Running a GNU parallel blast uses only ~2% of my memory per core. My system has a quad-core 24 GB RAM.
1.Can I affect the speed of blast process and reduce the time of run by alloting more memory to the process?
2. If yes, then how is it possible to scale up the memory usage?
Thanks.
From what you have said, I think that the problem you are computing, does not need so much computational memory. It rather needs computational power. Allocating more memory would not increase the computation time.
Dear Piotr,
Yes I checked the memory usage; the program used ~2% of my memory per core as I said before.
An update: I used blocks of 10000K and the blast ran for considerably lower run time (reduction of run time occurred by at least 500 hours). GNU Parallel is a saviour for computational biologists with limited resources.
However, I would like to re-iterate that this is memory problem needs an urgent solution and I am not the best suited person to do so. So, any help or suggestion will be highly appreciated.
Regards,
Hasnahana
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