Urania

One of the packages I use a lot in my research is the venerable PGPLOT package put together by Tim Pearson (currently at Caltech). You see evidence of this set of plotting routines in the figures in many astronomy papers from the 1980s onward. PGPLOT was written in FORTRAN and supports a wide variety of drivers to export its graphics, including color postscript, GIF, and Xwindows displays. In addition to using PGPLOT, I use PGPLOT.pm, a perl module for calling PGPLOT from perl scripts written by Karl Glazebrook.  I have used it to make interactive perl scripts for ‘marking’ spectral lines in HI spectra among other things.

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.

This is an upgraded tutorial to getting SSH2 support under PHP 5.3.0 that I wrote a while back. Getting SSH2 support in PHP is useful for maintaining WordPress blogs. It would be nice if such an extension were not necessary, but this is the only way WordPress supports SSH administration through their web interface.

The big difference is that I will now be using the built-in Apache2 and PHP 5.3.0 under MacOS 10.6.1. I have gotten tired of the fact that everytime MacPorts updates it PHP installation, it tends to clobber the php.ini file for the site, requiring me to re-setup everything. Furthermore, I am also a bit tired of having MacPorts install its own version of everything I already have under MacOS X (such as Apache2, PHP, and MySQL). I understand their philosophy (and the practicality of it), but I am trying to keep my computer as clean as possible. As such, I am only using MacPorts to provide libssh2 to the SSH2 extension for PHP.

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. If you haven’t already, start by installing libssh2 via MacPorts using the command:
   

   sudo port install libssh2

2. Download the necessary SSH2 PHP extension using the build in PECL command
   

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

   The sudo is necessary because a lock file needs to be created during the download in /usr/lib/php, which is a protected directory. However, the file is downloaded to the current directory. Once the download is complete, we will need to unpack the SSH2 extension and go into its directory:
   

   tar xzvf ssh2-0.11.0.tgz
   cd ssh2-0.11.0

   If you try to do the normal phpize/configure/make sequence for compiling PHP extensions at this point, you will get a string of error messages ending with something like
   

   /private/var/tmp/apache_mod_php/apache_mod_php-53~1/Build/tmp/pear/download/ssh2-0.11.0/ssh2.c:1105: warning: passing argument 4 of 'add_assoc_stringl_ex' discards qualifiers from pointer target type

   
   This is occuring because there is an incompatibility between this ssh2 extension code and PHP 5.3.0. It can be patched by downloading the ssh2-php53.patch file from http://remi.fedorapeople.org/ssh2-php53.patch and applying the patch from the command line in the ssh2-0.11.0 directory
   

   curl -o ssh2-php53.patch http://remi.fedorapeople.org/ssh2-php53.patch
   patch < ssh2-patch53.patch

   Once you have done that, you can finish the SSH2 PHP extension compilation using
   

   phpize
   ./configure --with-ssh2=/opt/local
   make
   sudo make install

   The final command informed me the ssh2.so library was placed in /usr/lib/php/extensions/no-debug-non-zts-20090626/

3. Now you need to make sure PHP loads the new module, so we open the PHP configuration file /etc/php.ini and edit the extension_dir line to point the extension directory above:
   

   extension_dir = "/usr/lib/php/extensions/no-debug-non-zts-20090626/"

   
   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 apachectl 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.

Nor Pirzkal has released another minor update to Scisoft OSX. He states in his blog that:

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