PyNE installation problems

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Ron Lavera

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Apr 5, 2023, 1:52:41 AM4/5/23

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Hello

I am hoping that you will be able to help me get PyNE installed.

I have a Windows 11 Pro, WSL2 Ubuntu system.

Under the Windows operating system, I have HDF5 installed.

I am trying to install PyNE-0.7.7 under the Ubuntu system.

I've tried 2 ways of installing the program, 1) downloading the taf file, and 2) using conda

1) After downloading the pyne-0.7.7.tar.gz file, I run this command line:

python setup.py install --user > log.txt

I get the following error on the display:

-- Include paths for /opt/pyne/pyne-0.7.7/pyne: /mnt/d/HDF5/include;/opt/anaconda3/3.10/anaconda3/lib/python3.10/site-packages/numpy/core/include;/opt/pyne/pyne-0.7.7/build/pyne;/opt/pyne/pyne-0.7.7/src
-- F2PY F90 FLAGS:
-- Include paths for /opt/pyne/pyne-0.7.7/pyne/xs: /mnt/d/HDF5/include;/opt/anaconda3/3.10/anaconda3/lib/python3.10/site-packages/numpy/core/include;/opt/pyne/pyne-0.7.7/build/pyne;/opt/pyne/pyne-0.7.7/src
In file included from /mnt/d/HDF5/include/hdf5.h:22,
from /opt/pyne/pyne-0.7.7/src/data.h:20,
from /opt/pyne/pyne-0.7.7/src/data.cpp:3:
/mnt/d/HDF5/include/H5public.h:173:19: error: conflicting declaration ‘typedef long long int ssize_t’
173 | typedef long long ssize_t;
| ^~~~~~~
In file included from /usr/include/stdlib.h:395,
from /usr/include/c++/11/cstdlib:75,
from /usr/include/c++/11/ext/string_conversions.h:41,
from /usr/include/c++/11/bits/basic_string.h:6608,
from /usr/include/c++/11/string:55,
from /usr/include/c++/11/bits/locale_classes.h:40,
from /usr/include/c++/11/bits/ios_base.h:41,
from /usr/include/c++/11/ios:42,
from /usr/include/c++/11/ostream:38,
from /usr/include/c++/11/iostream:39,
from /opt/pyne/pyne-0.7.7/src/data.h:8,
from /opt/pyne/pyne-0.7.7/src/data.cpp:3:
/usr/include/x86_64-linux-gnu/sys/types.h:108:19: note: previous declaration as ‘typedef __ssize_t ssize_t’
108 | typedef __ssize_t ssize_t;
| ^~~~~~~
make[2]: *** [src/CMakeFiles/pyne.dir/build.make:116: src/CMakeFiles/pyne.dir/data.cpp.o] Error 1

The log.txt file is attached.

2) using conda

/opt/anaconda3/3.10/anaconda3/bin/conda install -c conda-forge pyne=0.7.7`

environment variables:
CIO_TEST=<not set>
CONDA_DEFAULT_ENV=base
CONDA_EXE=/opt/anaconda3/3.10/anaconda3/bin/conda
CONDA_PREFIX=/opt/anaconda3/3.10/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/opt/anaconda3/3.10/anaconda3/bin/python
CONDA_ROOT=/opt/anaconda3/3.10/anaconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
LD_LIBRARY_PATH=/home/rlavera/.local/lib:/usr/lib/x86_64-linux-gnu/hdf5/serial:
LD_PRELOAD=<not set>
PATH=/home/rlavera/.local/bin:/home/rlavera/.local/bin:/opt/anaconda3/3.10/
anaconda3/bin:/opt/anaconda3/3.10/anaconda3/condabin:/usr/local/sbin:/
usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/game
s:/usr/lib/wsl/lib:/mnt/d/Intel/oneAPI/tbb/latest/redist/intel64/vc_mt
:/mnt/d/Intel/oneAPI/tbb/latest/redist/ia32/vc_mt:/mnt/d/Intel/oneAPI/
compiler/latest/windows/redist/intel64_win/compiler:/mnt/d/Intel/oneAP
I/compiler/latest/windows/redist/ia32_win/compiler:/mnt/c/Windows/syst
em32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System
32/WindowsPowerShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Progr
am Files (x86)/NVIDIA Corporation/PhysX/Common:/mnt/c/Program
Files/dotnet:/mnt/d/Strawberry-PERL/c/bin:/mnt/d/Strawberry-
PERL/perl/site/bin:/mnt/d/Strawberry-PERL/perl/bin:/mnt/e/Python-VS-
2019/VC/Tools/MSVC/14.29.30133/bin/Hostx64/x86:/mnt/d/MatLab2022b/bin:
/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/m
nt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/System32/O
penSSH:/mnt/d/GitW64/cmd:/mnt/d/HDF5/bin:/mnt/d/HDF5:/mnt/d/VTK:/mnt/d
/VTK/bin:/mnt/d/TIFF-4-
5/libtiff/Release:/mnt/c/Users/Ron/AppData/Local/Microsoft/WindowsApps
:/mnt/d/Microsoft VS Code/bin:/mnt/e/MCNP620/MCNP_CODE/MCNP620/Utiliti
es/EVENTLOG_ANALYZER:/mnt/d/Strawberry-PERL/perl/lib:/mnt/d/Anaconda3-
W11/Scripts:/mnt/e/PyNE:/mnt/e/cmake-3-26-
1/bin:/mnt/d/HDFVIEW/app:/mnt/d/HDFVIEW/runtime/bin:/mnt/d/MiKTeX/mikt
ex/bin/x64:/mnt/c/Program Files/CMake/bin:/mnt/c/Users/Ron/AppData/Loc
al/Programs/Python/Python39/Scripts:/mnt/e/PyNE/pyne:/snap/bin:/opt/an
aconda3/3.10/anaconda3/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>

active environment : base
active env location : /opt/anaconda3/3.10/anaconda3
shell level : 1
user config file : /home/rlavera/.condarc
populated config files : /home/rlavera/.condarc
conda version : 23.1.0
conda-build version : 3.23.3
python version : 3.10.9.final.0
virtual packages : __archspec=1=x86_64
__cuda=12.0=0
__glibc=2.35=0
__linux=5.15.90.1=0
__unix=0=0
base environment : /opt/anaconda3/3.10/anaconda3 (writable)
conda av data dir : /opt/anaconda3/3.10/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/anaconda3/3.10/anaconda3/pkgs
/home/rlavera/.conda/pkgs
envs directories : /opt/anaconda3/3.10/anaconda3/envs
/home/rlavera/.conda/envs
platform : linux-64
user-agent : conda/23.1.0 requests/2.28.1 CPython/3.10.9 Linux/5.15.90.1-microsoft-standard-WSL2 ubuntu/22.04.2 glibc/2.35
UID:GID : 1000:1000
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

Your help would be appreciated.

Thanks.

Ron

log.txt

Ron Lavera

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Apr 5, 2023, 10:46:08 AM4/5/23

to pyne...@googlegroups.com

This is a follow up to my previous email.

I was able to get PyNE to install by removing the Windows PATH statements pointing to my HDF5 installation on the Windows D: volume.

However, the installation then threw a number of warning messages I thought you might be interested in knowing about.

Please see the attached files.

Ron

pyne-install-screenshot.txt

pyne-install-log.txt

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