On 09/26/12 19:14, Jérémie Dubois-Lacoste wrote:
Dear All,
Hi!
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.
it would seem that there is a malloc(glibc) behaviour ...
i seen in other list an advice to use :
export MALLOC_ARENA_MAX=1
export MALLOC_MMAP_THRESHOLD=131072
in order to decrease the used memory ..
HTH,
Adrian
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
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