Subject: Cluster of PCs for Gaussian

From: Alessandra Ricca <[email-masked]>
Date: Fri, 9 Mar 2001 07:57:33 -0800 (PST)

Dear CCL members:

Thanks to all who replied to my original question:

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We have two clusters of intel based machines.

Cluster 1 
 * Intel Pentium III 600 MHz CPU with fan
 * ASUS P3B-F Motheroard
 * 512MB SDRAM PC100MHz (2x256MB), Cas III Type and Low Profile.
 * 22GB IBM IDE HDD 7200RPM
 * 4MB AGP ATI Display Card
cluster 2
 * (1)Intel Pentium III 800MHz CPU with fan, 256K cache
 * Intel L440GX+ Dual Pentium III Motherboard
 * SCSI, Lan and VGA on Board
 * 1024MB SDRAM PC100MHz (4x256MB), ECC Register
 * 40GB IBM IDE HDD 7200RPM

We ran gaussian98 in parallel using linda on cluster 1 
using redhat 6.1 for several months and everything appeared 
to function perfectly.  Cluster 2 came with redhat 6.2, and 
initially everything seemed to be fine, so cluster 1 was upgraded
to 6.2.  Under 6.2 gaussian jobs fail on cluster 1 with
a relatively short mean time between failure.  We have
now discovered that cluster 2 also seems to have problems
under 6.2, but the mean time between failures is much
longer.  
The failures come in two types: 1) the calculation appears
to run but values are all garbage (the values print as "nan")
2) one of the processes dies, most commonly, the message
is process 0 failed to complete.

Before restoring 6.1 to the machine, does anyone know
what this problem is and how to fix it?
-------------------------------------------------------------

Here are the answers I got:

---------------------------------------------------------------------------
Yes, it looks like the same thing we had on our linux machines. I searched
for quite a while suspecting hardware problems, but the kernel shipped with
redhat6.2 is bugged and gives random numbers on floating point operations.
Upgrade to a newer kernel and try again.

Cheers,
Peter

--
Dr. D.P. Tieleman, Assistant Professor, AHFMR Scholar
Department of Biological Sciences, University of Calgary
2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
web: www.ucalgary.ca/~tieleman  fax: (403)289-9311

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	Hi all,

		We have a five-node, heterogeneous cluster of pentium boxes. All of these 
have RH 6.0 but the kernel was updated to 2.2.16. Since we don't have pgf77 
Gaussian sent us the binaries, so we didn't compile the program. Linda 
version is 3.1.
		All is working fine. Many of our calculations take several days to 
converge and we didn't note any problem related to memory or phantom process.
		It seems that migrating from RH 6.0 to 6.2 would be the problem (I don't 
kown why, though).

		Regards,

							Reinaldo
-----------------------------------------------------------------------------------------  

Hi Alessandra

I requested some help for the same problem i couple of weeks ago.

The problem is the kernel that comes with RH6.2, aparently 6.0 has no problem.

You must upgrade to the newest Kernel to correct the problem, I solved the
problem upgrading to the whole RH7.0 and gaussian runs nice, and without any
problem. I had a lot of problem to upgrade the kernel alone because of an
incompatibility with SCSI disk.

Now, since you have a couple of clusters you may want to try NWChem, its nice
and it's supposed to work really well on multiprocessor tasks.
http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html
I don't have a lot of experience because i don't have any cluster, but it may
be good and it's free and easy to use. You may want to take a look at the web
page, it has good info.

Best Regards
Max
---------------------------------------------------------------------------

Everyone running rh6.2 with the stock kernel (2.2.14 something) should
upgrade the kernel to either 2.2.16-3 or 2.2.17 something.
rh 2.2.14 will give random floating point errors.

this is a faq

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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First I'd just test the hardware really well with memtest86 from sgi. 
If the memory comes back without errors then we can take the next step
and see what compilers you used.  If you recompiled g98 after the
upgrade.  What kernel version you are using under 6.2 vs 6.1 etc...  I
have g98 running on our 212 proc cluster and have had to work through a
lot of the bugs in g98 and linda but have been able to come up with a
fairly good working set of binaries.

-----------------------------------------------------------------

I advice not to use kernel 2.2.16, it has too many bags. Try to upgrade
to 2.2.17 now available.
-- 
Dr. Irena Efremenko
Wolfson Department of Chemical Engineering
Technion - Israel Institute of Technology
Haifa 32000, Israel
Phone: 972-4-8293561
Fax: 972-4-8230476

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Thanks again.

Alessandra

Alessandra Ricca                 Mail:  NASA Ames Research Center    
Senior Research Scientist               Mail Stop 230-3 	
ELORET Corporation                      Moffett Field, CA 94035-1000 
http://www.eloret.com

Ph:  +1-650-604-5410             Email: [email-masked]
Fax: +1-650-604-0350