Dear All,
We recently reinstalled our computing cluster. We were using CentOS 5.3 (32 bits). It is now CentOS 6.3 (64 bits), installed from the CentOS 6.2 x64 CD, then upgraded to 6.3.
We have some issues with the memory needs of our running jobs. They require much more than before, it may be due to the switch from 32 to 64 bits, but to me this cannot explain the whole difference.
Here are our investigations.
We used the following simple benchmark:
1. Run a python script and check the memory that it requires (field "VIRT" of the "top" command). This script is: ---- import time time.sleep(30) print("done") ----
2. Similarly, run and check the memory of a simple bash script: ---- #!/bin/bash sleep 30 echo "done" ----
3. Open a R session and check the memory used
I asked 10 of our users to run these three things on their personal PCs. They are running different distributions (mainly ubuntu, slackware), half of them use a 32 bits system, the other half a 64 one. Here is a summary of the results:
Bash script: Avg Min Max 32 bits 5400 4192 9024 64 bits 12900 10000 16528
Python script: Avg Min Max 32 bits 8500 5004 11132 64 bits 32800 30000 36336
R: Avg Min Max 32 bits 26900 21000 33452 64 bits 100200 93008 97496
(as a side remark, the difference between 32 and 64 is surprisingly big to me...).
Then we ran the same things on our CentOS cluster, getting surprisingly high results. I installed a machine from scratch with the CentOS CD (6.2 x64) to be sure another component of the cluster was not playing a role. On this freshly installed machine I get the following results: SH: 103MB PYTHON: 114MB R: 200MB
So, compared to the highest of our users (among the 64 bits ones), we have a ratio of ~7, ~3, ~2, respectively.
It is very problematic for us because many jobs now cannot run properly, because they lack memory on most of our computing nodes. So we really cannot stand the situation...
Do you see any reason for this? Do you have suggestions?
Sincerely,
Jérémie