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-m option not working properly with large values #70
SortMeRNA uses memory mapping (mmap) to load reads into RAM. Memory mapping works with contiguous blocks of memory. Some users are reporting issues setting the -m parameter to larger values where the program appears to stall on the following mmap call,
char* raw = (char*)mmap ( 0, partial_file_size, PROT_READ, MAP_SHARED, fd, offset_map );
referenced this issue
Feb 18, 2015
Sorry, but I am not sure if I should write in this thread or open a new one.
Anyhow, I am facing an issue with this parameter as well. While playing around with the values, we noticed that if one supplies a value more than half the memory available (as per displayed in "-help"), then the program throws an error. I don't know if this information would help in any way. I will keep you posted if I find any other strange behaviour...
@ekopylova, no worries. Please do take your time. Meanwhile, I do have some additional observations to report.
I attempted running
On a side note: I have a bunch of data sets like these (of similar size) and most of them ran through