative Mac OS X applications for scientists, of which his recently released new program Papers is a prime example, it won Mekentosj’ third Apple Design Award. Visit our website to learn more.

• Aqua 10.4 Tiger (Universal)
• Aqua 10.5 Leopard (Universal)
• X11 10.4 Tiger (Universal)
• X11 10.5 Leopard (Universal)
• X11 10.5 Leopard (Universal) with Firewall

The release notes for SAOImage DS9 don’t necessarily suggest dramatic changes in this version relative to version 5.3.

1. CATALOGS: removed support for Chandra Source Catalog at request of Ian Evans of CXC (only added on October 3, 2008).
2. MASKS: add support for mask transparency.
3. MASKS: add new mask properties.
4. GRID: add grid title support.

My previously posted notes on integrating upgrades of DS9 into the Scisoft OS X installation still work. Just note that newer releases of Scisoft OS X place the binaries in /Applications/scisoft/i386/bin/ instead of /scisoft/i386/bin/ and if you are installing the X11 binary that is compatible with the firewall, you have to install both the ds9 and ds9.zip file in the bin/ directory of Scisoft OSX.

1. Fixed a parsing bug that prevented the loading of any Clear Sky Chart for sites containing parentheses or periods in their names. It was this bug that was interfering with the loading of our observatory’s Clear Sky Clock.
2. Since the Clear Sky Chart is quite large and many people will use the widget on laptops with small screens, I added a “Half-size mode“. All you do is click on the “Toggle Size” link on the widget. This shrinks the charge and saves screen real estate.
3. With Attilla Danko’s permission, I added a Built-in Legend (copied from his site) for interpreting the Clear Sky Chart to the widget. Just click on the charge and the legend appears. Click again and it goes away.
4. I also added a link to the Clear Sky Charge site page, so if I wanted more detailed information, I can get it there.

I hope a few Mac-owning astronomers in the U.S. and Canada find this widget useful.

• Aqua 10.4 Tiger (Universal)
• Aqua 10.5 Leopard (Universal)
• X11 10.4 Tiger (Universal)
• X11 10.5 Leopard (Universal)
• X11 10.5 Leopard (Universal) with Firewall

To quote the release notes on the SAOImage DS9 website, the changes in the newly released version 5.3 are

Regions: Regions now support a centroid function. The centroid function can be manually invoked or regions can automatically snap to a centroid when moved or edited. Regions now have a DASH line property.

Colorbar: Now supports a vertical colorbar layout option, via the View Menu. Users can configure the font type and size of the colorbar, via the View Menu.

GUI: Now supports a vertical button bar, when in vertical layout mode.

Aqua MacOSX 10.5 firewall: The MacOSX Aqua 10.5 Leopard port of DS9 can be used with the MacOSX 10.5 firewall enabled.

X11 MacOSX 10.5: There are now two versions available for X11 MacOSX 10.5 Leopard. The non-firewall version is recommended for all unless you wish to enable the 10.5 firewall. [Juan's Note: While not stating this, they mean specifically the application-specific version of the MacOS firewall. See my notes on this problem here.] In that case, please use the firewall enabled version. Please note: this version consist of 2 files, ds9 and ds9.zip. It is very important that ds9.zip be placed in the same directory as the ds9 binary at all times.

Contours: Contours now have a DASH line option.

I have previously posted notes for integrating upgrades of DS9 into the Scisoft OS X installation and they still work just fine except that newer releases of Scisoft OS X place the binaries in /Applications/scisoft/i386/bin/ instead of /scisoft/i386/bin/ and if you are installing the X11 binary that is compatible with the firewall, you have to install both the ds9 and ds9.zip file in the bin/ directory of Scisoft OSX.

should resolve a few outstanding problems created when changing the location of scisoft from /scisoft to /Applications/scisoft/. Packages such as MIDAS and Gnuplot should now work properly.

This version removes some remaining dependencies on the HPC OSX compilers, which I had on my machine but which most users do not have (and do not want to have).

I compared the /Application/scisoft/i386/Packages directory from this release of Scisoft OSX to the last one and there are no new packages installed. The few issues I noted with the Scisoft OSX 2008.8.1 release all appear to still be valid. Notably:

1. Permission Problems Persist: When the installer installs /Applications/scisoft, it appears that a bug in Apple’s Installer program triggers a change in ownership of the /Applications directory to that of the second user on the system. I strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using:
   

   sudo chown username:admin /Applications
   

   
   (where “username” is the primary administrative users username, in most cases, your username) to perform the repair.
2. ds9 command line executable missing: This release has the same glitch I noticed in version 2008.8.1 in that /Applications/scisoft/i386/bin doesn’t appear to have a ds9 binary installed. You can fix this by installing the X11 version of ds9 there or by linking to the Aqua version of ds9 that was installed using the command line
   

   ln -s "/Applications/scisoft/i386/Applications/SAOImage DS9.app/Contents/MacOS/ds9" /Applications/scisoft/i386/bin/ds9

I have placed a copy of this release in my Scisoft OSX Mirror in case the main Scisoft OSX repository gets bogged down.

There are a few changes in this version and all packages have been updated to the latest available versions. Starting with this version, Scisoft is installed in /Applications/scisoft (it previously was installed in /scisoft). Make sure that you remove any old /scisoft installation and properly update your startup files to source the Setup.csh or Setup.bash from their new locations.

In the README file you are told

Once the collection is successfully installed csh and tcsh users should invoke the command:

source /Applications/scisoft/all/bin/Setup.csh

to gain access to all the software and configure their environment correctly.

Users of the “bash” shell should instead use:

. /Applications/scisoft/all/bin/Setup.bash

Personally, to avoid problems in tcsh with a script breaking or with modifying my PATH multiple times by repeated execution of the Setup.csh script, I use the following line in my .tcshrc to first check for the existence of the Setup.csh script and SCISOFT environmental variables before executing it.

if (! $?SCISOFT) then
test -r /Applications/scisoft/all/bin/Setup.csh && source /Applications/scisoft/all/bin/Setup.csh
endif

Permission Problems Persist
This version addresses all the issues I noticed with Scisoft OSX 2008.5.1 except for one annoying one, the reassignment of ownership of the enclosing directory on installation. If you installed the old version of Scisoft OSX, it would reassign ownership of the root (/) directory to the second user on the system (in my case, since their is none, it showed the user as “502″). I beta-tested various versions of Scisoft OSX but Nor was not able to stamp out this particular problem. I believe Nor has come to the conclusion after extensive testing that this is a problem with Apple’s software for constructing installer packages. By moving the Scisoft OSX installation to /Applications/scisoft, it is the /Applications directory that gets its ownership changed instead of the root directory, which is less damaging. However, I would strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using:

sudo chown username:admin /Applications

(where “username” is the primary administrative users username, in most cases, your username) to perform the repair.

A Quick-Fix for any Legacy Scisoft-related scripts
If you had a few scripts that relied on Scisoft OSX being located in /scisoft and you don’t want to edit them all is you can make /scisoft point to /Applications/scisoft. This can be accomplished by first moving the old version of Scisoft OSX before installing 2008.8.1 via the command line:

sudo mv /scisoft /scisoft_old

and then once you have installed the new Scisoft OSX in 2008.8.1, create a symbolic link from the old location to the new by typing (again from the command line)

sudo ln -s /Applications/scisoft /scisoft

This will allow any scripts that refer to items in /scisoft to continue to work for the most part.

What’s New?
An investigation of the /Application/scisoft/i386/Packages directory as well as the NEWS file reveals the following changes to this version of SciSoft OSX over the 2008.5.1 version.

• DS9 updated from 5.1 to 5.3beta
  
• FV updated from 5.1 to 5.2.1
• ATLAS updated to version 3.8.2
• MIDAS updated to 08FEBpl1.1
• cdsclient was updated to version 2.87
• OpenMotif updated to 2.1.32_compat
• cfitsio library updaed from 3.090 to 3.090 (the current version is 3.100)
• pango library updated from version 1.20.2 to 1.21.3
• pixman library updated from 0.10.0 to 0.11.2
  
• expat library updated from 2.0.0 to 2.0.1
  
• fontconfig library updated from 2.3.2 to 2.6.0
• freetype library updated from 2.2.1 to 2.3.6
• gettext library updated from 0.14.5 to 0.17
• gtk+ updated from 2.12.9 to 2.12.10
• libpng library updated from 1.2.10 to 1.2.29
• netCDF library version 3.6.2 added
• pkg-config updated from 0.20 to 0.23
• TclTk package updated from 8.4.13 to 8.4.19
• wcstools library updated from 3.6.4 to 3.7.3 (current version is 3.7.5)
• IRAF package rvsao updated t version 2.5.7 to 2.6.4
• Python was updated to 2.5.2 and the following Python libraries were updated:
  
• • ScientificPython updated to 2.6.1

Minor Glitches
The only other minor glitch I noticed was that /Applications/scisoft/i386/bin doesn’t appear to have a ds9 binary installed. You can fix this by installing the X11 version of ds9 there or by linking to the Aqua version of ds9 that was installed using the command line

ln -s "/Applications/scisoft/i386/Applications/SAOImage DS9.app/Contents/MacOS/ds9" /Applications/scisoft/i386/bin/ds9

Unfortunately, there are very few “external” users of the Hectospec, so the software pipeline available for reducing Hectospec observations, called SPECROAD, was only geared to run on SAO computers. I spent a considerable amount of time last summer and this summer getting that software into a much more portable form, documenting how to use it, and removing bugs from the code.

All this work resulted in the creation of a new version of the Hectospec data pipeline I dubbed “External SPECROAD” or “E-SPECROAD” for short. There were several major problems with the original SPECROAD code that I addressed in E-SPECROAD:

1. Nonportability: The SPECROAD scripts were only designed to run on a Solaris computer at the SAO, with files in specific hard-coded locations using a specific IRAF environment with all the IRAF parameters set before the scripts were run. This has been addressed by trying to assume almost nothing about a user’s IRAF environment from the start except that they have the proper packages installed.
2. Lack of Documentation: The documentation for SPECROAD is frankly inadequate. It was an in-house tool for the SAO, so the publically-available documentation consists mostly of one webpage describing what the scripts do. I have now written up both an installation guide (because there are a lot of pre-requisite pieces of code to install) and a E-SPECROAD user’s guide.
3. No Installation Instructions: There were several IRAF packages to install (available here). The shell scripts required not only the installation of several IRAF packages and the compilation of several C programs, they used korn shell (ksh) which I was unfamiliar with. And, as I would also soon discover, the ksh installed on the Mac had serious bugs in its list handling. There is now a fairly compete installation guide laying out all the pre-requisites and addressing installations on both Macs and Linux boxes.
4. Undocumented Bugs: The available SPECROAD scripts had major bugs whose workarounds were undocumented and only available when I would email someone at the SAO to inquire about them. In one case, you had to know to actually break out of the script with Control-C, then run some of the reduction in IRAF, and then restart the script! E-SPECROAD has been fairly extensively debugged. It’s not bug free, but the exterminator has made some serious passes at the code.
5. Assumed Availability of Spectral Templates: The SPECROAD scripts typically relied on pre-set spectral line databases for different grating/central wavelength configurations instead of having the user exploit the IRAF identify command to build a database. E-SPECROAD is geared toward the user who is going to wavelength calibrate their observations by building the spectral line database for themselves.
6. Assumed Use of Low Resolution Spectra: The SPECROAD scripts were mostly pre-configured for working with 270gpm gratings and required some tweaking for 600gpm. E-SPECROAD can work with either configuration without editing the code.
7. Inconvienent Backups As Data Reduction Progresses: If one of the scripts executed by SPECROAD crashed, you had to dig around subdirectories to “backtrack” the changes before restarting the script. With disk space not an issue, I prefer monolithic backups of the entire data directory at certain key points in the data reduction pipeline. Since you may not like this form of backup (as they consume a lot of disk space), they are optional.

Today, I am posting E-SPECROAD online as a beta release along with installation instructions and a user’s guide. All the other external users of Hectospec I am aware of, all two of you, can enjoy or complain to me about this code. The ones I am unaware of are free to use the code as well.

As such, for now, since I prefer the X-windows version of SAOImage DS9, I am leaving the the Firewall off for now, I’m not too concerned.

The first one I noticed was the updating of Xquartz to version 2.3.0. Xquartz is the updated version of X11 for the Mac OS (even ahead of Apple’s own installed versions) that I prefer to use, largely because bug-fixes get rolled in here before they appear in Mac OS. This version requires Mac OS 10.5.4 and has a couple of caveats attached to it for programmers, notably:

The software supporting the deprecated imake build system is not provided in this package. If you need imake and xmkmf, please install the X11 package that came with your Leopard DVD before installing this version. Alternatively, you can compile these packages on your own or get them from a third party such as Fink or MacPorts. The darwin configuration files used by the imake build system are outdated and not supported. Developers using this build system are advised to migrate to autoconf.

[Added July 24, 2008: Apparently, this version of Xquartz changed the X11.app Icon so it now X11 looks like this

when it is on the Dock. Interesting, but it threw me for a second. The only documentation I found of this change is in a Ticket filed with XQuartz's bug reporting system. Still, I think this is a good idea, as it gives a visual cue that you are using XQuartz as opposed to the default X11 installation.]

Along with a bunch of library changes, the key update appears to be having the Xserver updated to the 1.4 branch of Xorg. There is also “support for adding new $DISPLAY sockets after the server is running” (which I think means using the DISPLAY variable will not break things) and “/usr/X11/bin/Xquartz is just a stub that will ‘do the right thing’,” whatever that means. I have upgraded to it and as a reminder, if you upgrade MacOS after installing Xquartz, you will need to reinstall Xquartz to get it back.

The other interesting software release for Mac-based astronomers I noticed today was SAOImage DS9 which has released version 5.3beta, which appears to be, based on the statement on their homepage that “MacOSX 10.5 users with firewall enabled, please use version 5.3 beta”, geared toward addressing the issue I noticed this April with version 5.2 where launching SAOimage DS9 with a certain firewall setting on the Mac could result in the the application becoming irreparably damaged at launch.

• Upgraded the freetype library to version 2.3.6, which fixes “A bunch of potential security problems have been found [and fixed in this release”
• Upgraded to pixman library to version 0.11.4.
• Xquartz fixes from xorg-server-1.3.0-apple21, the key fix being support for monitor hotplugging, although several security fixes also occurred.

Again, if you upgrade MacOS (say to version 10.5.4, which is supposed to be released soon in order to support iPhone G3 and MobileMe), you will likely need to reinstall Xquartz (unless Apple has upgraded their X11 installation to match Xquartz).

The latest update to Scisoft OSX is now available. This includes an update to Pyraf (v. 1.6), GSL, pygsl, Gunplot, and a few backend libraries.

I went ahead and decided to install it today to investigate the improvements. As is usually my procedure, I first moved the directory containing my functional SciSoft OSX install temporarily out of the way via the command line:

sudo mv /scisoft /scisoft_old

Having done that I double-clicked on the installer package and let it do its thing, installing everything in the /scisoft directory. I poked around a bit an realized almost immediately that /scisoft/i386/Applications directory was empty! This one is kind of a show stopper as it means DS9 and FV are unavailable. I copied the files back from the previous installation without too much of a hitch. I did check, the installer package file with Pacifist and it does appear to contain those files in it, so I am not sure why they didn’t appear to install. I hope this is an isolated incident and not a recurring issue with the installer.

Other minor glitches I noticed:

• I discovered that /scisoft/i386/Packages, /scisoft/NEWS and /scisoft/i386/share are set to have owner 502:502 instead of root:admin. This glitch is easily fixed by issuing the following command from the Terminal
  

  sudo chown -R root:admin /scisoft/

• I also noticed that in addition to the x11iraf-1.5DEV installation, the entire x11iraf-1.3.2 installation is still sitting in the /scisoft/i386/Packages directory. All the x11iraf binaries in /scisoft/i386/bin/ are linked to x11iraf-1.5DEV instead of the older 1.3.2 binaries. I suspect this is an oversight.

An investigation of the /scisoft/i386/Packages directory as well as the NEWS file reveals the following changes to this version of SciSoft OSX over the 2008.3.1 version.

• GSL updated from 1.9 to 1.11
• DS9 updated from 4.13 to 5.1 (The current version of SAOImage DS9 is actually version 5.2, you can read about how to update the SciSoft version of DS9 in this post)
• GNUPlot updated from 4.0.0 to 4.2.3
• Swarp updated from version 2.15.7 to 2.17.1
• WeightWatcher updated from version 1.7 to 1.8.7
• pyraf updated from version 1.3 to version 1.6
• The following Python libraries were updated:
• • pygtk updated from 2.8.6 to 2.12.1
  • matplotlib updated from 0.90 to 0.91.2
• atk library updated from 1.10.3 to 1.22.0
• cairo library updated from 1.1.6 to 1.6.4
• cfitsio library updaed from 3.040 to 3.080
• glib library updated from 2.8.6 to 2.16.3
• glib-1.2.10 library added as well (possibly for a particular package needing older version of library)
• gtk+ library updated from 2.8.19 to 2.12.9
• gtk+-1.2.10 library added as well (possibly for a particular package needing older version of library)
• pango library updated from version 1.10.4 to 1.20.2
• pixman 0.10.0 library added
• libtiff library upgraded from 3.7.4 to 3.8.2

Hats off to the SciSoft OSX folks for keeping this package up to date. I have placed a copy in my SciSoft OSX mirror in case there are any access issues.