PyNe Installation error

[Suharyana Suharyana]

Hi my name is Suharyana from Physics Department Sebelas Maret University Indonesia. I want to install  PyNe , but failed. I typed ./ubuntu.sh stable when installing. Could you please tell me what should I do to fix this problem? Thank you very much.

Best regards

-- Install configuration: "Release"
############### Begin Python Install ###############
-- Python installer:
  PYTHON_EXECUTABLE: /home/pc07/mambaforge/bin/python
  CMAKE_INSTALL_PREFIX: /home/pc07/.local
  CMAKE_CURRENT_BINARY_DIR: /home/pc07/opt/pyne/pyne-repo/build
/home/pc07/opt/pyne/pyne-repo/build/setup_sub.py:9: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses
  import imp
/home/pc07/opt/pyne/pyne-repo/build/pyne/__init__.py:22: Warning: Error importing PyNE: you should not try to import PyNE from its source directory; please exit the PyNE source tree, and relaunch your python interpreter from there.
  warn(msg, Warning)
Traceback (most recent call last):
  File "/home/pc07/opt/pyne/pyne-repo/build/setup_sub.py", line 26, in <module>
    from pyne.pyne_version import PYNE_VERSION
  File "/home/pc07/opt/pyne/pyne-repo/build/pyne/__init__.py", line 14, in <module>
    from .pyne_config import *
ImportError: libhdf5.so.103: cannot open shared object file: No such file or directory
CMake Error at cmake/SetupSubPyInstall.cmake:15 (message):
  Process setup_sub.py install failed, res_var = '1'
Call Stack (most recent call first):
  cmake_install.cmake:41 (include)


make: *** [Makefile:86: install] Error 1

--------------------

If you are having issues building pyne, please report your problem to pyne...@googlegroups.com or look for help at http://pyne.io

--------------------
Traceback (most recent call last):
  File "/home/pc07/opt/pyne/pyne-repo/setup.py", line 481, in <module>
    main()
  File "/home/pc07/opt/pyne/pyne-repo/setup.py", line 464, in main
    main_safe(ns)
  File "/home/pc07/opt/pyne/pyne-repo/setup.py", line 456, in main_safe
    main_body(ns)
  File "/home/pc07/opt/pyne/pyne-repo/setup.py", line 440, in main_body
    rtn = subprocess.check_call(["make", "install"], cwd=ns.build_dir)
  File "/home/pc07/mambaforge/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make', 'install']' returned non-zero exit status 2.
./ubuntu.sh: /home/pc07/.local/bin/nuc_data_make: /home/pc07/enter/bin/python: bad interpreter: No such file or directory


Testing test_ace.py:

Traceback (most recent call last):
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/loader.py", line 417, in loadTestsFromName
    module = self.importer.importFromPath(
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/mambaforge/envs/openmc-env/lib/python3.11/imp.py", line 235, in load_module
    return load_source(name, filename, file)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/mambaforge/envs/openmc-env/lib/python3.11/imp.py", line 172, in load_source
    module = _load(spec)
             ^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 721, in _load
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/pc07/opt/pyne/pyne-repo/tests/test_ace.py", line 7, in <module>
    import pyne.ace
ModuleNotFoundError: No module named 'pyne'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/pc07/.local/bin/nosetests", line 8, in <module>
    sys.exit(run_exit())
             ^^^^^^^^^^
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/core.py", line 118, in __init__
    unittest.TestProgram.__init__(
  File "/home/pc07/mambaforge/envs/openmc-env/lib/python3.11/unittest/main.py", line 101, in __init__
    self.parseArgs(argv)
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/core.py", line 179, in parseArgs
    self.createTests()
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/core.py", line 193, in createTests
    self.test = self.testLoader.loadTestsFromNames(self.testNames)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/loader.py", line 481, in loadTestsFromNames
    return unittest.TestLoader.loadTestsFromNames(self, names, module)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/mambaforge/envs/openmc-env/lib/python3.11/unittest/loader.py", line 220, in loadTestsFromNames
    suites = [self.loadTestsFromName(name, module) for name in names]
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/mambaforge/envs/openmc-env/lib/python3.11/unittest/loader.py", line 220, in <listcomp>
    suites = [self.loadTestsFromName(name, module) for name in names]
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/loader.py", line 426, in loadTestsFromName
    return suite([Failure(exc[0], exc[1], exc[2],
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/suite.py", line 423, in __call__
    tests = self.wrapTests(tests)
            ^^^^^^^^^^^^^^^^^^^^^
  File "/home/pc07/.local/lib/python3.11/site-packages/nose/suite.py", line 541, in wrapTests
    if isinstance(tests, collections.Callable) or isinstance(tests, unittest.TestSuite):
                         ^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'collections' has no attribute 'Callable'
Testing failed on test_ace.py
Run 'source ~/.bashrc' to update environment variables. PyNE may not function correctly without doing so.
(base) pc07@PC-07:~$

[Ahnaf Tahmid]

Hi Suharyana,

It seems you are using python 3.11 which is not compatible with PyNE stable version. Try to use Python 3.8. However, there is a script available to install DAGMC, OpenMC and PyNE in a virtual environment named nuclear-boy. The script is intended to simplify the installation process for these dependencies and improve reproducibility. The script has been tested on Ubuntu 22.04 (Python 3.10.6) and should work on other Linux systems that support apt-get as well.