Dear samtools community,
I looked up in help, logs in digests, but I can’t find an answer to my problem,
so I am going to ask.
As far as I can tell, samtools uses merge sort and rumor has it that it is
multithreaded.
I am using:
samtools sort -m 1G -T tfoo -o foo.bam -@32 bfoo.bam
I have been checking on the calculation and I see no evidence of parallelism.
No threads are spawned, no use of CPU above 100%.
I tried all sort of numbers after @, with and without spaces and it never seems
to be making any difference.
There are 32 cores(dual AMD Abu Dhabi at 2.5 GHz) and 64 GB of RAM per node.
Threaded calculations have been run before successfully (not with samtools).
If anyone could help me understand what is happening I would be very grateful.
Sincerely,
Lorenzo
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