Hi,
I am not really happy with the current external basecalling pipeline.
Hardware: 48 cores (AMD Opteron Processor 6176 SE), 256GB RAM
System: Linux, 64bit, make 3.82, OLB 1.9.3
No other load on the machine, data is stored locally (xfs).
Apart from the fact that 'make' is probably the wrong tool for this task,
what are your experiences with external basecalling using OLB?
For a current Hiseq run (2x101bp+index, roughly 160K CIF files) 'make'
needs appr. 4 days to read the makefile and its includes (preparing the
execution of the actual basecalling step) using one CPU. When it has
finished the actual basecalling starts multithreaded and is usually finished
overnight (a few hours).
Any comments on that?
thanks,
Sven
I am not really happy with the current external basecalling pipeline.
Hardware: 48 cores (AMD Opteron Processor 6176 SE), 256GB RAM
System: Linux, 64bit, make 3.82, OLB 1.9.3
No other load on the machine, data is stored locally (xfs).
Apart from the fact that 'make' is probably the wrong tool for this task,
what are your experiences with external basecalling using OLB?
For a current Hiseq run (2x101bp+index, roughly 160K CIF files) 'make'
needs appr. 4 days to read the makefile and its includes (preparing the
execution of the actual basecalling step) using one CPU. When it has
finished the actual basecalling starts multithreaded and is usually finished
overnight (a few hours).
Any comments on that?
thanks,
Sven
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