memory issue

[SooLee]

We had an occasion where >15GB mem was required for 749.2 MB hic file. Could it be optimized a bit more?

[sameet]

As a followup, what are general memory requirements for such a conversion?

[carlvitzthum]

@sameet I have released version 0.4.0, which takes big steps towards improving memory usage and overall runtime. In my tests, hic files up to 10GB consumed up to 2 GB of memory locally. I will leave this issue open for now, since I have further memory and speed optimizations in mind that I will implement in a future version.

[Phlya]

I'm just trying to convert the biggest files from Rao et al 2014. I am doing it on a cluster where I request 32Gb memory, but the job dies with the following memory error:

Traceback (most recent call last):
  File "/exports/igmm/eddie/wendy-lab/ilia/condaenvs/dotfinder/bin/hic2cool", line 11, in <module>
    load_entry_point('hic2cool==0.5.1', 'console_scripts', 'hic2cool')()
  File "/exports/igmm/eddie/wendy-lab/ilia/condaenvs/dotfinder/lib/python3.6/site-packages/hic2cool/__main__.py", line 80, in main
    hic2cool_convert(args.infile, args.outfile, args.resolution, args.warnings, args.silent)
  File "/exports/igmm/eddie/wendy-lab/ilia/condaenvs/dotfinder/lib/python3.6/site-packages/hic2cool/hic2cool_utils.py", line 870, in hic2cool_convert
    buf = mmap.mmap(req.fileno(), 0, access=mmap.ACCESS_READ)
OSError: [Errno 12] Cannot allocate memory

After requesting 64Gb, it seems to be running, and maxvmem it uses is 38Gb! That is almost the size of the hic file (~40Gb). This seems a bit extreme! Is this normal?

$ hic2cool --version
hic2cool 0.5.1

[carlvitzthum]

Thanks for reporting this! You may be the first to use hic2cool to convert a file of that size and your feedback is helpful. I will look into why such a memory requirement is so high when I get a chance.

Best, Carl

[Phlya]

Maybe the format has changed, but that's the filesize of original Rao et al 2014 .hic files, I'm sure people have converted them to coolers... I just got them from here https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525