Add Cython version of `MmReader` #1825

arlenk · 2018-01-04T04:07:21Z

Very naive version of mmreader in cython.

From some profiling, when simply looping through an uncompressed mm corpus, 60% of the time is spent splitting each line and converting the strings to ints (or floats). For a compressed corpus, about 45% of the time is spent in splitting and converting to ints/floats.

This version simply performs those two steps in cython using sscanf. The rest of the code is pretty much unchanged -- though still compiled in cython for simplicity. This change has a decent impact on performance, especially for uncompressed files. The table below shows some profiling results for looping through a few different corpuses in mm format (the tfidf corpus is used to make sure the code works with an mm file that has floats as well).

	num_docs	num_terms	compressed?	time (current)	time (new)	speed up
enron	40k	28k	no	22.3	2.6	8.7
			yes	37.3	14.4	2.6
nytimes	300k	100k	no	419.3	49.2	8.5
			yes	686.2	275.1	2.5
text8	2k	250k	no	25.4	2.5	10.1
			yes	41.9	17.0	2.5
text8 (tfidf)	2k	250k	no	30.0	5.5	5.4
			yes	47.8	21.1	2.3

In theory, the rest of the code could be converted into c code as well, though that would require writing c code to handle all the different file types that the mmreader accepts (eg, compressed files) and from profiling results, that portion of the code only accounts for 10% (uncompressed files) to 30% (compressed files) of the time.

The real world impact of this change is much more modest than the results above (unless for some reason you are just looping through a corpus...), but I have seen time savings of 15% in some real world uses of LDA with this change. Obviously the impact any user sees will depend on the size of their corpus and the type of model they are using.

piskvorky · 2018-01-04T11:01:42Z

This is great! Speeding up the "basic blocks" (MmCorpus included) is a much needed direction.

@arlenk Are there any cons to this change? What are the disadvantages, trade-offs?

@menshikh-iv shall we keep the old "pure-Python" version, or do we drop the slow versions and keep only the compiled code path? I'm +1 for dropping, now that we offer a good system for binary (pre-compiled) wheels to Gensim users.

arlenk · 2018-01-06T02:45:19Z

@arlenk Are there any cons to this change? What are the disadvantages, trade-offs?

Here are the cons I can think of:

keeping both the python & cython versions means a fair amount of code duplication. Anyone fixing bugs or adding features would have to remember to update both files
keeping only the cython version, on the other hand, makes the code less accessible (in my opinion) to end users. Not sure how often people will care about looking at (or changing) the internals of mmreader, but keeping this only in cython will make that harder.
dealing with strings in c/cython always makes me worry about encoding issues. Since mm files should only have numbers, though, I can't think of a reason why we would ever run into non ascii files, but maybe others can think potential encoding issues.

menshikh-iv · 2018-01-08T10:37:50Z

@piskvorky I'm +1 for dropping too (because we have wheels right now), this has no sense to support 2 versions.

menshikh-iv

Great work 👍

menshikh-iv · 2018-01-08T10:39:23Z

setup.py

@@ -256,9 +256,12 @@ def finalize_options(self):
        Extension('gensim.models.doc2vec_inner',
            sources=['./gensim/models/doc2vec_inner.c'],
            include_dirs=[model_dir]),
+        Extension('gensim.corpora._mmreader',
+            sources=['./gensim/corpora/_mmreader.c'],
+            include_dirs=[model_dir]),


Why model_dir here? This isn't related to gensim/models.

menshikh-iv · 2018-01-08T10:40:26Z

gensim/corpora/_mmreader.pyx

+
+    def __init__(self, input, transposed=True):
+        """
+        Initialize the matrix reader.


Please use numpy-style docstrings (here and everywhere).

menshikh-iv · 2018-01-08T10:42:50Z

gensim/corpora/_mmreader.pyx

+logger = logging.getLogger(__name__)
+
+
+cdef class MmReader(object):


This is almost same as a pure-python version (sscanf different), maybe something else?

No, nothing else really. It's a very trivial change. Just a change to use sscanf instead of split() and int() and a few type definitions (eg, docid, termid, and previd in iter).

No doubt converting the actual file access to c would further improve performance, but that will require dealing with all the different file types that smart_open accepts. Also, I don't think this is the main hotspot in iter.

For example, here's a line profiler output of the current (develop branch) code when reading a raw text file:

Line # % Time Line Contents ============================== 907 0.0 with utils.file_or_filename(self.input) as lines: 908 0.0 self.skip_headers(lines) 911 8.6 for line in lines: 912 40.4 docid, termid, val = utils.to_unicode(line).split() # needed for python3 913 7.0 if not self.transposed: 914 termid, docid = docid, termid 915 # -1 because matrix market indexes are 1-based => convert to 0-based 916 22.5 docid, termid, val = int(docid) - 1, int(termid) - 1, float(val) 917 6.7 assert previd <= docid, "matrix columns must come in ascending order" 918 6.4 if docid != previd: 931 932 8.4 document.append((termid, val,)) # add another field to the current document 933

The majority of time is spent splitting the line and converting the resulting strings to ints (lines 912 and 916). sscanf handles both of these lines. Another 20% or so is taken up by the testing self.transposed and comparing docid and previd (lines 913, 917, and 918). Statically typing these variables in cython helps quite a bt too.

For a compressed text file, line 911 (for line in lines) takes up 33% of the time, but most of the time is still taken by line.split() and int().

Here's the line profile output when reading a compressed file

Line # % Time Line Contents ============================== 907 0.0 with utils.file_or_filename(self.input) as lines: 908 0.0 self.skip_headers(lines) 911 31.5 for line in lines: 912 30.6 docid, termid, val = utils.to_unicode(line).split() # needed for python3 913 5.1 if not self.transposed: 914 termid, docid = docid, termid 915 # -1 because matrix market indexes are 1-based => convert to 0-based 916 17.0 docid, termid, val = int(docid) - 1, int(termid) - 1, float(val) 917 4.9 assert previd <= docid, "matrix columns must come in ascending order" 918 4.6 if docid != previd: 932 6.3 document.append((termid, val,)) # add another field to the current document

menshikh-iv · 2018-01-09T06:41:57Z

@arlenk please update develop branch in your fork and merge fresh develop here (this needed for correct doc building).

arlenk · 2018-01-10T02:08:15Z

@menshikh-iv, i updated my develop branch

If you want to drop the python only version, let me know, and I can update the PR to only include the cython version (perhaps in a gensim.corpora.mmreader module).

menshikh-iv · 2018-01-11T06:32:37Z

@arlenk great, yes, please remove pure python version, and this LGTM, wdyt @piskvorky?

piskvorky · 2018-01-11T18:43:53Z

What are the compatibility implications of this? Any changes needed in existing user code? Does it support the same range of inputs (compressed etc)?

arlenk · 2018-01-12T03:34:21Z

What are the compatibility implications of this?

I don't think there are any compatibility implications. It should be a drop in replacement for the current mmreader.

Any changes needed in existing user code? Does it support the same range of inputs (compressed etc)?

Yes, the actual opening of the file and looping through the rows is still handled by python/smart_open. The only part that is in c is "splitting" each line and converting the values to ints/floats.

I added a few more unittests for MmCorpus as well, including one with a compressed file.

menshikh-iv

Right now, problem is

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "gensim/__init__.py", line 6, in <module>
    from gensim import parsing, matutils, interfaces, corpora, models, similarities, summarization, utils  # noqa:F401
  File "gensim/corpora/__init__.py", line 8, in <module>
    from .mmcorpus import MmCorpus  # noqa:F401
  File "gensim/corpora/mmcorpus.py", line 17, in <module>
    from gensim.corpora.mmreader import MmReader
ImportError: No module named mmreader

I'm not sure, but maybe "incule_dir" solve this problem.

menshikh-iv · 2018-01-12T05:45:25Z

setup.py

@@ -256,9 +256,11 @@ def finalize_options(self):
        Extension('gensim.models.doc2vec_inner',
            sources=['./gensim/models/doc2vec_inner.c'],
            include_dirs=[model_dir]),
+        Extension('gensim.corpora.mmreader',
+            sources=['./gensim/corpora/mmreader.c']),


Probably, "include_dirs" should be gensim/corpora

Thanks @menshikh-iv . It looks like it is failing on the bold line below in the tox config:

python -c "from gensim.models.word2vec import FAST_VERSION; print(FAST_VERSION)" python setup.py build_ext --inplace python -c "from gensim.models.word2vec import FAST_VERSION; print(FAST_VERSION)"

This tries to import word2vec before any of the cython modules are compiled. word2vec imports gensim.corpor, which import mmreader. Since I took out the python version of mmreader, this line is failing as the cython version isn't built yet (this happens on the next line of the tox config).

For now, I removed the bold line to confirm the build works. If the plan is to only include the c/cython versions of code, I am not sure if the bold line above is still necessary. If it is still necessary, then I can add a try/except to gensim.corpora.init, though that would only be used for this line in the tox file.

@arlenk aha, this means that now we can't use FAST_VERSION freely, this isn't good.

Probably, we need to move this constant (because this needed for checking that all compiled successfully), to a zone where we didn't receive an exception if something goes wrong.

Ok, I added back the FAST_VERSION check to the tox config, so the config is the same as before.

To make the test run, I had to add a try/except block to gensim.corpora.init as that file tries to import MmCorpus. Since this check happens before the c-extension is built, MmCorpus fails because there is no pure python MmReader any more. The except block in the init file just creates a dummy MmCorpus class so the code "works" (ie, the imports don't fail, but obviously the dummy classes will not work if used).

This is not a very elegant solution, but I can't think of a better option if that check in the tox file is necessary. Maybe there is a different way to check if the compilation step failed? Also, is the compilation step still necessary with a wheel distribution?

Yes, this is not a good solution.
Compilation step is a mandatory step for wheels, I agree, but we also have repo & developers who work with it.

As alternative, I propose to replace import in tox.ini to something like this from gensim.models.word2vec_inner import FAST_VERSION, i.e. direct import, this will be helpful for this case?

As alternative, I propose to replace import in tox.ini to something like this from gensim.models.word2vec_inner import FAST_VERSION, i.e. direct import, this will be helpful for this case?

That's a good idea, but unfortunately that fails too. Importing anything under gensim.* implicitly runs gensim/init.py, which imports gensim.corpora, which imports mmreader (which doesn't exist yet at this point in the tox process).

Do you know what this line in the tox config is meant to test?

python -c "from gensim.models.word2vec import FAST_VERSION; print(FAST_VERSION)" python setup.py build_ext --inplace python -c "from gensim.models.word2vec import FAST_VERSION; print(FAST_VERSION)" pytest {posargs:gensim/test}

It seems like it tests whether all the "pure python" code installed correctly, but I wonder if there is a different way to test that. Or is that test necessary since either the following line (the setup.py line) or the pytest line will fail if the install was not good.

Do you know what this line in the tox config is meant to test?

I added it when I write the first version of tox.ini for sanity checking only

Feel free to remove this (and also remove try/except block in python file)

Do you know what this line in the tox config is meant to test?

I added it when I write the first version of tox.ini for sanity checking only

ah, ok, that makes sense. I will remove this line for now and drop the try/except.

thanks

menshikh-iv · 2018-02-10T15:39:59Z

Hello @arlenk, sorry for waiting, can you make last changes

Merge fresh changes from develop
Return python version of MmReader (that will be used for backward compatibility until major release, will be dropped before next major).
Return FAST_VERSION first check too (same reason).

and PR will be ready to merge.

menshikh-iv · 2018-02-13T16:28:22Z

gensim/corpora/ucicorpus.py

@@ -15,7 +15,7 @@
 from gensim import utils
 from gensim.corpora import Dictionary
 from gensim.corpora import IndexedCorpus
-from gensim.matutils import MmReader


Please move MmReader to matutils (yes, this is wired, but needed for backward compatibility). We'll move it to corpora with major release.

ok done. I kept the cython version as "gensim.corpora._mmreader". Let me know if you want this renamed to gensim.corpora.mmreader or something else.

menshikh-iv · 2018-02-13T16:29:03Z

setup.py

@@ -256,9 +256,11 @@ def finalize_options(self):
        Extension('gensim.models.doc2vec_inner',
            sources=['./gensim/models/doc2vec_inner.c'],
            include_dirs=[model_dir]),
+        Extension('gensim.corpora._mmreader',
+            sources=['./gensim/corpora/_mmreader.c']),


include_dirs no needed here?

no, I don't think it's needed. The other pyx/c files include model_dir because they reference each other, but this module doesn't need to reference any of the other cython files.

menshikh-iv · 2018-02-14T08:38:29Z

gensim/corpora/mmcorpus.py

+    # try to load fast, cythonized code if possible
+    from gensim.corpora._mmreader import MmReader
+    FAST_VERSION = 1
+    logger.info('Fast version of MmReader is being used')


No need to log anything here (and after, because this will be shown for each import of gensim at all (because we import all stuff in __init__.py)

ok, will remove

menshikh-iv · 2018-02-14T08:38:58Z

gensim/corpora/mmcorpus.py

+try:
+    # try to load fast, cythonized code if possible
+    from gensim.corpora._mmreader import MmReader
+    FAST_VERSION = 1


No need FAST_VERSION here at all (this is connected with BLAS stuff, that isn't used here).

sounds good will remove this too

menshikh-iv · 2018-02-14T08:41:56Z

gensim/corpora/mmcorpus.py

@@ -19,21 +19,78 @@
 logger = logging.getLogger('gensim.corpora.mmcorpus')


-class MmCorpus(matutils.MmReader, IndexedCorpus):
+try:


Can you move this try/except section to matutils.py and restore all imports (this is simplest and clearest way)

I tried moving the import to matutils, but it causes some issues with circular imports.

For example, if I put the following in matutils.py:

try: # try loading cython version of mmreader from gensim.corpora._mmreader import MmReader except ImportError: # else fallback to python version class MmReader(object): pass

When the try block tries to import gensim.corpora._mmreader, that executes gensim.corpora.__init__, which tries to import gensim.corpora.mmcorpus.MmCorpus, which unfortunately tries to import matutils.MmReader, which isn't defined yet (as we are still in the try block).

You end up with a exception like:

----> 1 import gensim ~/Projects/gensim/gensim-mmreader/gensim/__init__.py in <module>() 4 """ 5 ----> 6 from gensim import parsing, matutils, interfaces, corpora, models, similarities, summarization, utils # noqa:F401 7 import logging 8 ~/Projects/gensim/gensim-mmreader/gensim/matutils.py in <module>() 33 try: 34 # try loading cython version of mmreader ---> 35 from gensim.corpora._mmreader import MmReader ~/Projects/gensim/gensim-mmreader/gensim/corpora/__init__.py in <module>() 6 from .indexedcorpus import IndexedCorpus # noqa:F401 must appear before the other classes 7 ----> 8 from .mmcorpus import MmCorpus # noqa:F401 9 from .bleicorpus import BleiCorpus # noqa:F401 ~/Projects/gensim/gensim-mmreader/gensim/corpora/mmcorpus.py in <module>() 21 ---> 22 class MmCorpus(matutils.MmReader, IndexedCorpus): 23 """ AttributeError: module 'gensim.matutils' has no attribute 'MmReader'

I couldn't think of an easy way around this, short of moving _mmreader out of the corpora package, but I'll keep playing around with it.

Oh, that's really sad, I understand what happens :( To avoid this, we need to move _mmreader from corpora (but I have no idea what's better place for it).

menshikh-iv · 2018-02-14T08:42:21Z

gensim/test/test_corpora.py

+        pass
+
+    def test_load(self):
+        self.assertRaises(ValueError, lambda: [doc for doc in self.corpus])


I don't catch, what is it?

Are you asking specifically about TestMmCorpusCorrupt? That's a test to confirm the code will raise an exception if the input file is malformed. The new code checks that sscanf reads in 3 values, so I just test that and raise an exception if fewer values are read.

As for the other tests, I added tests for:

the two compressed formats (gzip and bz2)

to make sure you can access docs by index for a corpus with an index

to check the values read back match what we expect (mostly, I was worried about floats getting truncated to ints)

menshikh-iv · 2018-02-14T08:43:03Z

gensim/test/test_corpora.py

@@ -215,10 +215,10 @@ def _get_slice(corpus, slice_):
            self.assertRaises(RuntimeError, _get_slice, corpus_, 1.0)


-class TestMmCorpus(CorpusTestCase):
+class TestMmCorpusWithIndex(CorpusTestCase):


what's about backward compatibility tests? Or we have no problems here because we change the only reader?

I confirmed that all the tests pass with the existing version of MmReader as well, so there shouldn't be any backward compatibility issues.

menshikh-iv · 2018-02-21T13:26:00Z

@CLearERR one more task for you (documenting), add this to "docsim PR", you need to go through files & cleanup docstrings after I merge this PR:

gensim/corpora/_mmreader.pyx
gensim/corpora/mmcorpus.py
gensim/matutils.py (MmReader & MmWriter)

Be accurate:

Don't forget to fetch fresh upstream with current changes
Don't forget to check how all rendered (especially for cython part).

menshikh-iv · 2018-02-21T13:28:12Z

@arlenk great work! I fixed import-error, will merge this after CI if all fine, let's return to LDA cythonization PR.

* simple cython version of mmreader * confirm MmCorpus read correct values from corpus file * remove unnecessary include dirs for _mmreader.c * add numpy-style docstrings * update conversion specifier for doubles for sscanf * drop plain python version of mmreader * additional unittests for mmcorpus * add gzipped mmcorpus unittest * add bzip compressed test corpus * remove tox test for non-compiled word2vec * add back tox test for non-compiled word2vec * add dummy classes for tox's non-compiled word2vec check * fix ordering of imports for gensim.corpora * remove tox test for non-compiled code * update MANIFEST to include cython mmreader * add back python only version of MmReader * mend * mend * move python version of MmReader back to matutils * fix import problems * fix import order

menshikh-iv · 2018-02-23T06:58:46Z

@arlenk great work, thank you very much 🔥!

piskvorky · 2018-03-01T12:13:40Z

@arlenk how did you create the text8 .mm corpus? Can you please share it? (or the code for how you generated it from the raw text8)

arlenk · 2018-03-02T02:22:42Z

@arlenk how did you create the text8 .mm corpus? Can you please share it? (or the code for how you generated it from the raw text8)

Sure, here are the files (I had to gzip the index file as well so that github would allow me to attach it).
text8.mm.gz
text8.mm.index.gz

Here's the code I used for creating the files from the original text8 corpus

import gensim.downloader as api
import gensim.corpora as gc

import numpy as np
logging.basicConfig(format='%(asctime)s : %(levelname)s : %(message)s', level=logging.INFO)

np.seterr(all='raise')

# load data
_corpus_path = '~/corpora/'

def save_corpus(name='text8'):
    texts = api.load(name)

    print("creating dictionary")
    dictionary = gc.Dictionary([[ word.lower() for word in text ] for text in texts ])
    outfile = os.path.join(_corpus_path, "{}.dict".format(name))
    print("saving dictionary to: {}".format(outfile))
    dictionary.save(outfile)

    print("converting to corpus")
    corpus = [ dictionary.doc2bow([ word.lower() for word in text]) for text in texts ]
    outfile = os.path.join(_corpus_path, "{}.mm".format(name))
    print("saving corpus to {}".format(outfile))
    gc.MmCorpus.serialize(outfile, corpus)

arlenk · 2018-03-02T02:35:48Z

and here's the code for the tfidf version. I created this version just to make sure there were no issues with floating point numbers in the input file.

import gensim.models as gm
import gensim.corpora as gc
corpus = gc.MmCorpus('~/corpora/text8.mm',)
tfidf = gm.TfidfModel(corpus)
corpus_tfidf = [ tfidf[doc] for doc in corpus ]
gc.MmCorpus.serialize('~/corpora/text8.tfidf.mm', corpus_tfidf)

piskvorky · 2018-03-02T08:16:15Z

Thanks a lot @arlenk !

simple cython version of mmreader

270e7bc

arlenk changed the title ~~simple cython version of mmreader~~ [WIP] simple cython version of mmreader Jan 4, 2018

Merge branch 'develop' into mmreader

e28c3b7

arlenk added 2 commits January 5, 2018 21:33

confirm MmCorpus read correct values from corpus file

fc1a9ed

Merge branch 'mmreader' of github.com:arlenk/gensim into mmreader

e6f3c80

menshikh-iv suggested changes Jan 8, 2018

View reviewed changes

arlenk added 2 commits January 8, 2018 23:12

remove unnecessary include dirs for _mmreader.c

c445d72

add numpy-style docstrings

8139236

arlenk added 2 commits January 9, 2018 20:50

update conversion specifier for doubles for sscanf

666de77

Merge remote-tracking branch 'upstream/develop' into mmreader

6ac9388

arlenk added 3 commits January 11, 2018 22:19

drop plain python version of mmreader

b43b946

additional unittests for mmcorpus

95b0ecd

add gzipped mmcorpus unittest

5be1de9

Merge branch 'develop' into mmreader

02a5538

menshikh-iv suggested changes Jan 12, 2018

View reviewed changes

arlenk added 7 commits January 14, 2018 21:10

add bzip compressed test corpus

a437acc

remove tox test for non-compiled word2vec

5ad5dab

add back tox test for non-compiled word2vec

4c4bec0

add dummy classes for tox's non-compiled word2vec check

fb84cf1

fix ordering of imports for gensim.corpora

fc0617e

remove tox test for non-compiled code

9965aef

update MANIFEST to include cython mmreader

0977b6d

arlenk added 4 commits February 11, 2018 10:12

Merge remote-tracking branch 'upstream/develop' into mmreader

214caa7

add back python only version of MmReader

73af360

mend

aac8648

mend

ff729a5

menshikh-iv suggested changes Feb 13, 2018

View reviewed changes

move python version of MmReader back to matutils

d9f5922

menshikh-iv suggested changes Feb 14, 2018

View reviewed changes

menshikh-iv mentioned this pull request Feb 15, 2018

Refactor API reference gensim.corpora #1671

Closed

14 tasks

menshikh-iv added 3 commits February 21, 2018 17:11

fix import problems

3fe6856

fix import order

3c13976

Merge branch 'develop' into mmreader

548a217

menshikh-iv changed the title ~~[WIP] simple cython version of mmreader~~ Add Cython version of Mmreader Feb 21, 2018

menshikh-iv changed the title ~~Add Cython version of Mmreader~~ Add Cython version of MmReader Feb 21, 2018

menshikh-iv merged commit c3f08c1 into piskvorky:develop Feb 21, 2018

arlenk deleted the mmreader branch February 23, 2018 02:17

piskvorky mentioned this pull request May 10, 2018

Performance question on sorting on Dictionary.doc2bow and MmWriter.write_vector #2043

Closed

		logger = logging.getLogger(__name__)


		cdef class MmReader(object):

Add Cython version of MmReader #1825

Add Cython version of MmReader #1825

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Add Cython version of `MmReader` #1825

Add Cython version of `MmReader` #1825

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