Comment 6 for bug 2057780

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
>
>