[CentOS] High memory needs

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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