PyFluent on Linux: Unable to install via pip.

[ypatel-qa]

1. • Linux machine name: lebfluintrh08 (RH8.5)
2. • /usr/bin/pip3
3. • pip 9.0.3 from /usr/lib/python3.6/site-packages (python 3.6)

While installing PyFluent via pip3 on Linux, I am getting this error:

[ypatel@lebfluintrh08][/net/nfs.lebisilon/home/ypatel/pyfluent/pyfluent]> pip3 install -e .
Obtaining file:///net/nfs.lebisilon/home/ypatel/pyfluent/pyfluent
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/net/nfs.lebisilon/home/ypatel/pyfluent/pyfluent/setup.py", line 4, in <module>
        from setuptools import find_namespace_packages, setup
    ImportError: cannot import name 'find_namespace_packages'

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /net/nfs.lebisilon/home/ypatel/pyfluent/pyfluent/
[ypatel@lebfluintrh08][/net/nfs.lebisilon/home/ypatel/pyfluent/pyfluent]> pip3 install pyfluent
Collecting pyfluent
  Using cached https://files.pythonhosted.org/packages/06/4b/96f9ac3237ed70648da3194c8da59c514c4a325031f32948b9b1a99b950a/pyfluent-0.2.1.tar.gz
Collecting msgpack-python>=0.3.0 (from pyfluent)
  Using cached https://files.pythonhosted.org/packages/8a/20/6eca772d1a5830336f84aca1d8198e5a3f4715cd1c7fc36d3cc7f7185091/msgpack-python-0.5.6.tar.gz
Installing collected packages: msgpack-python, pyfluent
  Running setup.py install for msgpack-python ... error
    Complete output from command /usr/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-ml6yrf4n/msgpack-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-h_hfoypv-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/msgpack
    copying msgpack/_version.py -> build/lib.linux-x86_64-3.6/msgpack
    copying msgpack/__init__.py -> build/lib.linux-x86_64-3.6/msgpack
    copying msgpack/exceptions.py -> build/lib.linux-x86_64-3.6/msgpack
    copying msgpack/fallback.py -> build/lib.linux-x86_64-3.6/msgpack
    running build_ext
    building 'msgpack._packer' extension
    creating build/temp.linux-x86_64-3.6
    creating build/temp.linux-x86_64-3.6/msgpack
    gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D__LITTLE_ENDIAN__=1 -I. -I/usr/include/python3.6m -c msgpack/_packer.cpp -o build/temp.linux-x86_64-3.6/msgpack/_packer.o
    msgpack/_packer.cpp:4:10: fatal error: Python.h: No such file or directory
     #include "Python.h"
              ^~~~~~~~~~
    compilation terminated.
    WARNING: Failed to compile extension modules.
    msgpack uses fallback pure python implementation.
    command 'gcc' failed with exit status 1
    building 'msgpack._unpacker' extension
    gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D__LITTLE_ENDIAN__=1 -I. -I/usr/include/python3.6m -c msgpack/_unpacker.cpp -o build/temp.linux-x86_64-3.6/msgpack/_unpacker.o
    msgpack/_unpacker.cpp:4:10: fatal error: Python.h: No such file or directory
     #include "Python.h"
              ^~~~~~~~~~
    compilation terminated.
    WARNING: Failed to compile extension modules.
    msgpack uses fallback pure python implementation.
    command 'gcc' failed with exit status 1
    running install_lib
    creating /usr/local/lib64/python3.6
    error: could not create '/usr/local/lib64/python3.6': Permission denied

    ----------------------------------------
Command "/usr/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-ml6yrf4n/msgpack-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-h_hfoypv-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-ml6yrf4n/msgpack-python/
[ypatel@lebfluintrh08][/net/nfs.lebisilon/home/ypatel/pyfluent/pyfluent]>

[ypatel-qa]

@seanpearsonuk - I am not sure if I should try with "sudo" access or ask IT to install it? Do we expect our Linux users to have "sudo" access?

[seanpearsonuk]

Is this a regression or the first time you've tried? Presumably some folks have been doing this on Linux already.

[seanpearsonuk]

please run pip list and report the version of setuptools in particular

[seanpearsonuk]

also I believe we require Python version >3.6 as indicated in setup.py

[seanpearsonuk]

find_namespace_packages was introduced in v40.1.0 of setuptools

[dnwillia-work]

Try it again with a virtual environment and install new setuptools? eg: if your shell is a bash, it's like this I think:

python -m venv venv
. venv/bin/activate
pip install setuptools

That should get around needing sudo. Though, Sean is right, we don't support anything older than 3.7:
https://dev.docs.pyansys.com/guidelines/version_support.html

maybe we can make a check for this in setup.py

[ypatel-qa]

@seanpearsonuk @dnwillia-work Thank you.

IT has upgraded the Python version on lebfluintrh08.

[ypatel@lebfluintrh08][/net/nfs.lebisilon/home/ypatel]> pip3 list
Package Version

---

pip 19.3.1
setuptools 41.6.0
[ypatel@lebfluintrh08][/net/nfs.lebisilon/home/ypatel]> python --version
Python 3.8.8
[ypatel@lebfluintrh08][/net/nfs.lebisilon/home/ypatel]>

However, I still get this error,

[ypatel@lebfluintrh08][/net/nfs.lebisilon/home/ypatel/pyfluent/pyfluent]> pip3 install -e .
Obtaining file:///net/nfs.lebisilon/home/ypatel/pyfluent/pyfluent
Collecting grpcio>=1.30.0
Using cached https://files.pythonhosted.org/packages/5b/92/a00eed89bae16e48644f514c842b1cc6deaf0f79cb7dcfeda2dc514e11af/grpcio-1.44.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Collecting numpy>=1.21.5
Using cached https://files.pythonhosted.org/packages/38/c0/c45c5eb0e25247d5fbb333fd0b56e570ba21cf0e3dca3abad174fb780e8c/numpy-1.22.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Collecting protobuf>=3.12.2
Using cached https://files.pythonhosted.org/packages/d5/c8/64de54ef0121a1ff6309f102124c6b5a89260dc584e1871341f5199b7b85/protobuf-3.19.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Collecting six>=1.5.2
Using cached https://files.pythonhosted.org/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl
Installing collected packages: six, grpcio, numpy, protobuf, ansys-fluent-solver
ERROR: Could not install packages due to an EnvironmentError: [Errno 13] Permission denied: '/usr/local/lib/python3.8'
Consider using the --user option or check the permissions.

[ypatel@lebfluintrh08][/net/nfs.lebisilon/home/ypatel/pyfluent/pyfluent]>

[ypatel-qa]

@seanpearsonuk @dnwillia-work Use of virtual environment seems working fine to launch PyFluent (without sudo access). Let me follow up on testing using vnev.

[dnwillia-work]

@ypatel-qa Is there anything left to do on this?

[ypatel-qa]

Hi @dnwillia-work venv is working fine on Linux without sudo access. This issue can be closed.

Just wondering if we need to document this information for users?

[dnwillia-work]

Yeah right. Let’s at least see if there is a way to check for the interpreter version.

[jorgepiloto]

Glad to see @dnwillia-work and @seanpearsonuk provided guidance on how to solve this. Just a couple of comments before closing this, @ypatel-qa:

• Avoid executing sudo python ... or sudo pip .... The output of this commands might break your default Python installation, the one being used by the system usually.

• Use which python to check for the Python interpreter you are running. Make sure it does not point to /usr/bin/python, as this is the system's one.

This issue is related with ansys/pyansys-dev-guide#50.

[ypatel-qa]

Thank you @jorgepiloto .