[GE users] Error: libc.so.6: failed to map segment from shared object:

reuti reuti at staff.uni-marburg.de
Wed Feb 25 15:19:55 GMT 2009


Am 25.02.2009 um 15:43 schrieb prentice:

> reuti wrote:
>> Am 24.02.2009 um 19:11 schrieb prentice:
>>
>>> My cluster nodes have 16GB of RAM, which SGE detects as 15.7G. I
>>> want to
>>> set h_vmem as consumable, so I set h_vmem on all my nodes to a value
>>> safely below that limit, say 15G (I've also tried 15.5G and 15.7G,
>>> with
>>> the same effect):
>>>
>>> for i in $(seq -w 64); do qconf -mattr exechost complex_values
>>> h_vmem=15G node${i}; done
>>>
>>> I then set h_vmem to be consumable:
>>>
>>> h_vmem              h_vmem     MEMORY      <=    YES         YES
>>> 0        0
>>>
>>> Now when I run an MPI test job (a simple "hello, world" type  
>>> program,
>>> that I've been using as a test case for months now), I get this  
>>> error:
>>>
>>> mpirun: error while loading shared libraries: libc.so.6: failed  
>>> to map
>>> segment from shared object: Cannot allocate memory
>>
>> If h_vmem is set, it's also often necessary to request -l h_stack=32M
>> or 128M.
>>
>
> I've found that I need to set -l h_stack=128M. When h_vmem is set  
> to be
> consumable, I get this error:
>
>  main|node01|W|job 2785 exceeds job hard limit "h_vmem" of queue
> "all.q at node01.aurora" (123715584.00000 > limit: 0.00000) - send
> ing SIGKILL
>
> I get this error when I set the default h_vmem to 0 or 1.8G or 1.9G,
> both of which should be within the limits per node ((1.9g x 8) <  
> 15.7 G).

This is only what is granted. If this wouldn't be available, the job  
wouldn't be scheduled. So, the job was started and consumed more than  
granted. With a limit of 0 not surprising - did you define it in the  
queue definition?

>
> Any idea what's causing this error?

Be aware, that the limit is your program code plus your data.

-- Reuti


> h_vmem for each node us currently
> set to 15.7G.
>
>
> -- 
> Prentice
>
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