debug log

[RodenLuo]

For lorenzo-rovigatti#31

[RodenLuo]

$ file /Users/yangx0i/miniconda3_arm64/envs/oxpy_arm/bin/python
/Users/yangx0i/miniconda3_arm64/envs/oxpy_arm/bin/python: Mach-O 64-bit executable arm64

[RodenLuo]

$ /Users/yangx0i/miniconda3_arm64/envs/oxpy_arm/bin/python -V
Python 3.10.4
$ git clone https://github.com/lorenzo-rovigatti/oxDNA.git
$ vi oxDNA/oxpy/CMakeLists.txt # remove the linking
$ /Applications/CMake.app/Contents/bin/cmake -version
cmake version 3.24.1

CMake suite maintained and supported by Kitware (kitware.com/cmake).
$ /Applications/CMake.app/Contents/bin/cmake .. -DDebug=True -DPython=ON -DPYTHON_INCLUDE_DIRS=/Users/yangx0i/miniconda3_arm64/envs/oxpy_arm/include/python3.10 -DPYTHON_EXECUTABLE=/Users/yangx0i/miniconda3_arm64/envs/oxpy_arm/bin/python

$ make -j98
$ make install

$ ~/.local/bin/oat config
INFO: oxDNA_analysis_tools version: 2.0.3
INFO: running config.py installed at:  /Users/yangx0i/.local/lib/python3.10/site-packages/oxDNA_analysis_tools/config.py
INFO: Python version: 3.10.4
INFO: Package Numpy found. Version: 1.23.3
INFO: Package MatPlotLib found. Version: 3.5.3
INFO: Package BioPython found. Version: 1.79
INFO: Package SciKit-Learn found. Version: 1.1.2
INFO: Package oxpy found. Version: 3.4.3.dev0+g6794178.d20220912
INFO: No dependency issues found.

INFO: Analyses will be computed in chunks of 20 configurations at a time
INFO: You can modify this number by running oat config -n <number>, which will be persistent between analyses.



$ ~/.local/bin/oat mean -h
usage: mean.py [-h] [-p num_cpus] [-o output_file] [-d deviation_file]
               [-i index_file] [-a alignment_configuration]
               trajectory

Computes the mean structure of a trajectory file

positional arguments:
  trajectory            The trajectory file you wish to analyze

options:
  -h, --help            show this help message and exit
  -p num_cpus           (optional) How many cores to use
  -o output_file, --output output_file
                        The filename to save the mean structure to
  -d deviation_file, --deviations deviation_file
                        Immediatley run oat deviations from the output
  -i index_file         Compute mean structure of a subset of particles from a
                        space-separated list in the provided file
  -a alignment_configuration, --align alignment_configuration
                        The id of the configuration to align to, otherwise
                        random


$ ~/.local/bin/oat mean -o mean_all.dat hairpin.conf 
INFO: oxDNA_analysis_tools version: 2.0.3
INFO: running config.py installed at:  /Users/yangx0i/.local/lib/python3.10/site-packages/oxDNA_analysis_tools/config.py
INFO: Python version: 3.10.4
INFO: Package Numpy found. Version: 1.23.3
INFO: No dependency issues found.
INFO: Processing in blocks of 20 configurations
INFO: You can modify this number by running oat config -n <number>, which will be persistent between analyses.
Starting up 1 processes for 1 chunks
All spawned, waiting for results
--- 0.6535718441009521 seconds ---