[Beowulf] hang-up of HPC Challenge

Mikhail Kuzminsky kus at free.net
Mon Aug 18 11:20:16 PDT 2008

I ran a set of HPC Challenge benchmarks on ONE dual socket quad-core 
Opteron2350 (Rev. B3) based server (8 logical CPUs).
RAM size is 16 Gbytes. The tests performed were under SuSE 
10.3/x86-64, for LAM MPI 7.1.4 and MPICH 1.2.7 from SuSE distribution, 
using Atlas 3.9. Unfortunately there is only one such cluster node, 
and I can't reproduce the run on another node :-(

For N (matrix size) up to 10000 all looks OK. But for more large N 
(15000/20000/...) hpcc execution 
(mpirun -np 8 hpcc) leads to Linux hang-up.

In the "top" output I see 8 hpcc examplars each eating about 100% of 
CPU, and reasonable amounts of virtual and RSS memory per hpcc 
process, and the absense of swap using. Usually there is no PTRANS 
results in hpccoutf.txt results file, but in a few cases (when I 
"activelly looked" to hpcc execution by means of ps/top issuing) I see 
reasonable PTRANS results but absense of HPLinpack results. One time I 
obtained PTRANS, HPL and DGEMM results for N=20000, but hangup later - 
on STREAM tests. May be it's simple because of absense (at hangup) of 
final writing of output buffer to output file on HDD.

One of possible reasons of hang-ups is memory hardware problem, but 
what is about possible software reasons of hangups ? 

The hpcc executable is 64-bit dynamically linked. 
/etc/security/limits.conf is empty. stacksize limit (for user issuing 
mpirun) is "unlimited", main memory limit - about 14 GB, virtual 
memory limit - about 30 GB. Atlas was compiled for 32-bit integers, 
but it's enough for such N values. Even /proc/sys/kernel/shmmax is 

What else may be the reason of hangup ?

Mikhail Kuzminskiy
Computer Assistance to Chemical Research Center
Zelinsky Institute of Organic Chemistry



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