University of Glasgow

Roderic Page

![winebottler.png](http://lh3.ggpht.com/_Gct8lVAxKqQ/TAvXvzjMYUI/AAAAAAAAAqo/wEJNi0Q0NbI/winebottler.png?imgmax=800){border="0"
width="128" height="128" align="right"}  
In an [earlier
post](http://iphylo.blogspot.com/2009/08/nexus-data-editor-and-windows-vista.html)
I expressed my amazement that my venerable [Nexus Data
Editor](http://taxonomy.zoology.gla.ac.uk/rod/NDE/nde.html) (NDE) still
had users, meaning I had to rebuild the installer so users could install
NDE on Windows Vista. Now, Thomas Hauser has gone one better and created
an installer for Mac OS X. Given that NDE is a Windows-only program,
this is quite a feat. Thomas uses Mike Kroenenberg\'s
([@k3erg](http://twitter.com/k3erg))
[WineBottler](http://winebottler.kronenberg.org/) to create a version of
NDE that can be run on a Mac. WineBottler builds on
[Wine](http://en.wikipedia.org/wiki/Wine_(software)), which enables
Windows software to run on Unix-like operating systems.  
  
To run NDE on a Mac, first download WineBottler from
<http://winebottler.kronenberg.org/> and install. Then grab the file
[NDE.dmg](http://dl.dropbox.com/u/582882/NDE.dmg) Thomas has created.
Install the file NDE in your Applications file and run it. Note that you
will need X11 installed on your Mac. If you don\'t have this it should
be on the installation disk that came with your computer. After a short
pause you should see NDE appear in a X11 window. Below is a screen shot
showing NDE editing the example file (Bembidion.nex) that comes with the
program:  

::: {style="text-align:center;"}
![ndemac.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/TAvcxUiIj5I/AAAAAAAAAqw/Hu85swtmvCQ/ndemac.png?imgmax=800){border="0"
width="400"}
:::

  
Many thanks to Thomas for his efforts in packaging NDE with Winebottler,
and for making available the NDE.dmg file he created.


In an earlier post  I expressed my amazement that my venerable Nexus Data Editor (NDE) still had users, meaning I had to rebuild the installer so users could install NDE on Windows Vista. Now, Thomas Hauser has gone one better and created an installer for Mac OS X. Given that NDE is a Windows-only program, this is quite a feat. Thomas uses Mike Kroenenberg's (@k3erg) WineBottler to create a version of NDE that can be run on a Mac.

Nexus Data Editor running on Mac OS X

Thinking about ways to improve the performance of some of my web servers
I\'ve begun to toy with Memcached. These notes are to remind me how to
set it up (I\'m using Mac OS X 10.5, Apache 2 and PHP 5.2.10, as
provided by Apple). Erik\'s blog post [Memcached with PHP on Mac OS
X](http://af-design.com/blog/2008/10/18/memcached-with-php-on-mac-os-x/)
has a step-by-step guide, based on the post [Setup a Memcached-Enabled
MAMP Sandbox
Environment](http://www.lullabot.com/articles/setup-memcached-mamp-sandbox-environment)
by Nate Haug, and I\'ve basically followed the steps they outline.  

1.  **Install the Memcached service on Mac OS X:** Follow the
    instructions in Nate Haug\'s
    [post](http://www.lullabot.com/articles/setup-memcached-mamp-sandbox-environment).

2.  **Install Memcache PHP Extension:** Apple\'s PHP doesn\'t come with
    the PECL package for memcache so [download
    it](http://pecl.php.net/package/memcache). To compile it go:  

        phpize
        ./configure
        make
        sudo make install

      
    One important point. If you are running 64-bit Mac OS X (as I am),
    ./configure by itself won\'t build a usable extension. However, [a
    comment by
    Matt](http://af-design.com/blog/2008/10/18/memcached-with-php-on-mac-os-x/#comment-719)
    on Erik\'s original post provides the solution. Instead of just
    ./configure, type this at the command prompt:  

    ::: {style="font-family:Courier;font-size:12px;"}
      
    MACOSX_DEPLOYMENT_TARGET=10.5 CFLAGS=\"-arch ppc -arch ppc64 -arch
    i386 -arch x86_64 -g -Os -pipe -no-cpp-precomp\" CCFLAGS=\"-arch ppc
    -arch ppc64 -arch i386 -arch x86_64 -g -Os -pipe\" CXXFLAGS=\"-arch
    ppc -arch ppc64 -arch i386 -arch x86_64 -g -Os -pipe\"
    LDFLAGS=\"-arch ppc -arch ppc64 -arch i386 -arch x86_64
    -bind_at_load\" ./configure
    :::

      
      
    Then follow the rest of Erik\'s instructions for adding the
    extension to your copy of PHP.

3.  **Restart Apache:** You can do this by restarting Web sharing in
    System preferences. Use the
    [phpinfo();]{style="font-family:Courier;"} command to check that the
    extension is working. You should see something like this:  

    ::: {style="text-align:center;"}
    ![memcache.png](http://lh3.ggpht.com/_Gct8lVAxKqQ/Stm5R4EuiFI/AAAAAAAAAkc/jlbYMibXRYQ/memcache.png?imgmax=800){border="0"
    width="380"}
    :::

      
    If you don\'t see this, something\'s gone wrong. The Apache web log
    may help (for example, that\'s where I discovered that I had the
    problem reported by several people who commented on [Erik\'s
    post](http://af-design.com/blog/2008/10/18/memcached-with-php-on-mac-os-x/).

4.  You can start the memcached daemon like this:  

        # /bin/sh
        memcached -m 1 -l 127.0.0.1 -p 11211 -d

  
Now, I just need to explore how to actually use this\...


Thinking about ways to improve the performance of some of my web servers I've begun to toy with Memcached.

Memcached, Mac OS X, and PHP

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2q_M2pIIbG8jOStxkt1tcWbmXcYjxMlN0iQptRglKVJAWLL7_VgcGRdchOwBj7T69yIfCirprynA1Bz2dVMyAg8mXgEUOODhKciGtThdoan2ZTBMf37qow4wbc6NSgVymMJC3/s320/sun.sparcstation5.12.jpg){#BLOGGER_PHOTO_ID_5126087534069653298
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"
width="200"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2q_M2pIIbG8jOStxkt1tcWbmXcYjxMlN0iQptRglKVJAWLL7_VgcGRdchOwBj7T69yIfCirprynA1Bz2dVMyAg8mXgEUOODhKciGtThdoan2ZTBMf37qow4wbc6NSgVymMJC3/s1600-h/sun.sparcstation5.12.jpg)  
No, not taxonomy the discipline (although I\'ve [given a
talk](http://iphylo.blogspot.com/2005/12/google-yahoo-and-end-of-taxonomy.html)
asking this question), but
[taxonomy.zoology.gla.ac.uk](http://taxonomy.zoology.gla.ac.uk/), my
long-running web server hosting such venerable software projects as
[TreeView](http://taxonomy.zoology.gla.ac.uk/rod/treeview.html),
[NDE](http://taxonomy.zoology.gla.ac.uk/rod/NDE/nde.html), and
[GeneTree](http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html),
along with my [home
page](http://taxonomy.zoology.gla.ac.uk/rod/rod.html).  
  
A series of power cuts in my building while I was away finally did for
my ancient Sun Sparcstation5, running the CERN web server (yes, it\'s
**that** old). I can remember the thrill (mixed with mild terror) of
taking delivery of the Sparcstation and having to manually assemble it
(the CD ROM and floppy drives came separately), and the painful
introduction to the Unix command line. The joy of getting a web server
to run (way back in late 1995), followed by Samba, AppleTalk, and CVS.  
  
For the time being a backup copy of the documents and software hosted on
the Sparcstation are being served from a Mac. The only tricky thing was
setting up the CVS server that I use for version control for my
projects. Yes, I know CVS is also ancient, and that [Linus Torvalds will
think me a moron](http://www.youtube.com/watch?v=4XpnKHJAok8), but for
now it\'s what I use. CVS comes with Apple\'s developer tools, but I
wanted to set up remote access. I found the articles by Daniel Côté
[Setting up a CVS server on Mac OS X](http://www.novajo.ca/cvs.html) and
on Mac OSX Hints [Enable CVS pserver on
10.2](http://www.macosxhints.com/article.php?story=20020918055124794) to
be helpful. Basically I initialised a new CVS repository, then copied
across the backed repository from a DVD. I then replaced some files in
CVSROOT that listed things like the modules in the repository and
notifications sent when code is comitted. Getting the pserver up and
running required some work. I created a file called cvspserver inside
/etc/xinetd.d/, with the following contents.  
  

``` {style="border: 1px solid #c7cfd5;background: #f1f5f9;padding:15px;"}
service cvspserver
{
        disable = no
        socket_type     = stream
        wait            = no
        user            = root
        server          = /usr/bin/cvs
        server_args     = -f --allow-root=/usr/local/CVS pserver
        groups          = yes
        flags           = REUSE
}
```

  
Then I started the service:  

``` {style="border: 1px solid #c7cfd5;background: #f1f5f9;padding:15px;"}
sudo /sbin/service cvspserver start
```

  
So far, so good, but I couldn\'t log in to CVS. Discovered that this is
because [Mac OS X uses ShadowHash
authentication_authority](http://www.macosxhints.com/comment.php?mode=display&format=threaded&order=ASC&pid=32077).
Hence, on a Mac CVS won\'t use the system user names and passwords
(probably a good thing). Therefore, we uncomment the line  

``` {style="border: 1px solid #c7cfd5;background: #f1f5f9;padding:15px;"}
# Set this to "no" if pserver shouldn't check system users/passwords
SystemAuth=no
```

  
in the file CVSROOT/config, then create a file CVSROOT/passwd. This file
contains the username, hash password, and the actual Mac OS X username
(nicely explained in [Daniel Côté\'s
article](http://www.novajo.ca/cvs.html)). To generate a hash password,
do this:  
  

``` {style="border: 1px solid #c7cfd5;background: #f1f5f9;padding:15px;"}
darwin: openssl passwd
Password: 123
Verifying - Password: 123
yrp85EUNQl01E
```

  
At last it all seems to work, and I can get back to coding. This is
about as geeky as this blog gets, but if you want a real geek overload,
spend some time listening to this talk by Linus Torvalds.  
  


No, not taxonomy the discipline (although I've given a talk asking this question), but taxonomy.zoology.gla.ac.uk, my long-running web server hosting such venerable software projects as TreeView, NDE, and GeneTree, along with my home page.A series of power cuts in my building while I was away finally did for my ancient Sun Sparcstation5, running the CERN web server (yes, it's
<b>
 that
</b>
old). I can remember the thrill (mixed with mild terror)

Taxonomy is dead, long live taxonomy

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuxEZ6JGUwLNcr1J_JgCKOOiKxReuYkIl-vny13DPXiDoSu1iHrbInrTU9OsOJKdtyDYJ_OYkFOhrhFDyRYrI6c4-4yIHJJikRplUla4UvmzEP__zEvIdfvIfGzZMHHnTK-d5n/s320/Parallels.jpg){#BLOGGER_PHOTO_ID_5111962867581410562
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuxEZ6JGUwLNcr1J_JgCKOOiKxReuYkIl-vny13DPXiDoSu1iHrbInrTU9OsOJKdtyDYJ_OYkFOhrhFDyRYrI6c4-4yIHJJikRplUla4UvmzEP__zEvIdfvIfGzZMHHnTK-d5n/s1600-h/Parallels.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Quick note to say how much fun it is to use [Parallels
Desktop](http://www.parallels.com/). It\'s a great advantage to have
Windows XP and Fedora Core 7 running on my Mac. As much as I dislike
Internet Explorer, it caught some bugs in my code. It\'s always useful
to try different environments when debugging code, either stand alone or
for the Web.


Quick note to say how much fun it is to use  Parallels Desktop. It's a great advantage to have Windows XP and Fedora Core 7 running on my Mac. As much as I dislike Internet Explorer, it caught some bugs in my code. It's always useful to try different environments when debugging code, either stand alone or for the Web.

Publicaciones de Rogue Scholar

Nexus Data Editor running on Mac OS X

Memcached, Mac OS X, and PHP

Taxonomy is dead, long live taxonomy

Parallels