Another little pointer for those searching madly for Linux installation help. Working on OpenSuse installations on a number of ASUS K8N-DL motherboards. On these boards, Suse installation goes just fine for all of 30 seconds, then freezes cold. After much searching, it was discovered that the BIOS requires updating. The fix is as follows (it’s a good idea to update the board BIOS anyway when you first buy it. No telling how long the board sat on a shelf somewhere before you got to it).
1. Go to www.asus.com.
2. Click on DOWNLOADS (or just click HERE as long as the link works).
3. Type K8N-DL in the “Input Model to Searc” (sic) search box (or whatever board you have).
4. Click on the available K8N-DL link and download the first file (should be K8NDL1007.zip, version 1007, 2005/10/26 update or whatever the latest one is).
5. Put the unzipped file D8003a00.700 on a floppy.
6. Reboot the machine in question.
7. Hit Alt-F2 to get to the FlashBIOS update.
8. Let the update go and wait patiently.
After this, OpenSuse 10.0 will/should install just fine.
In the process of setting up the CIA cluster for DMol3 (Accelrys) and Gaussian calculations. The use of a batch queuing system is recommended by Accelrys to take advantage of available resources (as they become available). The only open-source package they put their name to is OpenPBS (at openpbs.org). Compilation on a 64bit dual core AMD Opteron box (or any 64bit Linux system) gives the following error message.
a] [../OpenPBS ]# ./configure
creating cache ./config.cache
checking host system type... Invalid configuration `ia64-pc-linux-gnuoldld': machine `ia64-pc' not recognized
Invalid configuration `ia64-pc-linux': machine `ia64-pc' not recognized
configure: error: config.sub failed on ia64-pc-linux
The problem is that OpenPBS’s (terribly out-of-date) auto-config script for configure doesn’t know 64bit Linux out of the box. The solution to this is to not let configure guess the machine type. This is done by modifying a single line in the config.guess file located in the OpenPBS “../buildutils/” directory.
You can either go into the config.guess file and change the line
b] #UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
or download the altered config.guess file HERE. The downloaded file has a .txt extension to it (in case your browser gets confused) which you’ll have to delete when you download it
d] mv config.guess.txt config.guess
Just replace the existing config.guess file with this new one and ./configure away.
P.S. I’m doing this (these) installation(s) with OpenSuse 10.0. The default installation for OpenSuse was not designed for programmers (as I rant about HERE). You’ll need to Yast gcc and tcl/tk packages to make OpenPBS (and just about everything else) compile. If you’ve not gotten that far yet, just install everything and accept the lost 6 GBs to peace of mind (and don’t ask about fortran).
The OpenSuse 10.0 CD set, still the only distro to install cleanly on my Precision M70, DOESN’T contain lots of useful developmental software and libraries some of ye olde quantum chemical codes need to run. This is painfully apparent to those who have downloaded the pre-compiled GAMESS-US code and found it not to do run (and what’s with the OSX in the README?) because of missing libg2c files. Yes, even real tech geeks are too lazy to make some days. That may have come out wrong.
If your goal is just to get the program running, the quick fix is to feed your machine just the libraries (a proper compilation or, uh, more complete Linux installation would also work, but that’s beyond the scope of this blog). This involves the following:
1. Go to rpm.pbone.net or your favorite rpm search engine.
2. Search for “libg2c”
3. Download the libg2c-3.3.6-3.i586.rpm (or machine specific) rpm. Version 3.3.X because the precompiled GAMESS-US code was done with g77 3.3 and why risk any more hassle. I’ve one local i586 copy on this site for when I’m in the middle of nowhere and don’t want to bother with problematic rpm repositories.
4. On the problematic Linux box, login as root (su). With the libg2c file in the current directory, install the rpm.
rpm -i libg2c-3.3.6-3.i586.rpm
(or whatever flavor you have).
5. Wait patiently.
6. Upon completion, GAMESS-US should work just fine in single-processor mode (that is to say, if you’ve got a dual core or dual chip, you should still be having some MPI issues to resolve with Suse).