Hello everyone,
I have a problem on stat1002.eqiad.wmnet using https://github.com/Wikidata/QueryAnalysis/blob/master/tools/hourlyFieldValue... on two files (1.1 GB and 2.4 GB respectively); the processed ends with Killed. My guess is that my script uses too much memory. However, it was my understanding that csv.DictReader reads line-by-line, so the file sizes should not matter.
If anyone can tell me why my script is taking up so much memory or if there is any other reason for the script getting killed I'd be grateful.
Greetings,
Adrian
Hi Adrian,
2017-05-12 14:55 GMT+02:00 Adrian Bielefeldt < Adrian.Bielefeldt@mailbox.tu-dresden.de>:
Hello everyone,
I have a problem on stat1002.eqiad.wmnet using https://github.com/Wikidata/QueryAnalysis/blob/master/ tools/hourlyFieldValue.py on two files (1.1 GB and 2.4 GB respectively); the processed ends with Killed. My guess is that my script uses too much memory. However, it was my understanding that csv.DictReader reads line-by-line, so the file sizes should not matter.
If anyone can tell me why my script is taking up so much memory or if there is any other reason for the script getting killed I'd be grateful.
I checked dmesg on stat1002 and the Kernel OOM killer is the one that ended your process. I didn't check very carefully but maybe the problem are the size of the structs in https://github.com/Wikidata/QueryAnalysis/blob/master/tools/hourlyFieldValue... ?
I'd also check the usage of zip, since from https://docs.python.org/2/library/functions.html#zip it seems that it unpacks all the items of your csv dictionaries in one go.
Hope that helps!
Luca
Hey Adrian.
It looks like your script also buffers all the output values in memory before the final loops + sort phase that outputs to a file.
If you stream the output to your files that should really help.
Since you have a sorting requirement, look at https://docs.python.org/dev/library/collections.html#collections.OrderedDict for your key inserts. It is more compute heavy on inserts, but that’s a reasonable tradeoff given the problem you’re having.
For the values you can use SortedList from the sortedcontainers or blist module for doing your value inserts and maintain sorted order. Those modules are not part of the standard Python SDK, so if that’s not an option then sorted() for the values lists, provided no given list is too large, is probably fine.
I agree with the zip comment below also. DictReader is a generator object, but when you send it to zip() Python will iterate all the contents of the generator and defeat it’s purpose. Checkout itertools.izip() to return an iterator instead of a materialized list.
From: Analytics analytics-bounces@lists.wikimedia.org on behalf of Luca Toscano ltoscano@wikimedia.org Reply-To: "A mailing list for the Analytics Team at WMF and everybody who has an interest in Wikipedia and analytics." analytics@lists.wikimedia.org Date: Friday, May 12, 2017 at 9:26 AM To: "A mailing list for the Analytics Team at WMF and everybody who has an interest in Wikipedia and analytics." analytics@lists.wikimedia.org Subject: Re: [Analytics] python script killed on large file - stat1002.eqiad.wmnet
Hi Adrian,
2017-05-12 14:55 GMT+02:00 Adrian Bielefeldt <Adrian.Bielefeldt@mailbox.tu-dresden.demailto:Adrian.Bielefeldt@mailbox.tu-dresden.de>: Hello everyone,
I have a problem on stat1002.eqiad.wmnet using https://github.com/Wikidata/QueryAnalysis/blob/master/tools/hourlyFieldValue...https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Wikidata_QueryAnalysis_blob_master_tools_hourlyFieldValue.py&d=DwMFaQ&c=gFTBenQ7Vj71sUi1A4CkFnmPzqwDo07QsHw-JRepxyw&r=XYb0dICC34f7i19sp8q3kXzrSJMkWJPZqcu5o_ACx1c&m=AFL9GcHLAPJEERowF-1Tj-6IPuTiPl2NpgDbh7gf9bI&s=oJiLgVPbomYWg-v0Ej-FiBIpXNEJIMUTVZtkUNuk6fQ&e= on two files (1.1 GB and 2.4 GB respectively); the processed ends with Killed. My guess is that my script uses too much memory. However, it was my understanding that csv.DictReader reads line-by-line, so the file sizes should not matter.
If anyone can tell me why my script is taking up so much memory or if there is any other reason for the script getting killed I'd be grateful.
I checked dmesg on stat1002 and the Kernel OOM killer is the one that ended your process. I didn't check very carefully but maybe the problem are the size of the structs in https://github.com/Wikidata/QueryAnalysis/blob/master/tools/hourlyFieldValue...https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Wikidata_QueryAnalysis_blob_master_tools_hourlyFieldValue.py-23L34-2DL36&d=DwMFaQ&c=gFTBenQ7Vj71sUi1A4CkFnmPzqwDo07QsHw-JRepxyw&r=XYb0dICC34f7i19sp8q3kXzrSJMkWJPZqcu5o_ACx1c&m=AFL9GcHLAPJEERowF-1Tj-6IPuTiPl2NpgDbh7gf9bI&s=zcR7tvm5mlwhcSLC3l6s0RMUtElQTk8icCIQAv_LHEo&e= ?
I'd also check the usage of zip, since from https://docs.python.org/2/library/functions.html#ziphttps://urldefense.proofpoint.com/v2/url?u=https-3A__docs.python.org_2_library_functions.html-23zip&d=DwMFaQ&c=gFTBenQ7Vj71sUi1A4CkFnmPzqwDo07QsHw-JRepxyw&r=XYb0dICC34f7i19sp8q3kXzrSJMkWJPZqcu5o_ACx1c&m=AFL9GcHLAPJEERowF-1Tj-6IPuTiPl2NpgDbh7gf9bI&s=ejUGUdfcQX8Au0UCy_LK-64ihsfsRXMzAOcKfycltjY&e= it seems that it unpacks all the items of your csv dictionaries in one go.
Hope that helps!
Luca