Urania

I am having an interesting problem. In my last post, I noted that on some Macs with Leopard installed, deactivating the lines calling /usr/libexec/path_helper in the /etc/profile file fixed LaTeXit hanging at launch. A bit more investigation by Antonio Molins (posted in the comments to that post) revealed it was possible to add an ASCII file in the /etc/paths.d directory. We could create a file called /etc/paths.d/macports containing the only the line

/opt/local/bin

and it should automatically add everything in macports to most user’s PATH variables. However, when I tried this, all my calls to /usr/libexec/path_helper -s always locked up the command.

Some further investigation revealed new user accounts on my Macs didn’t have this problem. I surmised that since I was setting up the PATH and MANPATH variables in my environment at login, that this could apparently lock up path_helper. Since I use tcsh by default (instead of Apple’s default bash shell), I issued the following two commands from the command line

unsetenv PATH
unsetenv MANPATH 

and sure enough path_helper worked without an issue. So something is buggy in path_helper, or at least hypersensitive to pre-existing PATH environmental variables. I’ll have to investigate this more later. One thing I did discover is that

/usr/libexec/path_helper -c 

will produce the commands to set up tcsh’s environment.

/usr/libexec/path_helper -s 

returns those for the default bash shell.

[A better fix to this problem is to upgrade to LaTeXit 1.15, which was released on April 16, 2008.  It fixes the problems with Leopard and allows you to keep the default /etc/profile file for Leopard.]

Apparently, LaTeXIt, which I use to generate equations with Latex which can then be copied into Apple’s Keynote and Pages documents, locks up on launch a vanilla install of Leopard. This post on MacOSXHints.com provides a hack, but it wasn’t that nice, since it involves re-installing a particular version of latex. It turns out the solution was really much simpler and shows up in the comments on that page. In the comments, user Paolo Bosetti notes that

There is actually a much easier workaround: simply change your /etc/profile commenting the following lines (add the “#” at the begining):

# if [ -x /usr/libexec/path_helper ]; then
# eval `/usr/libexec/path_helper -s`
# fi

and adding the following two:

PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/local/bin:/usr/X11/bin"
export PATH

Why so? Apple changed the Leopard way to set the PATH variable, and now it uses the /usr/libexec/path_helper command, which seems having troubles with LaTeXiT spawned bash scripts. If you make this modification to your /etc/profile, you are simply dropping the new path_helper in favour of the plain old way to set the PATH variable.

This also explains why I wasn’t seeing this on my laptop, since it kept the old /etc/profile file during the upgrade.

Another user comments that the fix could also be done without hacking the /etc/profile but instead just changing ~/.profile such that /opt/local/bin appears in the path last, since /usr/libexec/path_helper is supposed to read ~/.profile. However, I was unable to get this approach to work.

Since switching to Leopard on my server earlier this week, I have noticed that file transfers over the Ethernet LAN at work are insanely slow. I frequently synchronize files (over AFS File Sharing) over an Ethernet LAN between my server and my MacBook Pro. My MacBook Pro has been running Leopard for several months while my server was running MacOS 10.4.11 until this week. Having been happy with Leopard on my MBP, I decided to upgrade my server. Since then, file transfers between the two computers have been a royal disaster. When I initially connected I was getting speeds of up to 1.5 MB/s, but it quickly drops to 30KB/s or less. This was much less than the 10MB/s speeds I was typically seeing before upgrading my server to Leopard. I couldn’t quite figure out the pattern. It did seem the speed uploading files to my server was not as affected as downloading from my server.

Given the fact I didn’t see any file transfer issues between the two computers before upgrading the server to Leopard (MacOS 10.5.2), I suspected the issue was solely with the server (or possibly due to the communication between two computers running Leopard). On a hunch that the “self-tuning” networking heralded (quietly) on Apple’s Leopard Features page might be the problem, I tried to turn it off by tinkering with the “Advanced” settings in the Network Preference Pane. Specifically I changed the settings to look like this:

Notably, I forced the configuration to be manual (instead of “Automatic”), I set the “Speed” to “100BaseT” which is my LAN’s speed (instead of “autoselect”), and I set the “Duplex” to “full-duplex” without “flow control”. I left the “MTU” at “Standard (1500)”.

Making these changes seems to have done the trick. For the last hour my network has maintained speeds of about 10 MB/s on download, something it hasn’t been able to do for the last few days. I suspect Apple has some work to do on their “self-tuning” Network code.

[Followup Post: Yes,this pretty much fixes my network slowdowns. I just did some Bandwidth tests online, I'm back up to my pre-Leopard speeds.]

There is a great article online at Scientific American’s website investigating the claim that Arthur Eddington and Frank Dyson might have “cooked” the data from their solar eclipse observations in 1919 in a way that supported Einstein’s (then new) General Theory of Relativity:

On May 29, 1919, two British expeditions, positioned on opposite sides of the planet, aimed telescopes at the sun during a total eclipse. Their mission: to test a radical theory of gravity dreamed up by a former patent clerk, who predicted that passing starlight should bend toward the sun. Their results, announced that November, vaulted Albert Einstein into the public consciousness and confirmed one of the most spectacular experimental successes in the history of science.

In recent decades, however, some science historians have argued that astronomer Sir Arthur Eddington, the junior member of the 1919 expedition, believed so strongly in Einstein’s theory of general relativity that he discounted data that clashed with it. [From Fact or Fiction: Did Researchers Cook Data from the First Test of General Relativity?]

The nice thing is this article illustrates one of the less well-appreciated challenges facing the functional scientist: distinguishing between bad data and data that conflicts with your theoretical expectations. Bad data, like other things in life, just happens. And when it happens, it can be a pain to deal with. How do you know when the data is “bad” (that is, the result of a problem at the telescope or a glitch in your software) versus when the data simply conflicts with your theory? In one case, getting rid of the data makes sense. However, being over-eager to reject conflicting data may make you reject a completely compatible alternative interpretation to your observation. Furthermore, if your data seem to support a controversial theory, you should be fairly confident your results are not the result of “bad” data. As Carl Sagan said in Cosmos , “Extraordinary claims require extraordinary evidence.” You have to be pretty confident you haven’t made a mistake if your data strays far from what you expect. Knowing the difference between “bad” data and data that supports a different theory the human part of the science I try to teach my students about. It is also the reason peer-review is such an incredibly important part of the scientific process.

By the way, the verdict of the article’s author is that Eddington and Dyson did the right thing. It turns out it was actually Dyson, who was initially inclined against Einstein’s theory, who made the decision to toss the bad data out. The final results when published^[1] supported Einstein’s General Theory of Relativity, which still stands as the most well-supported model for gravitation to this day.

The nice thing about MacOS X 10.5 Leopard is that it comes with PHP 5.2.4 pre-installed. Unfortunately one of the features Apple choose not to compile in was support for the GD graphics library, which I use extensively. Furthermore compiling in new features has proven to be somewhat troublesome. When I tried to configure PHP 5.2.5 on my Leopard box which the following commands (a variant of the configure command I would issue under Tiger with no complaints):

The result was a failed configure due to an error in mysql configuration. I pinned this down to a request for a library at /usr/local/mysql/lib/mysql/libmysqlclient.15.dylib which is actually located one directory up. This can be fixed via the command line using:

cd /usr/local/mysql/lib
mkdir mysql
cp libmysqlclient.15.dylib mysql/libmysqlclient.15.dylib

Then the ./configure worked just fine. Unfortunately, when I did a

make
make test

to compile the PHP and test it, there was no happiness. There were over 50 errors, some of them major. Crud. This is just the setup. See, all I needed was GD graphics library support in PHP for my website. Well, after googling for some time for some master hacker’s notes on getting PHP 5.2.5 to compile on Leopard, I discovered a fellow named Hill Pei had hacked GD support into the Leopard PHP without too much effort. His method simply requires some comfort with the command line and editing text files. In five minutes, I had GD support with Leopard’s built-in PHP. Excellent! [Despite a report in the comments to the contrary. This still appears to be necessary if you apply Security Update 2008-002, which installs PHP version 5.2.5. In which case, you should grab the php 5.2.5 code and work from there. I can confirm Hill Pei's instructions do work after Security Update 20008-002 if you grab the PHP-5.2.5 code instead of 5.2.4 as he suggests.]

I have taken part of my day to get my main web server upgraded to MacOS X 10.5 (aka Leopard). I spent quite a bit of time waiting, removing programs I knew were incompatible, and so on. Still, this upgrade was not without a few bumps:

• Check Hardware Compatibility: My Sonnet Tempo SATA X4P card (which I use to provide an external SATA [eSATA] interface for my RAID of data drives) was incompatible with Leopard and would cause the installer to hang. I finally discovered a firmware upgrade was available that fixed this. This was a stupid rookie mistake. Rule of Thumb: Always check the non-Apple hardware for updates before making a major OS X upgrade.
• Watch out for /home: I had been using a symbolic link from /home to /Users because in my old Unix days, I hardcoded a lot of my software to look for my home directory in /home. Leopard expects /home to be available as mount point for the automount service, so getting with the modern era and not relying on /home to point to /User is required if you adopt Leopard.
• Rebuild Web Server Configuration: One problem I was prepared for is that the web server was updated to Apache2. This in itself was not bad, but the configuration files for Apache (version 1) were stored in /etc/httpd and the new configuration files for Apache2 are in /etc/apache2 and they were NOT migrated. I don’t fault Apple for not migrating the files, but I kicked this around on my laptop quite a bit in order to tweak the configuration files back to something I liked. One thing I immediately did was that this MacOS comes with PHP 5.2.4 preinstalled, but not enabled in Apache2. I enabled it by editting the /etc/apache2/httpd.conf file (which you might have to create) and uncommenting the line with # LoadModule php5_module (by removing the ‘#’ symbol from the beginning of the line). Once that was done, I restarted the Apache2 server and all my PHP code (including this blog) was running again.
• Tweak MySQL for Leopard: The PHP 5.2.4 included with MacOS X is compiled with support for MySQL. This is nice in that you can just download the MySQL package installer and quickly get a LAMP server running. However, it was set up with the MacOS X Server version of MySQL in mind, which means it expects the socket to be in a different location than the vanilla MySQL. This can be solved by either tweaking the MySQL configuration (as outlined in the MySQL section of the blog post at http://remysharp.com/2007/10/27/lamp-in-leopard-osx-105-php5-and-apache-22/ ) or by tweaking the PHP configuration by editing the /etc/php.ini file (if it doesn’t exist, first copy /etc/php.ini.default to /etc/php.ini) and search for the line containing mysqli.default_socket = to read
  

  mysqli.default_socket = /private/tmp/mysql.sock
  

  This solution seemed more straight forward, so I did this.
• Reinstall MacPorts: Since I am aficionado of MacPorts, I reinstalled it and rebuilt all the ports. Some of the issues I had before with MacPorts on Leopard on my MacBook Pro cropped up again on my PowerMac G5, notably
• • gv still needs to be patched as I noted here.
  • sqlite3 still does know about its dependence on nawk.
  • xterm doesn’t install unless you update your X11 installation using the latest version of Xquartz (currently at version 2.1.4).
• Update to latest version of Xquartz: Since I don’t like X11 headaches, I updated to the latest version of Xquartz (currently at version 2.1.4).

So the adventure continues. Back to research, I have invested about 5 hours of my spring break into this upgrade, that is enough for now.

Just a quick note that xephem now works when installed via MacPorts on Leopard (MacPorts Bug Report Ticket #13498). As noted by user “jmr” in that bug report, the error was apparently that

The build.args need to be set as described in the INSTALL file.

So I updated the ports files via an

sudo port -d sync

Followed by

sudo port install xephem

and xephem was installed via MacPorts again. I then removed manual install I had performed earlier with

sudo rm -rf /usr/local/bin/xephem /usr/local/xephem /usr/local/man/man1/xephem.1

I also removed the ~/.xephem directory and let the preferences rebuild. Now I am running with the MacPorts version of xephem again.