Dear all, I am scratching my head but apart from getting splinters into my fingers I cannot find a good answer for the following problem: I am running a DFT program (NWChem) in parallel on our cluster (AMD Opterons, single quad cores in the node, 12 GB of RAM, Gigabit network) and at certain stages of the run top is presenting me with that:
top - 15:10:48 up 13 days, 22:20, 1 user, load average: 0.26, 0.24, 0.19 Tasks: 106 total, 1 running, 105 sleeping, 0 stopped, 0 zombie Cpu0 : 8.0% us, 2.7% sy, 0.0% ni, 82.7% id, 0.0% wa, 1.3% hi, 5.3% si Cpu1 : 4.1% us, 1.4% sy, 0.0% ni, 94.6% id, 0.0% wa, 0.0% hi, 0.0% si Cpu2 : 2.7% us, 0.0% sy, 0.0% ni, 97.3% id, 0.0% wa, 0.0% hi, 0.0% si Cpu3 : 0.0% us, 0.0% sy, 0.0% ni, 100.0% id, 0.0% wa, 0.0% hi, 0.0% si Mem: 12250540k total, 5581756k used, 6668784k free, 273396k buffers Swap: 16779884k total, 0k used, 16779884k free, 3841688k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 16885 sassy 15 0 3928m 1.7g 1.4g S 4 14.4 312:19.92 nwchem 16886 sassy 15 0 3928m 1.7g 1.4g S 4 14.5 313:08.77 nwchem 16887 sassy 15 0 3920m 1.7g 1.4g S 3 14.4 316:18.24 nwchem 16888 sassy 15 0 3923m 1.6g 1.3g S 3 13.3 316:13.55 nwchem 16890 sassy 15 0 2943m 1.7g 1.7g S 3 14.8 104:32.33 nwchem It is not a few seconds it does it, it appears to be for a prolonged period of time. I checked it randomly for say 1 min and the performance is well below 50 % (most of the time around 20 %). I have not noticed that when I am running the job within one node. I have the suspicion that the Gigabit network is the problem, but I really would like to pinpoint that so I can get my boss to upgrade to a better network for parallel computing (hence my previous question about Open-MX). Now how, as I am not an admin of that cluster, would I be able to do that? Thanks for your comments. Best wishes from Glasgow! Jörg -- ************************************************************* Jörg Saßmannshausen Research Fellow University of Strathclyde Department of Pure and Applied Chemistry 295 Cathedral St. Glasgow G1 1XL email: jorg.sassmannshau...@strath.ac.uk web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
