As you can see the rss memory was only 31M, so it was not aggregating memory

On Wed, 20 Mar 2024 at 08:56, Hans-Henrik Stærfeldt <
<email address hidden>> wrote:

> Tried out del elem[:], same result;
>
> [hzys@ip-10-79-219-18 build]( entrez-xml-parser-fail)$ python memorybug.py
> Testing lxml.etree.iterparse with cleanup
> count: 4931000/4931000 eta:0:00:00
> mem:31.52M/mnt/docker/All_Mammalia.xml:-1924384678:38:FATAL:PARSER:ERR_NO_MEMORY:
> Memory allocation failed
> Traceback (most recent call last):
>   File "/develop/hzys/bdas/etl/entrez/mammals/elastic/build/memorybug.py",
> line 101, in <module>
>     raise excpt
>   File "/develop/hzys/bdas/etl/entrez/mammals/elastic/build/memorybug.py",
> line 98, in <module>
>     test_lxml_iterate(argparser().parse_args())
>   File "/develop/hzys/bdas/etl/entrez/mammals/elastic/build/memorybug.py",
> line 49, in test_lxml_iterate
>     for _, elem in lxml.etree.iterparse(  # pylint:
> disable=c-extension-no-member
>   File "src/lxml/iterparse.pxi", line 208, in lxml.etree.iterparse.__next__
>   File "src/lxml/iterparse.pxi", line 193, in lxml.etree.iterparse.__next__
>   File "src/lxml/iterparse.pxi", line 228, in
> lxml.etree.iterparse._read_more_events
>   File "src/lxml/parser.pxi", line 1451, in lxml.etree._FeedParser.feed
>   File "src/lxml/parser.pxi", line 624, in
> lxml.etree._ParserContext._handleParseResult
>   File "src/lxml/parser.pxi", line 633, in
> lxml.etree._ParserContext._handleParseResultDoc
>   File "src/lxml/parser.pxi", line 743, in lxml.etree._handleParseResult
>   File "src/lxml/parser.pxi", line 672, in lxml.etree._raiseParseError
>   File "/mnt/docker/All_Mammalia.xml", line -1924384678
> lxml.etree.XMLSyntaxError: Memory allocation failed
>
> On Fri, 15 Mar 2024 at 18:35, scoder <email address hidden> wrote:
>
>> Thanks. Does it change anything if you replace the "elem.clear()" in
>> your code with "del elem[:]" ?
>>
>> --
>> You received this bug notification because you are subscribed to the bug
>> report.
>> https://bugs.launchpad.net/bugs/2057780
>>
>> Title:
>>   lxml.etree.XMLSyntaxError: Memory allocation failed - but no memory
>>   used
>>
>> Status in lxml:
>>   New
>>
>> Bug description:
>>   Python              : sys.version_info(major=3, minor=10, micro=8,
>> releaselevel='final', serial=0)
>>   lxml.etree          : (5, 1, 0, 0)
>>   libxml used         : (2, 12, 3)
>>   libxml compiled     : (2, 12, 3)
>>   libxslt used        : (1, 1, 39)
>>   libxslt compiled    : (1, 1, 39)
>>
>>
>>   I am parsing a very large XML (500G) file using lxml.etree.iterparse
>> like this
>>   The individual records are not very large. This runs for about an hour,
>> memory
>>   not getting close to 100M while it runs. Machine has hundreds of
>> gigabytes of
>>   memory, and its mostly not utilised while this ran.
>>
>>
>>   with open(largexmlfilepath, "rb") as xmlstream:
>>      for _, elem in lxml.etree.iterparse(  # pylint:
>> disable=c-extension-no-member
>>          xmlstream, events=("end",), remove_blank_text=True, tag=tagname
>>      ):
>>         # Don't actually try to do anything
>>         assert elem
>>         elem.clear()
>>         while elem.getprevious() is not None:
>>             del elem.getparent()[0]
>>
>>
>>   After about 4931000 records processed, I get this
>>   ...
>>     File "src/lxml/iterparse.pxi", line 210, in
>> lxml.etree.iterparse.__next__
>>     File "src/lxml/iterparse.pxi", line 195, in
>> lxml.etree.iterparse.__next__
>>     File "src/lxml/iterparse.pxi", line 230, in
>> lxml.etree.iterparse._read_more_events
>>     File "src/lxml/parser.pxi", line 1432, in lxml.etree._FeedParser.feed
>>     File "src/lxml/parser.pxi", line 609, in
>> lxml.etree._ParserContext._handleParseResult
>>     File "src/lxml/parser.pxi", line 618, in
>> lxml.etree._ParserContext._handleParseResultDoc
>>     File "src/lxml/parser.pxi", line 728, in lxml.etree._handleParseResult
>>     File "src/lxml/parser.pxi", line 657, in lxml.etree._raiseParseError
>>     File "/mnt/docker/All_Mammalia.xml", line -1924384678
>>   lxml.etree.XMLSyntaxError: Memory allocation failed
>>
>>   It is very reproducible. It seems to fail exactly at the same place.
>>
>> To manage notifications about this bug go to:
>> https://bugs.launchpad.net/lxml/+bug/2057780/+subscriptions
>>
>>