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gt1 / biobambam2

Tools for early stage alignment file processing
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Question - bammarkduplicates2 - does it invoke 'top'? #32

Closed keiranmraine closed 8 years ago

keiranmraine commented 8 years ago

Hi,

Just found a very odd log, which appears to include the output of top, that indicated a memory allocation error.

AutoArray<unsigned char,alloc_type_cxx> failed to allocate 268435456 elements (268435456 bytes)
current total allocation 306663325

Is biobambam invoking 'top' or do I need to raise this with our systems group?

Thanks

gt1 commented 8 years ago

Hi Keiran,

it invokes top in case a memory allocation fails. I added this at some point to see whether there were other programs around taking too much memory in case an allocation fails.

Best,

German

On 05.10.2016 13:13, Keiran Raine wrote:

Hi,

Just found a very odd log, which appears to include the output of top, that indicated a memory allocation error.

|AutoArray<unsigned char,alloc_type_cxx> failed to allocate 268435456 elements (268435456 bytes) current total allocation 306663325 |

Is biobambam invoking 'top' or do I need to raise this with our systems group?

Thanks

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keiranmraine commented 8 years ago

Okay, thanks