[phenixbb] iotbx.merging_statistics on Python 3: too memory consuming

Martin Malý martin.maly at ibt.cas.cz
Mon Nov 29 08:25:43 PST 2021


Dear PHENIX & CCTBX developers and users,

I tried to calculate merging statistics with CCTBX tools using Python 3.
I realized that the memory requirements are much higher comparing with
Python 2... I closed all programs firstly so I had just 1.6 GB RAM used
of 7.6 GB total RAM. Then I ran these two lines of code in the
cctbx.python shell:

import iotbx.merging_statistics
i_obs = iotbx.merging_statistics.select_data(file_name="XDS_ASCII.HKL",
data_labels=None)

Python 2.7: The RAM usage went to 4.8 GB and then I was able to
calculate merging statistics.
Python 3.7: The module import was successful. Then the RAM usage went to
total 7.6 GB and then the process was killed by the operating system
(CentOS 7).

Please, do you have any suggestion how to use this module "more
carefully" and save memory?
Thank you!
Best regards,
Martin Malý
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