This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is It Possible To Mmap A Recarray In Python 2.7?

I have a large global recarray totaling 30GBs of data in a programme running via qsub on a cluster with 256GBs of RAM. I am currently the only user on this cluster so there are no conflicts with the allocation of RAM. When looping over this recarray the system appears to shunt the object to the disc, not keep it held in RAM, thus slowing the loop in excess of 5 fold. I have been looking at using mmap on the object in the following ways and received the following errors.

m = mmap.mmap(myrecarray, 0)
MMAP TypeError: only length-1 arrays can be converted to Python scalars

m = mmap.mmap(myrecarray.fileno(), 0)
AttributeError: record array has no attribute fileno

is it possible to use mmap to hold a recarray object in the RAM, or is this a total misuse of the mmap method or can this only be done for other object types, like strings or files?

many thanks

python
• 4,239 views • link
updated by Matt Shirley Matt Shirley • written by t.c.a.smith • t.c.a.smith

This is a hardcore programming question, definitely there are python cracks around here, but I think you are better served with asking this on stackoverflow. Also, if you want to keep this question open here, please construct a plausible sounding ;) connection to bioinformatics.

• 0 views • link
written by Michael Dondrup Michael Dondrup

Thanks for your response. I have already asked it on the stack, but so far received no response, so i thought I'd try Biostars as we are often dealing with large amounts of data, so maybe someone had previously come across a similar issue. To relate it to biology, this recarray is a local genome build, to which I am mapping millions of mutations and carrying out quantitative genetic analyses. I hope that clears things up.

• 0 views • link
written by t.c.a.smith • t.c.a.smith

Thanks Michael, hopefully someone out there has some experience with locking objects into RAM.

• 0 views • link
written by t.c.a.smith • t.c.a.smith

afaik, the mmap POSIX system call can map files and devices to memory, but then they are just a pointer to a vector of bytes, nothing high level like a python data structure.

• 0 views • link
written by Michael Dondrup Michael Dondrup

1 answer

Do you need random access to the entire array? If so then you'll need to use something like an sqlite database. The mmap module simply makes a file available as a mutable string and/or a file object that you can seek/peek on bytes. Your recarray doesn't have a file handle because it's not a file-like object. You could read the file line-by-line and do what you need with it.

• 267 views • link
written by Matt Shirley Matt Shirley

OK, thanks for the answer, it would be preferable to have access to the full array, there are many other options to overcome the problem. I was initially looking to the recarray system as it is a superfast way to construct the array in the first place and the field names make it perfect for intuitive access. but maybe going line by line using the more conventional indexing method will be preferable. FYI, I managed to use...

m = mmap(-1,13000000000, MAP_PRIVATE)
m.write(myrecarray)

and "top" showed the correct increase in RAM in the "virt" column but a lesser increase in the "res" column, however the loop time did not not decrease, suggesting that that RAM had been been reserved for the proccess but the object had not fully been mapped to it. Time try a different approach I think. Thanks a lot for your time

• 0 views • link
written by t.c.a.smith • t.c.a.smith

If your data are highly structured already on disk you might still be able to get away with a mmap object. Say each field in your data file is 16 bytes long. You could then access the nth field by either seeking to the 16 x n byte or indexing the 16 x n position of the mmap object.

• 0 views • link
written by Matt Shirley Matt Shirley

Log in to answer this question.

More posts like this

No similar posts found.