search

capreolus-ir / capreolus

A toolkit for end-to-end neural ad hoc retrieval
https://capreolus.ai
Apache License 2.0
95 stars 32 forks source link

canada compute - GLIBC_2.29 error when installing #169

Closed nimasadri11 closed 3 years ago

nimasadri11 commented 3 years ago

After using this tutorial, I tried python -m capreolus.run rank.print_config to test the installation on Canada Compute, however, I am getting the below error: 

Traceback (most recent call last):
  File "/home/nsadri/anaconda3/lib/python3.8/runpy.py", line 185, in _run_module_as_main
    mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
  File "/home/nsadri/anaconda3/lib/python3.8/runpy.py", line 111, in _get_module_details
    __import__(pkg_name)
  File "/home/nsadri/capreolus/capreolus/__init__.py", line 5, in <module>
    from profane import ConfigOption, Dependency, ModuleBase, constants, config_list_to_dict, module_registry
  File "/home/nsadri/.local/lib/python3.8/site-packages/profane/__init__.py", line 1, in <module>
    import profane.base
  File "/home/nsadri/.local/lib/python3.8/site-packages/profane/base.py", line 5, in <module>
    import numpy as np
  File "/home/nsadri/anaconda3/lib/python3.8/site-packages/numpy/__init__.py", line 150, in <module>
    from . import core
  File "/home/nsadri/anaconda3/lib/python3.8/site-packages/numpy/core/__init__.py", line 48, in <module>
    raise ImportError(msg)
ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.8 from "/home/nsadri/anaconda3/bin/python"
  * The NumPy version is: "1.21.0"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /home/nsadri/anaconda3/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so)
crystina-z commented 3 years ago

@nimasadri11 heyy thanks for this feedback. I'm testing the script on my end. During this time, a few questions to help identify the problem:

  1. could u please check the current version and installation source (e.g. pip / conda) of packages numpy, spacy, scispacy, torch and tensorflow?
  2. was the setup-cc.sh running smoothly or it got interrupted and hv to rerun?
  3. which CC cluster was it running on?

Thanks!

nimasadri11 commented 3 years ago

Thanks for the response @crystina-z . Please see my answers below.

  1. This answer is a bit complicated so I will put it at the end
  2. I didn't have to rerun. But it did have issues with some Numpy, Spacy versions so it did take quite a long time for pip to backtrace and resolve them.
  3. Cedar

Answer to Q1:

setup-cc.sh installs tensorflow in the capreolus conda environment, but the docs don't say I need to run python -m capreolus.run ... inside the capreolus conda environment. So I just ran it in conda's base environment. Given that, I will give versions of my packages in the base and also in the capreolus coda environments.

Conda Base Env

Name: numpy
Version: 1.21.0+computecanada

Name: spacy
Version: 3.1.0+computecanada

Name: scispacy
Version: 0.4.0

Name: torch
Version: 1.9.0+computecanada

Tensorflow is not installed

Conda Capreolus Env

Name: numpy
Version: 1.21.1

Name: spacy
Version: 2.3.7

scispacy is not installed

Name: torch
Version: 1.4.0

Name: tensorflow
Version: 2.3.0

Quick Question: Should I be running python -m capreolus.run ... from the capreolus conda environment or the base conda environment?

crystina-z commented 3 years ago

@nimasadri11 Thx! Just to know the installation source, when u do conda list | grep -E 'numpy|spacy|torch|tensorflow' in the caperolus env, does it gives a pypi or conda-forge in the last column?

For the question: the command python -m .. would need to be run on capreolus env. Sorry for not mentioning it clear in the doc

nimasadri11 commented 3 years ago

@crystina-z It's pypi with the exception of spacy which is conda-forge. Screenshot below: Screen Shot 2021-07-29 at 1 02 22 PM

FYI, when I activated the capreolus conda env, it actually told me that profane is not installed (maybe the script does not install it when the conda env is activated. So I installed profane>=0.2.0 and ended up with the initial error of GLIBC_2.29 (the same one I mentioned in the original post).

crystina-z commented 3 years ago

@nimasadri11 great thx for the information. will get back to u once I got this reproduced and find the solution.

crystina-z commented 3 years ago

@nimasadri11 hi! I've tested the previous tutorial on my end and did encounter some issues (tho not the same one) which I hvn't find an easy solution, but the good news is that the following lines seem to work for me on cedar. 

module load python/3.7
module load scipy-stack

ENVDIR=/tmp/capreolus-env
virtualenv --no-download $ENVDIR
source $ENVDIR/bin/activate

cat requirements.txt | xargs -n 1 pip install
pip install profane>=0.2.0 pyjnius>=1.2.1 colorlog pyserini==0.12.0 ir_datasets==0.3.3 gdown pymagnitude tensorflow_ranking pytrec_eval
pip install --no-index torch numpy==1.21.0

These are pretty rough lines and have only been tested with python -m capreolus.run rank.print_config (I'm trying to test the model training etc but the sbatch hasn't been granted.) Hopefully this could be a quick solution for u, but do lmk if it doesn't or some other issue pop up. I'll also continue test it on my end and clean them up.

nimasadri11 commented 3 years ago

Thanks for the workaround @crystina-z . python -m capreolus.run rank.print_config runs without an error : ) Going to try to train on MSMARCO and fingers crossed it would work. I'll report back.

d1shs0ap commented 3 years ago
Screen Shot 2021-08-06 at 12 14 52 PM

I got this error while trying to run the above script (after running the original script indicated in setup-cc.md).

nimasadri11 commented 3 years ago

@d1shs0ap I suggest deleting the previous virtual environment and only run the script Crystina suggested. It worked for me on Cedar.

crystina-z commented 3 years ago

@nimasadri11 thanks for helping!

@d1shs0ap seems to be the java version problem (anserini and pyserini required at least Java 11). Tho not sure why the java prepared in the setup-cc.md was not working, module load java/11 should solved the problem I guess.

d1shs0ap commented 3 years ago

@crystina-z @nimasadri11 it worked! Thank you guys so much!

A question for @crystina-z, how could you tell that it was a java version problem by looking at the error above? Thanks in advance!

crystina-z commented 3 years ago

@d1shs0ap nice to hear! and I was guessing it's the java version since the error seems to using the /usr/lib/jvm/java-1.8.0... from the error message :P

crystina-z commented 3 years ago

@d1shs0ap @nimasadri11 The issue seems solved. I'll close this comment for now, but feel free to re-open it if there is any further problem with this.

crystina-z commented 3 years ago

Heyy @nimasadri11 @d1shs0ap I just wrote a hopefully cleaner version in the setup-cc.md. Could you please help testing if this version works on your end? The scripts are supposed to finish in 10~30 mins.

python -m capreolus.run rank.print_config would be enough for the test.

Thanks!

nimasadri11 commented 3 years ago

@crystina-z Of course. I will test this as soon as the training job is finished : )

nimasadri11 commented 3 years ago

@crystina-z I tried this but I get 'ModuleNotFoundError: No module named 'tensorflow_ranking'. Tried to install with it with pip install tensorflow_ranking, but it gives an error: 

ERROR: Could not find a version that satisfies the requirement tensorflow<3,>=2.6.0 (from tensorflow-serving-api<3.0.0,>=2.0.0->tensorflow_ranking) (from versions: 2.4.1+computecanada, 2.5.0+computecanada)
ERROR: No matching distribution found for tensorflow<3,>=2.6.0 (from tensorflow-serving-api<3.0.0,>=2.0.0->tensorflow_ranking)
crystina-z commented 3 years ago

@nimasadri11 Thanks! to confirm, did this happen when create a new venv environment and installing the first step pip install tf-models-official==2.5?

nimasadri11 commented 3 years ago

@crystina-z yes! I followed the steps in the code markdown block here, with the only change being to change the environment name, ENVDIR, to avoid overwriting the environment I already have. However, when running pip install tf-models-official==2.5 I did get the following error:

Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/oauthlib-3.1.1+computecanada-py2.py3-none-any.whl
Building wheels for collected packages: google-crc32c
  Building wheel for google-crc32c (PEP 517) ... done
  Created wheel for google-crc32c: filename=google_crc32c-1.1.2-py3-none-any.whl size=13195 sha256=2d048b660412107bc52bb9463935b28860a7aed0363afb0efafd57d1a99fb757
  Stored in directory: /home/nsadri/.cache/pip/wheels/b9/ad/6c/86e27bce4da73265f59aee70ca6194177c9dd76bbcd1a1388f
Successfully built google-crc32c
ERROR: tensorboard 2.6.0+computecanada has requirement google-auth<2,>=1.6.3, but you'll have google-auth 2.0.1 which is incompatible.
ERROR: tensorflow 2.5.0+computecanada has requirement grpcio~=1.34.0, but you'll have grpcio 1.38.1+computecanada which is incompatible.
ERROR: tensorflow 2.5.0+computecanada has requirement numpy~=1.19.2, but you'll have numpy 1.21.0+computecanada which is incompatible.
ERROR: tensorflow 2.5.0+computecanada has requirement six~=1.15.0, but you'll have six 1.16.0 which is incompatible.
ERROR: tensorflow-metadata 1.2.0 has requirement absl-py<0.13,>=0.9, but you'll have absl-py 0.13.0+computecanada which is incompatible.
crystina-z commented 3 years ago

@nimasadri11 thx for the very prompt reply!

The message looks wierd in terms of at this point, there shouldn't be any preinstalled tf or numpy tho...could u help checking which pip it's using ?

nimasadri11 commented 3 years ago

@crystina-z It's using ~/venv/capreolus-env-new/bin/pip (I named my new environment capreolus-env-new. I tested one more time, using another environment apreolus-env-new-new, and same thing happened. Here's the exact commands I executed (and their output).

(capreolus-env-new) (base) [nsadri@cedar1 ~]$ deactivate
(base) [nsadri@cedar1 ~]$ module load java/11
(base) [nsadri@cedar1 ~]$ module load python/3.7
(base) [nsadri@cedar1 ~]$ module load scipy-stack
(base) [nsadri@cedar1 ~]$ ENVDIR=$HOME/venv/capreolus-env-new-new
(base) [nsadri@cedar1 ~]$ virtualenv --no-download $ENVDIR
created virtual environment CPython3.7.9.final.0-64 in 5186ms
  creator CPython3Posix(dest=/home/nsadri/venv/capreolus-env-new-new, clear=False, global=False)
  seeder FromAppData(download=False, pip=latest, setuptools=latest, wheel=latest, via=copy, app_data_dir=/home/nsadri/.local/share/virtualenv/seed-app-data/v1.0.1)
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
(base) [nsadri@cedar1 ~]$ source $ENVDIR/bin/activate
(capreolus-env-new-new) (base) [nsadri@cedar1 ~]$ pip install tf-models-official==2.5
Ignoring pip: markers 'python_version < "3"' don't match your environment
Looking in links: /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/avx2, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic
Collecting tf-models-official==2.5
  Using cached tf_models_official-2.5.0-py2.py3-none-any.whl (1.6 MB)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/psutil-5.8.0+computecanada-cp37-cp37m-linux_x86_64.whl
Collecting tensorflow-datasets
  Using cached tensorflow_datasets-4.4.0-py3-none-any.whl (4.0 MB)
Requirement already satisfied: pandas>=0.22.0 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from tf-models-official==2.5) (1.3.0+computecanada)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/tensorflow_hub-0.12.0+computecanada-py2.py3-none-any.whl
Requirement already satisfied: six in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/ipykernel/2021a/lib/python3.7/site-packages (from tf-models-official==2.5) (1.16.0)
Requirement already satisfied: Pillow in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from tf-models-official==2.5) (8.3.1+computecanada)
Requirement already satisfied: matplotlib in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from tf-models-official==2.5) (3.4.2+computecanada)
Requirement already satisfied: scipy>=0.19.1 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from tf-models-official==2.5) (1.7.0+computecanada)
Requirement already satisfied: Cython in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from tf-models-official==2.5) (0.29.24+computecanada)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/tensorflow_addons-0.13.0+computecanada-cp37-cp37m-linux_x86_64.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/seqeval-1.2.2+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/py_cpuinfo-4.0.0+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/oauth2client-4.1.3+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/opencv_python_headless-4.5.3.56+computecanada-cp37-cp37m-linux_x86_64.whl
Collecting tf-slim>=1.1.0
  Using cached tf_slim-1.1.0-py2.py3-none-any.whl (352 kB)
Processing ./.cache/pip/wheels/62/d6/58/5853130f941e75b2177d281eb7e44b4a98ed46dd155f556dc5/kaggle-1.5.12-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/PyYAML-5.4.1+computecanada-cp37-cp37m-linux_x86_64.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/pycocotools-2.0.2+computecanada-cp37-cp37m-linux_x86_64.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/tensorflow-2.5.0+computecanada-cp37-cp37m-linux_x86_64.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/gin_config-0.4.0+computecanada-py3-none-any.whl
Collecting tensorflow-model-optimization>=0.4.1
  Using cached tensorflow_model_optimization-0.6.0-py2.py3-none-any.whl (211 kB)
Collecting google-cloud-bigquery>=0.31.0
  Using cached google_cloud_bigquery-2.24.1-py2.py3-none-any.whl (198 kB)
Requirement already satisfied: numpy>=1.15.4 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from tf-models-official==2.5) (1.21.0+computecanada)
Collecting google-api-python-client>=1.6.7
  Using cached google_api_python_client-2.17.0-py2.py3-none-any.whl (7.3 MB)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/sentencepiece-0.1.96+computecanada-cp37-cp37m-linux_x86_64.whl
Collecting sacrebleu
  Using cached sacrebleu-2.0.0-py3-none-any.whl (90 kB)
Collecting tensorflow-metadata
  Using cached tensorflow_metadata-1.2.0-py3-none-any.whl (48 kB)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/protobuf-3.17.3+computecanada-py2.py3-none-any.whl
Collecting importlib-resources; python_version < "3.9"
  Using cached importlib_resources-5.2.2-py3-none-any.whl (27 kB)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/absl_py-0.13.0+computecanada-py3-none-any.whl
Requirement already satisfied: attrs>=18.1.0 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from tensorflow-datasets->tf-models-official==2.5) (21.2.0+computecanada)
Requirement already satisfied: requests>=2.19.0 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from tensorflow-datasets->tf-models-official==2.5) (2.26.0+computecanada)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/dill-0.3.4+computecanada-py3-none-any.whl
Requirement already satisfied: typing-extensions; python_version < "3.8" in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from tensorflow-datasets->tf-models-official==2.5) (3.10.0.0+computecanada)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/termcolor-1.1.0+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/promise-2.3+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/future-0.18.2+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/tqdm-4.62.1-py2.py3-none-any.whl
Requirement already satisfied: python-dateutil>=2.7.3 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/ipykernel/2021a/lib/python3.7/site-packages (from pandas>=0.22.0->tf-models-official==2.5) (2.8.1)
Requirement already satisfied: pytz>=2017.3 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from pandas>=0.22.0->tf-models-official==2.5) (2021.1+computecanada)
Requirement already satisfied: cycler>=0.10 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from matplotlib->tf-models-official==2.5) (0.10.0+computecanada)
Requirement already satisfied: pyparsing>=2.2.1 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from matplotlib->tf-models-official==2.5) (2.4.7+computecanada)
Requirement already satisfied: kiwisolver>=1.0.1 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from matplotlib->tf-models-official==2.5) (1.3.1+computecanada)
Collecting typeguard>=2.7
  Using cached typeguard-2.12.1-py3-none-any.whl (17 kB)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/scikit_learn-0.24.2+computecanada-cp37-cp37m-linux_x86_64.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/pyasn1_modules-0.2.8+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/rsa-4.7.2+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/pyasn1-0.4.8+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/httplib2-0.19.1+computecanada-py3-none-any.whl
Requirement already satisfied: urllib3 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from kaggle>=1.3.9->tf-models-official==2.5) (1.26.6+computecanada)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/python_slugify-5.0.2+computecanada-py2.py3-none-any.whl
Requirement already satisfied: certifi in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from kaggle>=1.3.9->tf-models-official==2.5) (2021.5.30+computecanada)
Requirement already satisfied: setuptools>=18.0 in ./venv/capreolus-env-new-new/lib/python3.7/site-packages (from pycocotools->tf-models-official==2.5) (46.1.3)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/Keras_Preprocessing-1.1.2+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/wheel-0.37.0+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/tensorflow_estimator-2.5.0+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/astunparse-1.6.3+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/google_pasta-0.2.0+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/h5py-3.1.0+computecanada-cp37-cp37m-linux_x86_64.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/grpcio-1.34.0+computecanada-cp37-cp37m-linux_x86_64.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/opt_einsum-3.3.0+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/wrapt-1.12.1+computecanada-cp37-cp37m-linux_x86_64.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/tensorboard-2.6.0+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/keras_nightly-2.5.0.dev2021032900+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/gast-0.4.0+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/flatbuffers-1.12+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/dm_tree-0.1.6+computecanada-cp37-cp37m-linux_x86_64.whl
Collecting proto-plus>=1.10.0
  Using cached proto_plus-1.19.0-py3-none-any.whl (42 kB)
Collecting google-cloud-core<3.0.0dev,>=1.4.1
  Using cached google_cloud_core-2.0.0-py2.py3-none-any.whl (27 kB)
Requirement already satisfied: packaging>=14.3 in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from google-cloud-bigquery>=0.31.0->tf-models-official==2.5) (21.0+computecanada)
Collecting google-resumable-media<3.0dev,>=0.6.0
  Using cached google_resumable_media-2.0.0-py2.py3-none-any.whl (75 kB)
Collecting google-api-core[grpc]<3.0.0dev,>=1.29.0
  Using cached google_api_core-2.0.0-py2.py3-none-any.whl (92 kB)
Collecting google-auth-httplib2>=0.1.0
  Using cached google_auth_httplib2-0.1.0-py2.py3-none-any.whl (9.3 kB)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/uritemplate-3.0.1+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/google_auth-2.0.1-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic/regex-2021.7.6+computecanada-cp37-cp37m-linux_x86_64.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/colorama-0.4.4+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/tabulate-0.8.9+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/portalocker-2.3.0+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/googleapis_common_protos-1.53.0+computecanada-py2.py3-none-any.whl
Requirement already satisfied: zipp>=3.1.0; python_version < "3.10" in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from importlib-resources; python_version < "3.9"->tensorflow-datasets->tf-models-official==2.5) (3.5.0+computecanada)
Requirement already satisfied: idna<4,>=2.5; python_version >= "3" in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from requests>=2.19.0->tensorflow-datasets->tf-models-official==2.5) (3.2+computecanada)
Requirement already satisfied: charset-normalizer~=2.0.0; python_version >= "3" in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from requests>=2.19.0->tensorflow-datasets->tf-models-official==2.5) (2.0.2+computecanada)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/joblib-1.0.1+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/threadpoolctl-2.2.0+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/text_unidecode-1.3+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/cached_property-1.5.2+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/tensorboard_plugin_wit-1.8.0+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/Markdown-3.3.4+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/google_auth_oauthlib-0.4.5+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/Werkzeug-2.0.1+computecanada-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/tensorboard_data_server-0.6.1+computecanada-py3-none-linux_x86_64.whl
Processing ./.cache/pip/wheels/b9/ad/6c/86e27bce4da73265f59aee70ca6194177c9dd76bbcd1a1388f/google_crc32c-1.1.2-py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/cachetools-4.2.2+computecanada-py3-none-any.whl
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/scipy-stack/2021a/lib/python3.7/site-packages (from markdown>=2.6.8->tensorboard~=2.5->tensorflow>=2.5.0->tf-models-official==2.5) (3.10.1+computecanada)
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/requests_oauthlib-1.3.0+computecanada-py2.py3-none-any.whl
Processing /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic/oauthlib-3.1.1+computecanada-py2.py3-none-any.whl
ERROR: tensorflow-metadata 1.2.0 has requirement absl-py<0.13,>=0.9, but you'll have absl-py 0.13.0+computecanada which is incompatible.
ERROR: tensorboard 2.6.0+computecanada has requirement google-auth<2,>=1.6.3, but you'll have google-auth 2.0.1 which is incompatible.
ERROR: tensorflow 2.5.0+computecanada has requirement numpy~=1.19.2, but you'll have numpy 1.21.0+computecanada which is incompatible.
ERROR: tensorflow 2.5.0+computecanada has requirement six~=1.15.0, but you'll have six 1.16.0 which is incompatible.
ERROR: tensorflow 2.5.0+computecanada has requirement typing-extensions~=3.7.4, but you'll have typing-extensions 3.10.0.0+computecanada which is incompatible.
ERROR: google-cloud-bigquery 2.24.1 has requirement grpcio<2.0dev,>=1.38.1, but you'll have grpcio 1.34.0+computecanada which is incompatible.
Installing collected packages: psutil, protobuf, googleapis-common-protos, absl-py, tensorflow-metadata, importlib-resources, dill, termcolor, promise, future, tqdm, tensorflow-datasets, tensorflow-hub, typeguard, tensorflow-addons, joblib, threadpoolctl, scikit-learn, seqeval, py-cpuinfo, pyasn1, pyasn1-modules, rsa, httplib2, oauth2client, opencv-python-headless, tf-slim, text-unidecode, python-slugify, kaggle, pyyaml, pycocotools, keras-preprocessing, wheel, tensorflow-estimator, astunparse, google-pasta, cached-property, h5py, grpcio, opt-einsum, wrapt, cachetools, google-auth, tensorboard-plugin-wit, markdown, oauthlib, requests-oauthlib, google-auth-oauthlib, werkzeug, tensorboard-data-server, tensorboard, keras-nightly, gast, flatbuffers, tensorflow, gin-config, dm-tree, tensorflow-model-optimization, proto-plus, google-api-core, google-cloud-core, google-crc32c, google-resumable-media, google-cloud-bigquery, google-auth-httplib2, uritemplate, google-api-python-client, sentencepiece, regex, colorama, tabulate, portalocker, sacrebleu, tf-models-official
  Attempting uninstall: wheel
    Found existing installation: wheel 0.34.2
    Uninstalling wheel-0.34.2:
      Successfully uninstalled wheel-0.34.2
Successfully installed absl-py-0.13.0+computecanada astunparse-1.6.3+computecanada cached-property-1.5.2+computecanada cachetools-4.2.2+computecanada colorama-0.4.4+computecanada dill-0.3.4+computecanada dm-tree-0.1.6+computecanada flatbuffers-1.12+computecanada future-0.18.2+computecanada gast-0.4.0+computecanada gin-config-0.4.0+computecanada google-api-core-2.0.0 google-api-python-client-2.17.0 google-auth-2.0.1 google-auth-httplib2-0.1.0 google-auth-oauthlib-0.4.5+computecanada google-cloud-bigquery-2.24.1 google-cloud-core-2.0.0 google-crc32c-1.1.2 google-pasta-0.2.0+computecanada google-resumable-media-2.0.0 googleapis-common-protos-1.53.0+computecanada grpcio-1.34.0+computecanada h5py-3.1.0+computecanada httplib2-0.19.1+computecanada importlib-resources-5.2.2 joblib-1.0.1+computecanada kaggle-1.5.12 keras-nightly-2.5.0.dev2021032900+computecanada keras-preprocessing-1.1.2+computecanada markdown-3.3.4+computecanada oauth2client-4.1.3+computecanada oauthlib-3.1.1+computecanada opencv-python-headless-4.5.3.56+computecanada opt-einsum-3.3.0+computecanada portalocker-2.3.0+computecanada promise-2.3+computecanada proto-plus-1.19.0 protobuf-3.17.3+computecanada psutil-5.8.0+computecanada py-cpuinfo-4.0.0+computecanada pyasn1-0.4.8+computecanada pyasn1-modules-0.2.8+computecanada pycocotools-2.0.2+computecanada python-slugify-5.0.2+computecanada pyyaml-5.4.1+computecanada regex-2021.7.6+computecanada requests-oauthlib-1.3.0+computecanada rsa-4.7.2+computecanada sacrebleu-2.0.0 scikit-learn-0.24.2+computecanada sentencepiece-0.1.96+computecanada seqeval-1.2.2+computecanada tabulate-0.8.9+computecanada tensorboard-2.6.0+computecanada tensorboard-data-server-0.6.1+computecanada tensorboard-plugin-wit-1.8.0+computecanada tensorflow-2.5.0+computecanada tensorflow-addons-0.13.0+computecanada tensorflow-datasets-4.4.0 tensorflow-estimator-2.5.0+computecanada tensorflow-hub-0.12.0+computecanada tensorflow-metadata-1.2.0 tensorflow-model-optimization-0.6.0 termcolor-1.1.0+computecanada text-unidecode-1.3+computecanada tf-models-official-2.5.0 tf-slim-1.1.0 threadpoolctl-2.2.0+computecanada tqdm-4.62.1 typeguard-2.12.1 uritemplate-3.0.1+computecanada werkzeug-2.0.1+computecanada wheel-0.37.0+computecanada wrapt-1.12.1+computecanada
crystina-z commented 3 years ago

@nimasadri11 Thanks for the double check! tho the outputs seems fine to me? like it doesn't contain the ERROR: No matching distribution found for tensorflow line. Does it mean that the print_config would actually works for this environment?

I also encounter the few package incompatible lines on my end as well, but seems they doesn't affect the program running etc.

nimasadri11 commented 3 years ago

@crystina-z ERROR: No matching distribution found for tensorflow happens when I run cat requirements.txt | cut -d '#' -f 1 | grep "\S" | xargs -n 1 -i sh -c 'pip install --no-index {} || pip install {}’.

There is a requirements.txt inside the docs/setup directory: /home/nsadri/scratch/capreolus/docs/setup/requirements.txt There is also one in the top directory: /home/nsadri/scratch/capreolus/requirements.txt

Does the requirements.txt in cat requirements.txt | cut -d '#' -f 1 | grep "\S" | xargs -n 1 -i sh -c 'pip install --no-index {} || pip install {}’ refer to the one in the top directory, correct? (i.e. /home/nsadri/scratch/capreolus/requirements.txt)

crystina-z commented 3 years ago

ahh I see. thanks! and yes, the requirement.txt refers to the one under top directory. In that case, could u help to try pip install tensorflow-ranking==0.4.2 before the line cat requirements.txt | cut -d '#' -f 1 | grep "\S" | xargs -n 1 -i sh -c 'pip install --no-index {} || pip install {}? So sorry for these troubles brought.

nimasadri11 commented 3 years ago

@crystina-z No worries at all. Happy I can help!

I just tried it, but still giving the same error. I run pip install tf-models-official==2.5 followed by pip install tensorflow-ranking==0.4.2, and I get:

ERROR: tensorflow 2.5.0+computecanada has requirement numpy~=1.19.2, but you'll have numpy 1.21.0+computecanada which is incompatible.
ERROR: tensorflow 2.5.0+computecanada has requirement six~=1.15.0, but you'll have six 1.16.0+computecanada which is incompatible.
ERROR: tensorflow 2.5.0+computecanada has requirement typing-extensions~=3.7.4, but you'll have typing-extensions 3.10.0.0+computecanada which is incompatible.
ERROR: tensorboard 2.6.0+computecanada has requirement google-auth<2,>=1.6.3, but you'll have google-auth 2.0.1 which is incompatible.
ERROR: google-cloud-bigquery 2.24.1 has requirement grpcio<2.0dev,>=1.38.1, but you'll have grpcio 1.34.0+computecanada which is incompatible.
ERROR: tensorflow-serving-api 2.6.0 has requirement tensorflow<3,>=2.6.0, but you'll have tensorflow 2.5.0+computecanada which is incompatible.

To confirm, I have not ran cat requirements.txt | cut -d '#' -f 1 | grep "\S" | xargs -n 1 -i sh -c 'pip install --no-index {} || pip install {} yet on this environment.

crystina-z commented 3 years ago

@nimasadri11 these ERROR: lines should be fined tho as long as it doesn't block the installation. Could u continue with the cat requirement.txt .. line and see if the ERROR: No matching distribution found for tensorflow issue is still raised? Thanks a lot!

nimasadri11 commented 3 years ago

@crystina-z

SUCCESS! 🎉

print_config works! Seems like doing pip install tensorflow-ranking==0.4.2 before cat requirements.txt ... is crucial (at least in my case). We should probably add it to setup-cc.md.

crystina-z commented 3 years ago

@nimasadri11 great! Yup I'll definitely add it. Thanks soooo much for the help!

d1shs0ap commented 3 years ago

@crystina-z I was away for vacation for the last two weeks, sorry for the late reply! Do you still want me to test this?

In addition, my previous replication of monoBERT on MS MARCO (https://github.com/capreolus-ir/capreolus/blob/feature/msmarco_psg/docs/reproduction/MS_MARCO.md) ran without any errors, should I add to the replication logs?

Thanks so much!