Author Topic: Install problem  (Read 106 times)

sg

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Install problem
« on: February 04, 2021, 05:42:46 PM »
The pip3 install for nheri-simcenter failed for me:

Code: [Select]
Sanjays-MBP2020:~ sg$ pip3 install nheri-simcenter
Collecting nheri-simcenter
  Downloading nheri_simcenter-0.9.1-py3-none-any.whl (4.3 kB)
Collecting tqdm
  Downloading tqdm-4.56.0-py2.py3-none-any.whl (72 kB)
     |████████████████████████████████| 72 kB 4.2 MB/s
Collecting pandas<=1.1.5,>=1.1.0
  Downloading pandas-1.1.5-cp39-cp39-macosx_10_9_x86_64.whl (10.3 MB)
     |████████████████████████████████| 10.3 MB 20.7 MB/s
Collecting jpype1
  Downloading JPype1-1.2.1-cp39-cp39-macosx_10_9_x86_64.whl (379 kB)
     |████████████████████████████████| 379 kB 80.5 MB/s
Collecting sklearn
  Downloading sklearn-0.0.tar.gz (1.1 kB)
Collecting xlrd<=1.2.0
  Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
     |████████████████████████████████| 103 kB 75.7 MB/s
Collecting tables
  Downloading tables-3.6.1.tar.gz (4.6 MB)
     |████████████████████████████████| 4.6 MB 83.6 MB/s
    ERROR: Command errored out with exit status 1:
     command: /usr/local/opt/python@3.9/bin/python3.9 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9d/rzw8lm7100923j8xf9bllgpc0000gn/T/pip-install-ssk3fkux/tables/setup.py'"'"'; __file__='"'"'/private/var/folders/9d/rzw8lm7100923j8xf9bllgpc0000gn/T/pip-install-ssk3fkux/tables/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/9d/rzw8lm7100923j8xf9bllgpc0000gn/T/pip-pip-egg-info-epxvhxqs
         cwd: /private/var/folders/9d/rzw8lm7100923j8xf9bllgpc0000gn/T/pip-install-ssk3fkux/tables/
    Complete output (10 lines):
    /var/folders/9d/rzw8lm7100923j8xf9bllgpc0000gn/T/H5close9tul_kdb.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.0 (default, Nov 21 2020, 14:01:50)
    * USE_PKGCONFIG: True
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

adamzs

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Re: Install problem
« Reply #1 on: February 04, 2021, 05:55:47 PM »
Thank you for reporting this error!

Please let us know a few more details about your environment to help us figure out where the problem stems from:
- Is this a MacBook Pro? If yes, does it use the new M1 chip?
- Do you have multiple Python versions installed?
- Do you use Anaconda by any chance?

steveg

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Re: Install problem
« Reply #2 on: February 04, 2021, 09:01:54 PM »
The issue is with Python3.9. Currently, the module Tables (last updated on Oct 28, 2019) does not build on 3.9. Need to install Python 3.8.

adamzs

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Re: Install problem
« Reply #3 on: February 04, 2021, 09:10:04 PM »
Thanks, Steve, that is good to know!

Does this apply to both Windows and Mac? If yes, I would put a warning to our documentation to strengthen our recommendation to use Python 3.8 and not higher.

sg

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Re: Install problem
« Reply #4 on: February 05, 2021, 06:47:38 AM »
As Stevan noted it is a 3.9 issue.  Notwithstanding for the record: the machine runs Catalina 10.15.7. MacBookPro (2019).  The Python is from brew.