Urania

I often have to tell people I live in “Fargo-Moorhead” before they have a clue where I live. But then they think I live in North Dakota. This is why I live on the Minnesota side of the Red River.

Nor Pirzkal has apparently been busy fixing the issues I noted in last month’s release of Scisoft OSX given his blog entry:

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 5.2.1and properly installed.
• HEASARC StudentHera.app was updated from version 5.1 to version 5.2.1and 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.

When I first started this blog, I was using Apple’s built-in X11, but then with the transition to MacOS 10.5, there were some serious issues with Apple’s X11 implementation having to do with the transition from X11R6 to X.org. One of Apple’s programmers started putting out bleeding-edge updates to Apple’s X11 called XQuartz that fixed a lot of the programs and I have kept using it ever since.

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.x11

   NOTE: 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

     T>his 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.

This first Scisoft OSX release of 2009 has appeared. Despite the brief entry on the VersionTracker website which said that this update rolled in the recently released STSDAS and TABLES IRAF package updates. from reviewing the CONTENTS file distributed with the install, I found Nor Pirzkal made quite a few additional updates in this release. The changes from Scisoft OSX 2008.9.1 are:

• 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.

I just noticed that the XQuartz folks released X11 2.3.3, but when I attempted to install it, it said I needed Mac OS 10.5.7 installed, which hasn’t been released yet. I have confirmed this on the release notes page. The full release notes seem to describe to major changes, updated support for OpenGL and some bug fixes regarding Caps Lock and mouse tracking.

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.]

There are some older school astronomers on Macs who cut their teeth on Linux and as such really prefer the full-screen X-Windows display for running astronomical data reductions. This way of running X11 has been unavailable since MaxOS 10.5 (which switched from X11 code bases). Well, to quote Macros Huerta’s MacSingularity Blog:

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.

I have been a very happy user of Papers for organizing downloaded Journal articles for about a year. The program, by the Dutch software firm Mekentosj BV, makes it easy to search for journal articles on ADS and arXiv (although the arXiv support seems a bit twitchy at times), download them, and place them into a searchable database. The program does occasionally show is roots as a biomedical oriented tool, but it functions very well for this astronomer.

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.

We have had a very cold winter this year. We had one cold snap in December where the nighttime lows dropped to -25 Fahrenheit (that’s -31 Celsius for the rest of the world). However, this new cold snap has been a bit more brutal with daytime highs of about -13 Fahrenheit (-25 Celsius) for the last 4 days. It was so cold yesterday morning (January 15, 2009) here in Moorhead that the temperature at the Moorhead airport dipped to -31 Fahrenheit (-35 Celsius) at 8:14am. At our house in town, the thermometer failed.

It listed the outdoor temperature as “OFL” which means “Off Low End” (I think)… so it was colder than -25 Fahrenheit (-32 Celsius). For fun, the kids and I went outside and decided to throw hot tap water into the air to create clouds. When you throw hot water into air that is this cold, it instantly vaporizes, forming a cloud. The video of it isn’t the clearest, but I think it is pretty cool.

On YouTube I found “Sharon in Minnesota” used extremely hot water from a tea kettle and a spray gun, which makes the droplets much smaller and thus gives you a much clearer cloud.

Finally, a much clearer video of the phenomenon with a simple glass of hot water comes from this poor soul in Alaska where they are dealing with weather about 20 degrees colder than us.

I believe what is happening is an extreme form of what happens to your breath becoming visible on a cold day. The water when thrown suddenly gets a relatively large surface area (allowing cooling) and is scattered into small droplets. These droplets have enough energy to transition to a more solid state, which gives us a visible cloud of tiny particles of ice. A few of the larger drops make it to the ground. I’d appreciate some clarification.

I just upgraded the software on this blog to WordPress 2.7. The major new feature I am interested in is automatic upgrading, which could prove quite a time saver. Unfortunately, this automatic upgrading uses only FTP (which is totally insecure) or FTPS (which requires me to set up an SSL certificate).

I noticed that the WordPress code had ssh2 support built-in, so all I need to is activate SSH2 support in the MacPorts installed PHP and I should be able to use SFTP in WordPress to handle the upgrades. I poked around and found this posting outlining the process for adding ssh2 support to Ubuntu. It guided me in developing this list of hints:

1. Start by installing libssh2 via MacPorts using the command:
   

   sudo port install libssh2
   

2. Once it is activated, link the libssh and PHP together using the PECL module SSH2. Unfortunately, directly installing the module with PECL under MacPorts is troublesome, so I just used PECL to download the module.
   

   pecl download ssh2
   

   triggered the following error (since ssh2 is apparently beta),
   

   Failed to download pecl/ssh2 within preferred state "stable", latest release is version 0.11.0, stability "beta", use "channel://pecl.php.net/ssh2-0.11.0" to install
   Cannot initialize 'ssh2', invalid or missing package file
   Package "ssh2" is not valid
   download failed
   

   so I used
   

   pecl download channel://pecl.php.net/ssh2-0.11.0
   

   as suggested and was able to download the PHP library for SSH2. Once the download was complete, I started on the standard compilation sequence for a PHP library
   

   tar xzvf ssh2-0.11.0.tgz
   cd ssh2-0.11.0
   phpize
   ./configure --with-ssh2=/opt/local
   make
   sudo make install
   

   The final command informed me the ssh2.so library was placed in /opt/local/lib/php/extensions/no-debug-non-zts-20060613/
3. Now you need to make sure PHP loads the new module, so we open the PHP configuration file /opt/local/etc/php.ini and edit the extension_dir line to point the extension directory above:
   

   extension_dir = "/opt/local/lib/php/extensions/no-debug-non-zts-20060613/"
   

   and then add the following line to the end of the section on “Dynamic Extensions”:
   

   extension=ssh2.so
   

   If you edited everything properly, a simple php -v from the command line should NOT trigger any errors.
4. Finally, I restart the apache2 server so that the reconfigured PHP is loaded using
   

   sudo /opt/local/etc/LaunchDaemons/org.macports.apache2/apache2.wrapper restart
   

   At this point, I checked (via the phpinfo(); command to see if the web server was supporting SSH. Near the bottom of the phpinfo(); listing is a listed of “Registered PHP Streams”. As noted here, it should incude “ssh2.shell”, “ssh2.exec”, “ssh2.tunnel”, “ssh2.scp”, and “ssh2.sftp”. If it does, you have enabled SSH support for Apache2 driven PHP pages under MacPorts.
5. If you are doing this to get WordPress 2.7 automatic installation working, you will notice now when the automatic installation dialog box pops up, in addition to ftp and ftps, you now have an ssh option.
   

6. Now that I got this working, I’ll just have to keep an eye out for any future MacPort updates to PHP and make sure they don’t overwrite the

   /opt/local/etc/php.ini

   file or the extensions directory where I installed ssh2.

There is a problem with libxml2 from version 2.7.1 onward where it completely deletes any greater than (>) and less than symbols (<) sent to it. This is messing up my blog posting unless I do it within the WordPress interface since attempts to use xmlrpc.php use PHP, which is compiled against libxml2, and thus the posting gets mangled.

The solution suggested on the PHP boards is to compile PHP against expat. This would be kind of a pain for me since I am using the MacPorts install of PHP. So I looked into rolling back to an earlier version of libxml2 using MacPorts. The solution was originally outlined in this blog post by Stephen Chu on how to install earlier versions of ruby under DarwinPorts, I have updated it for MacPorts. The key is to create a local MacPorts repository with the version of the port you want copied over to it.

1. First I identified the version of the libxml2 portfile I wanted by going to http://trac.macports.org/browser/trunk/dports/textproc/libxml2/Portfile and entering revisions into the “View revision” box until I found the appropriate version of the Portfile linking to libxml2 2.6.32 instead of 2.7.1. This turned out to be revision 40211 (actually 39551).
2. I created a directory to contain my MacPorts repository at /Users/Shared/dports/ and after creating that directory, I edited the MacPorts configuration file /opt/local/etc/macports/sources.conf to include the line:

   file:///Users/Shared/dports

   and you should make this line appear before the “rsync” or svn” port listing in the config file, otherwise it defaults to using that version of the port during the install.

3. I then installed the old libxml2 port into my local MacPorts respository using subversion:

   svn co --revision 40211 http://trac.macports.org/browser/trunk/dports/textproc/libxml2/ textproc/libxml2/
   

   and then I updated the MacPorts index:

   portindex /Users/Shared/dports

   With this done, I can see the two versions of libxml2 in my ports list, when I issue a

   port list libxml2

   the result is:

   libxml2 @2.7.2 textproc/libxml2 libxml2 @2.6.32 textproc/libxml2

   showing the current libxml2 version in MacPorts and the older one in my repository.

4. Now I can install the older version of libxml2 by first forcing removal of the current version and then installing the old version:

   sudo port -f uninstall libxml2 @2.7.2_1+darwin_9 sudo port install libxml2 @2.6.32

   [Warning: Unless you place the file:///Users/Shared/dports line before any rsync/svn lines of the config file noted in step 2, this port install command installs the current version instead of the old version]

5. I had to forcible uninstall and then reinstall libxslt but then my reinstall of php within MacPorts went fine. And I can now use WordPress again without any issues when using a remote blog editor.

I just figured in case anyone else wanted to use an older MacPort port they could use this to figure out how.

FreeType issues under Leopard Resolved: The MacPorts installation of FreeType will now compile a version under Leopard that does NOT throw a

The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec().
Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__() to debug.

error when fonts are used in PHP routines (fuller notes on this problem here although with my “hacked” fix, which is no longer needed). This problem as originally reported under Trouble Ticket #15909 on MacPorts.

Careful with that Apache2 upgrade, Eugene: I also discovered I have to be careful when updating apache2 under MacPorts in that it actually wiped out some of the configuration files stored in /opt/local/apache2/conf/, specifically it overwrote my modified versions of the /opt/local/apache2/conf/extra/httpd-dav.conf file and /opt/local/apache2/conf/extra/http-userdir.conf files. So now I am keeping copies of everything in /opt/local/apache2/conf backed up so I can roll back my changes after an upgrade of apache2 in MacPorts.

Fast on the heals of their release of version 5.3 about two weeks ago, the folks at the SAO have released version 5.4 of SAOImage DS9. Here are the links to the downloadable Mac-related SAOImage files

• 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.