[CentOS] High memory needs

Jérémie Dubois-Lacoste jeremie.dl at gmail.com
Wed Sep 26 12:50:04 EDT 2012


Hm, interesting suggestion. But didn't change anything. :(
Thanks anyway,

Jérémie



2012/9/26 Adrian Sevcenco <Adrian.Sevcenco at cern.ch>:
> 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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>>
>
>
>
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