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Test failure: TestLtrMsmarcoDocument on macOS 12.1 #938

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lintool opened this issue Jan 12, 2022 · 17 comments
Closed

Test failure: TestLtrMsmarcoDocument on macOS 12.1 #938

lintool opened this issue Jan 12, 2022 · 17 comments
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@lintool
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lintool commented Jan 12, 2022

Test failure on my iMac Pro, macOS Monterrey 12.1... any ideas?

% python -m unittest integrations.sparse.test_ltr_msmarco_document.TestLtrMsmarcoDocument
Attempting to initialize pre-built index msmarco-doc-per-passage-ltr.
/Users/jimmylin/.cache/pyserini/indexes/index-msmarco-doc-per-passage-ltr-20211031-33e4151.bd60e89041b4ebbabc4bf0cfac608a87 already exists, skipping download.
Initializing msmarco-doc-per-passage-ltr...
Using pre-defined topic order for msmarco-doc-dev
Running msmarco-doc-dev topics, saving to ltr_test/run.msmarco-pass-doc.bm25.txt...
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5193/5193 [48:00<00:00,  1.80it/s]
--2022-01-12 18:34:07--  https://rgw.cs.uwaterloo.ca/JIMMYLIN-bucket0/pyserini-models/model-ltr-msmarco-passage-mrr-v1.tar.gz
SSL_INIT
Resolving rgw.cs.uwaterloo.ca (rgw.cs.uwaterloo.ca)... 129.97.167.73
Connecting to rgw.cs.uwaterloo.ca (rgw.cs.uwaterloo.ca)|129.97.167.73|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 105024292 (100M) [application/gzip]
Saving to: ‘ltr_test/model-ltr-msmarco-passage-mrr-v1.tar.gz’

model-ltr-msmarco-passage-mrr-v1.tar.gz                                   100%[=====================================================================================================================================================================================>] 100.16M  54.5MB/s    in 1.8s    

2022-01-12 18:34:09 (54.5 MB/s) - ‘ltr_test/model-ltr-msmarco-passage-mrr-v1.tar.gz’ saved [105024292/105024292]

x msmarco-passage-ltr-mrr-v1/
x msmarco-passage-ltr-mrr-v1/metadata.json
x msmarco-passage-ltr-mrr-v1/output.json.gz
x msmarco-passage-ltr-mrr-v1/model.pkl
--2022-01-12 18:34:10--  https://rgw.cs.uwaterloo.ca/JIMMYLIN-bucket0/pyserini-models/model-ltr-ibm.tar.gz
SSL_INIT
Resolving rgw.cs.uwaterloo.ca (rgw.cs.uwaterloo.ca)... 129.97.167.73
Connecting to rgw.cs.uwaterloo.ca (rgw.cs.uwaterloo.ca)|129.97.167.73|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 252776626 (241M) [application/gzip]
Saving to: ‘ltr_test/model-ltr-ibm.tar.gz’

model-ltr-ibm.tar.gz                                                      100%[=====================================================================================================================================================================================>] 241.07M  52.6MB/s    in 4.5s    

2022-01-12 18:34:14 (53.3 MB/s) - ‘ltr_test/model-ltr-ibm.tar.gz’ saved [252776626/252776626]

x ibm_model/
x ibm_model/url_unlemm/
x ibm_model/url_unlemm/source.vcb
x ibm_model/url_unlemm/target.vcb
x ibm_model/url_unlemm/output.t1.5.bin
x ibm_model/body/
x ibm_model/body/source.vcb
x ibm_model/body/target.vcb
x ibm_model/body/output.t1.5.bin
x ibm_model/text_bert_tok/
x ibm_model/text_bert_tok/source.vcb
x ibm_model/text_bert_tok/target.vcb
x ibm_model/text_bert_tok/output.t1.5.bin
x ibm_model/title_unlemm/
x ibm_model/title_unlemm/source.vcb
x ibm_model/title_unlemm/target.vcb
x ibm_model/title_unlemm/output.t1.5.bin
Namespace(input='tools/topics-and-qrels/topics.msmarco-doc.dev.txt', min_query_token_qty=0, output='ltr_test/queries.dev.small.json')
{'herein', 'i', 'outside', 'hither', 'every', 'among', 'dost', 'never', 'hereabouts', 'also', 'on', 'us', 'thy', 'yourself', "doesn't", 'excepted', 'other', 'would', 'formerly', 'much', 'me', 'beyond', 'like', 'himself', 'of', 'till', 'before', 'furthest', 'is', 'between', 'lest', 'doing', 'after', 'excluding', 'beforehand', 'latterly', 'a', 'must', 'latter', 'thereabouts', 'kind', 'need', 'nonetheless', 'thereof', 'very', 'anyhow', 'canst', 'one', 'elsewhere', 'am', 'far', 'against', 'then', 'his', 'per', 'unable', 'several', 'inside', 'farthest', 'year', 'sang', 'thee', 'enough', 'whenever', 'whereof', 'doth', 'inasmuch', 'whichsoever', 'sprang', 'those', 'thereon', 'or', 'thence', 'to', 'itself', 'stave', 'really', 'so', "'s", 'further', 'whereby', 'most', 'somehow', 'few', 'he', 'in', 'this', 'ok', 'as', 'nevertheless', 'therein', 'round', 'were', 'thereto', 'sent', 'within', 'thus', 'during', 'howsoever', 'meantime', 'has', 'used', 'same', 'upwards', 'sprung', 'including', 'namely', 'underneath', 'ye', 'inward', 'worse', 'until', 'spoken', 'cannot', 'might', 'just', 'said', 'along', 'whole', 'more', 'av', 'upward', 'spoke', 'became', 'else', 'included', 'mostly', 'via', 'behind', 'hence', 'him', 'themselves', 'had', 'wherefrom', 'almost', 'becoming', 'less', 'ever', 'no', 'something', 'worst', 'whereunto', 'always', 'do', 'exclusive', 'thrice', 'slung', 'first', 'little', 'upon', 'forth', 'may', 'own', 'whereto', 'whichever', 'does', 'halves', 'my', 'saw', 'everyone', 'slunk', 'everything', 'amongst', 'anybody', 'into', 'beside', 'hardly', 'neither', 'herself', 'wherever', 'km', 'another', 'thereby', 'excepting', 'across', 'mr', 'well', 'go', 'cu', 'where', 'seemed', 'hereto', 'hath', 'spake', 'sometime', 'indeed', 'again', 'for', 'seldom', 'even', 'myself', 'nothing', 'et', 'etc', 'it', 'somewhat', 'hers', 'toward', 'by', 'seen', 'she', 'therefore', 'hereupon', 'whensoever', 'everybody', 'whereas', 'ie', 'why', "'ll", 'whose', 'perhaps', 'if', 'whew', 'furthermore', 'any', 'thyself', 'out', 'such', 'nobody', 'whoever', 'seems', 'been', 'since', 'yours', 'together', 'none', 'thou', 'once', 'many', 'will', 'indoors', 'whoa', 'how', 'and', 'yippee', 'provide', "'ves", 'hast', 'whereafter', 'others', 'because', 'whence', 'whosoever', 'not', 'ugh', 'yourselves', 'hindmost', 'contrariwise', 'whatever', "'m", 'wilt', 'be', 'can', 'let', 'using', 'your', 'thereupon', 'according', 'somewhere', 'yet', 'its', 'our', 'their', 'anything', 'these', 'whether', 'quite', 'nowadays', 'wherein', 'moreover', 'at', 'down', 'are', 'shown', 'ff', 'henceforth', 'thru', 'week', 'the', 'around', 'selves', 'insomuch', 'now', 'towards', 'too', 'alone', 'whereon', 'although', 'someone', 'all', 'some', 'slew', 'whomever', 'than', 'kg', 'whereat', 'but', 'thenceforth', 'see', 'an', 'apart', 'vs', 'dual', 'front', 'anyone', 'have', 'up', 'afterwards', 'that', 'supposing', 'could', 'slept', 'exception', 'sake', 'thereafter', 'unlike', 'use', "n't", 'her', 'about', 'ltd', 'include', 'rather', 'hitherto', 'staves', 'nope', 'noone', 'off', 'thereabout', 'ms', 'whomsoever', 'except', 'double', 'under', 'without', 'sometimes', "'re", 'already', 'while', 'still', 'ours', 'should', 'nor', 'plenty', 'them', 'above', 'besides', 'however', 'being', 'meanwhile', 'albeit', 'you', 'cos', 'with', 'which', 'become', 'from', 'wheresoever', 'wherewith', 'mrs', 'wherefore', 'shalt', 'day', 'cf', 'get', 'next', 'over', 'whatsoever', 'seem', 'we', 'forward', 'either', 'here', 'was', 'there', 'whereinto', 'spat', 'both', 'onto', 'often', 'though', 'whereabouts', 'whilst', 'seeing', 'save', 'what', 'below', 'inwards', 'whom', 'anywhere', 'whither', 'nowhere', 'ourselves', 'who', 'unless', 'exclude', 'ought', 'last', 'smote', 'only', 'anyway', 'whereupon', 'somebody', 'sideways', "'d", 'maybe', 'when', 'instead', 'notwithstanding', 'hereby', 'seeming', 'they', 'want', 'everywhere', 'hereafter', 'farther', 'wow', 'throughout', 'each', 'otherwise', 'becomes', 'certain', 'inc', 'choose', 'through'}
Disabled Spacy components:  ['ner', 'parser']
5193it [00:31, 167.26it/s]
Processed 5193 queries
analyzed contents
text_unlemm text_unlemm
text_bert_tok text_bert_tok
IBM model Load takes 14.84 seconds
IBM model Load takes 31.29 seconds
IBM model Load takes 312.11 seconds
IBM model Load takes 57.21 seconds
load dev
scripts/ltr_msmarco/ltr_inference.py:51: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  assert dev['qid'].dtype == np.object
scripts/ltr_msmarco/ltr_inference.py:52: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  assert dev['pid'].dtype == np.object
scripts/ltr_msmarco/ltr_inference.py:63: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  assert dev['qid'].dtype == np.object
scripts/ltr_msmarco/ltr_inference.py:64: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  assert dev['pid'].dtype == np.object
(5191286, 2)
(5193,)
rank    999.66994
rel     999.66994
dtype: float64
                     rank  rel
qid     pid                   
1000000 D1005950#0    454    0
        D100612#18    834    0
        D1007366#0    425    0
        D1007366#1    614    0
        D1011301#0     60    0
        D1011301#1     78    0
        D1027656#1    661    0
        D1027656#2    566    0
        D1063056#20   281    0
        D1067089#0    264    0
<class 'pandas.core.frame.DataFrame'>
MultiIndex: 5191286 entries, ('1000000', 'D1005950#0') to ('999942', 'D997465#3')
Data columns (total 2 columns):
 #   Column  Dtype
---  ------  -----
 0   rank    int32
 1   rel     int32
dtypes: int32(2)
memory usage: 228.4+ MB
None
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5193/5193 [00:29<00:00, 175.25it/s]
recall@10:0.0
recall@20:0.0
recall@50:0.0
recall@100:0.0
recall@200:0.0
recall@500:0.0
recall@1000:0.0
recall@2000:0.0
recall@5000:0.0
recall@10000:0.0
load queries
[thread 50435 also had an error]
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x0000000105767ffe, pid=67546, tid=82179
#
# JRE version: Java(TM) SE Runtime Environment (11.0.4+10) (build 11.0.4+10-LTS)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (11.0.4+10-LTS, mixed mode, tiered, compressed oops, g1 gc, bsd-amd64)
# Problematic frame:
# [thread 49667 also had an error]
[thread 81923 also had an error]
[thread 80899 also had an error]
[thread 51203 also had an error][thread 81667 also had an error]

[thread 82691 also had an error]
[thread 50691 also had an error]
[thread 51459 also had an error]
[thread 49411 also had an error]
[thread 81155 also had an error][thread 49923 also had an error][thread 50179 also had an error]
[thread 51715 also had an error][thread 81411 also had an error]



[thread 50947 also had an error]
[thread 82435 also had an error][thread 80131 also had an error]

[thread 54531 also had an error]
[thread 78339 also had an error]
[thread 78083 also had an error]
[thread 77571 also had an error]
[thread 77315 also had an error]
[thread 76803 also had an error]
[thread 55555 also had an error]
[thread 76291 also had an error]
[thread 75779 also had an error]
[thread 55811 also had an error]
[thread 56323 also had an error]
[thread 75267 also had an error]
[thread 75011 also had an error]
[thread 57091 also had an error]
C  [libomp.dylib+0x60ffe][thread 57347 also had an error]
  __kmp_suspend_initialize_thread+0x1e
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
[thread 73987 also had an error]
# An error report file with more information is saved as:
# /Users/jimmylin/workspace/pyserini/hs_err_pid67546.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
#
/Users/jimmylin/opt/anaconda3/envs/pyserini-dev/lib/python3.8/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '
Traceback (most recent call last):
  File "scripts/ltr_msmarco/generate_document_score_withmaxP.py", line 14, in <module>
    with open(args.input) as fin:
FileNotFoundError: [Errno 2] No such file or directory: 'ltr_test/run.ltr.msmarco-pass-doc.test.trec'
Traceback (most recent call last):
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 235, in <module>
    main(parser.parse_args())
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 222, in main
    metrics = compute_metrics_from_files(path_to_reference, path_to_candidate, exclude_qids)
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 184, in compute_metrics_from_files
    qids_to_ranked_candidate_documents = load_candidate(path_to_candidate)
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 98, in load_candidate
    with autoopen(path_to_candidate,'r') as f:
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 28, in autoopen
    return open(filename, mode)
FileNotFoundError: [Errno 2] No such file or directory: 'ltr_test/run.ltr.msmarco-pass-doc.test.tsv'
E
======================================================================
ERROR: test_reranking (integrations.sparse.test_ltr_msmarco_document.TestLtrMsmarcoDocument)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/jimmylin/workspace/pyserini/integrations/sparse/test_ltr_msmarco_document.py", line 56, in test_reranking
    result = subprocess.check_output(f'python tools/scripts/msmarco/msmarco_doc_eval.py --judgments tools/topics-and-qrels/qrels.msmarco-doc.dev.txt --run ltr_test/{outp_tsv}', shell=True).decode(sys.stdout.encoding)
  File "/Users/jimmylin/opt/anaconda3/envs/pyserini-dev/lib/python3.8/subprocess.py", line 415, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/Users/jimmylin/opt/anaconda3/envs/pyserini-dev/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'python tools/scripts/msmarco/msmarco_doc_eval.py --judgments tools/topics-and-qrels/qrels.msmarco-doc.dev.txt --run ltr_test/run.ltr.msmarco-pass-doc.test.tsv' returned non-zero exit status 1.

----------------------------------------------------------------------
Ran 1 test in 3437.703s

FAILED (errors=1)
@stephaniewhoo
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That's weird. Just rerun this test on orca and it passed

Done!
5191286it [00:07, 688446.36it/s]
100%|███████████████████████████████████████████████████████████████████| 5193/5193 [00:01<00:00, 4988.37it/s]
.
----------------------------------------------------------------------
Ran 1 test in 4216.341s

OK

@lintool
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lintool commented Jan 13, 2022

Seems to be a macOS problem... I'm trying to debug.

@stephaniewhoo do you have access to a macOS machine you can try also?

@lintool
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lintool commented Jan 13, 2022

Seems to be related to https://gcc.gnu.org/bugzilla/show_bug.cgi?id=92061

@lintool
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lintool commented Jan 13, 2022

This seems to be a known issue and doesn't appear to have been resolved yet: microsoft/LightGBM#4229

@yuki617
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yuki617 commented Jan 13, 2022

I also get it worked on orca. Will try on my macos machine too.

@lintool
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lintool commented Jan 13, 2022

Yes, confirmed that the test case passes on orca.

@stephaniewhoo
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score_tie occurs 208854 times in 5188 queries
recall@10:0.0
recall@20:0.0
recall@50:0.0
recall@100:0.0
recall@200:0.0
recall@250:0.0
recall@300:0.0
recall@333:0.0
recall@400:0.0
recall@500:0.0
recall@1000:0.0
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5193/5193 [00:16<00:00, 312.44it/s]
score_tie occurs 208854 times in 5188 queries
Done!
5191286it [00:07, 669016.70it/s]
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5193/5193 [00:01<00:00, 4888.41it/s]
.
----------------------------------------------------------------------
Ran 1 test in 10265.931s

OK

Finally the test is complete on my laptop (macOS) and it passes as well. My system is also MacOS Monterey 12.1 (21C52)

@yuki617
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yuki617 commented Jan 14, 2022

Same as Stephanie, the test also passed on my macos machine, my system is macOS Big Sur version 11.5.2

@lintool
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lintool commented Jan 15, 2022

Trying out the example here: microsoft/LightGBM#4229

% python
Python 3.8.12 (default, Oct 12 2021, 06:23:56) 
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from lightgbm import LGBMClassifier
>>> import numpy as np
>>> from concurrent.futures import ThreadPoolExecutor
>>> 
>>> x = np.random.random((200, 4))
>>> y = x.sum(axis=1) >= 2
>>> 
>>> 
>>> def myfunc(a=7):
...     test = LGBMClassifier().fit(x, y)
...     print(test.predict(x))
... 
>>> 
>>> with ThreadPoolExecutor(20) as tpe:
...     print(list(tpe.map(myfunc, range(20))))
... 
zsh: segmentation fault  python

Indeed, I get a seg fault - this is on macOS 12.1.

Additional details:

% pip list | grep lightgbm
lightgbm           3.3.2

% brew info libomp
libomp: stable 13.0.0 (bottled)
LLVM's OpenMP runtime library
https://openmp.llvm.org/
/usr/local/Cellar/libomp/13.0.0 (9 files, 1.6MB) *
  Poured from bottle on 2022-01-12 at 21:15:03
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/libomp.rb
License: MIT
==> Dependencies
Build: cmake ✘
==> Analytics
install: 52,037 (30 days), 228,792 (90 days), 1,152,680 (365 days)
install-on-request: 7,733 (30 days), 31,763 (90 days), 140,940 (365 days)
build-error: 10 (30 days)

@yuki617
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yuki617 commented Jan 15, 2022

I have tested the above script on my macOS with macOS version 11.5.2, libomp version 13.0.0 and lightgbm 3.2.2 . No segmentation fault is found, everything works just fine. The reason for the test failure was narrowed down to the version of macOS.

@lintool lintool changed the title Test failure: integrations.sparse.test_ltr_msmarco_document.TestLtrMsmarcoDocument Test failure: TestLtrMsmarcoDocument on macOS 12.1 Jan 15, 2022
@lintool
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lintool commented Jan 15, 2022

Waiting for upstream fixes. No further action for now.

@lintool
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lintool commented Apr 2, 2022

I just updated to libomp 14.0.0 via brew. Issue still persists.

@lintool
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lintool commented May 14, 2022

Update, still having this issue:

% python -m unittest integrations.sparse.test_lucenesearcher_check_ltr_msmarco_document.TestLtrMsmarcoDocument
...
recall@10:0.0
recall@20:0.0
recall@50:0.0
recall@100:0.0
recall@200:0.0
recall@500:0.0
recall@1000:0.0
recall@2000:0.0
recall@5000:0.0
recall@10000:0.0
Attempting to initialize pre-built index msmarco-doc-per-passage-ltr.
/Users/jimmylin/.cache/pyserini/indexes/index-msmarco-doc-per-passage-ltr-20211031-33e4151.bd60e89041b4ebbabc4bf0cfac608a87 already exists, skipping download.
Initializing msmarco-doc-per-passage-ltr...
Attempting to initialize pre-built index msmarco-doc-per-passage-ltr.
/Users/jimmylin/.cache/pyserini/indexes/index-msmarco-doc-per-passage-ltr-20211031-33e4151.bd60e89041b4ebbabc4bf0cfac608a87 already exists, skipping download.
Initializing msmarco-doc-per-passage-ltr...
analyzed contents
text_unlemm text_unlemm
text_bert_tok text_bert_tok
IBM model Load takes 14.59 seconds
IBM model Load takes 32.02 seconds
IBM model Load takes 315.10 seconds
IBM model Load takes 58.74 seconds
#
[thread 53763 also had an error]
[thread 78855 also had an error]
[thread 54019 also had an error]
[thread 76035 also had an error]
[thread 51207 also had an error]
[thread 75523 also had an error]
[thread 77827 also had an error]
[thread 51463 also had an error][thread 77059 also had an error]
[thread 52995 also had an error]# A fatal error has been detected by the Java Runtime Environment:
[thread 52739 also had an error][thread 77571 also had an error]

[thread 51715 also had an error]
[thread 77315 also had an error]


[thread 50951 also had an error][thread 78087 also had an error][thread 78599 also had an error]
[thread 50695 also had an error]
[thread 51971 also had an error][thread 50439 also had an error]


[thread 52483 also had an error]

[thread 53251 also had an error]
[thread 76291 also had an error][thread 76803 also had an error][thread 53507 also had an error]


[thread 76547 also had an error][thread 52227 also had an error]
#

#  SIGSEGV (0xb)[thread 75267 also had an error] at pc=0x0000000104abbffe
, pid=24960, tid=78343
#
# JRE version: Java(TM) SE Runtime Environment (11.0.4+10) (build 11.0.4+10-LTS)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (11.0.4+10-LTS, mixed mode, tiered, compressed oops, g1 gc, bsd-amd64)
# Problematic frame:
# [thread 71171 also had an error]
[thread 70659 also had an error]
[thread 70147 also had an error]
[thread 57347 also had an error]
[thread 69891 also had an error]
[thread 69635 also had an error]
C  [libomp.dylib+0x60ffe]  __kmp_suspend_initialize_thread+0x1e
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Users/jimmylin/workspace/pyserini/hs_err_pid24960.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
#
/Users/jimmylin/opt/anaconda3/envs/pyserini-dev/lib/python3.8/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '
Traceback (most recent call last):
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 235, in <module>
    main(parser.parse_args())
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 222, in main
    metrics = compute_metrics_from_files(path_to_reference, path_to_candidate, exclude_qids)
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 184, in compute_metrics_from_files
    qids_to_ranked_candidate_documents = load_candidate(path_to_candidate)
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 98, in load_candidate
    with autoopen(path_to_candidate,'r') as f:
  File "tools/scripts/msmarco/msmarco_doc_eval.py", line 28, in autoopen
    return open(filename, mode)
FileNotFoundError: [Errno 2] No such file or directory: 'ltr_test/run.ltr.msmarco-pass-doc.test.trec'
E
======================================================================
ERROR: test_reranking (integrations.sparse.test_lucenesearcher_check_ltr_msmarco_document.TestLtrMsmarcoDocument)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/jimmylin/workspace/pyserini/integrations/sparse/test_lucenesearcher_check_ltr_msmarco_document.py", line 50, in test_reranking
    result = subprocess.check_output(f'python tools/scripts/msmarco/msmarco_doc_eval.py --judgments tools/topics-and-qrels/qrels.msmarco-doc.dev.txt --run ltr_test/{outp}', shell=True).decode(sys.stdout.encoding)
  File "/Users/jimmylin/opt/anaconda3/envs/pyserini-dev/lib/python3.8/subprocess.py", line 415, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/Users/jimmylin/opt/anaconda3/envs/pyserini-dev/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'python tools/scripts/msmarco/msmarco_doc_eval.py --judgments tools/topics-and-qrels/qrels.msmarco-doc.dev.txt --run ltr_test/run.ltr.msmarco-pass-doc.test.trec' returned non-zero exit status 1.

----------------------------------------------------------------------
Ran 1 test in 4061.513s

FAILED (errors=1)

And:

% brew info libomp 
libomp: stable 14.0.0 (bottled)
LLVM's OpenMP runtime library

@lintool
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lintool commented May 14, 2022

Even with:

export LIBOMP_USE_HIDDEN_HELPER_TASK=0
export LIBOMP_NUM_HIDDEN_HELPER_THREADS=0

Per microsoft/LightGBM#4229 (comment) - didn't help.

@lintool
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lintool commented Sep 22, 2022

Trying this again:

% brew info libomp  
==> libomp: stable 14.0.6 (bottled)
LLVM's OpenMP runtime library

Still getting same error.

@lintool
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lintool commented Oct 9, 2022

Interestingly, on the M1 chip, lightgbm does work with the following install command:

conda install -c conda-forge lightgbm

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lintool commented Oct 15, 2024

Works fine on M series processors... simply solution, avoid x86 on Mac ;)

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