Closed UTNAK closed 1 month ago
@UTNAK I'm going to add these instructions into the dev container so recreating this environment is more consistent for developers and users.
Anaconda is found here: https://github.com/devcontainers/images/tree/main/src/anaconda
R and Quarto that works with VSCode found here: https://jamesgoldie.dev/writing/dev-containers-in-r/
Prepare Environment
Before you run simulations on your local computer, you need to setup simulation environments.
Install and Anaconda Python Install R and Quarto instruction is here Setup VSCode with quarto instruction is here
@UTNAK Python section of codespace is not working.
Getting an
OSError
after running Quarto notebook to calculate delta v section
This is due to the load of
from poliastro.twobody import Orbit
in src/analysis/analysisOrbit.py
I found that the this code works in python at terminal. In quarto notebook, this doesn't work
from poliastro.twobody import Orbit
This command returns error regarding to libstdc++.so.6
Traceback (most recent call last):
File "/opt/conda/envs/py39/lib/python3.9/site-packages/llvmlite/binding/ffi.py", line 136, in __getattr__
return self._fntab[name]
KeyError: 'LLVMPY_AddSymbol'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/py39/lib/python3.9/site-packages/llvmlite/binding/ffi.py", line 117, in _load_lib
self._lib_handle = ctypes.CDLL(str(lib_path))
File "/opt/conda/envs/py39/lib/python3.9/ctypes/__init__.py", line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /opt/conda/envs/py39/lib/python3.9/site-packages/llvmlite/binding/libllvmlite.so)
This command at terminal shows the list of "libstdc++.so"
find / -name "libstdc++.so*"
I found there is so many "libstdc++.so" files.
(py39) @UTNAK ➜ /workspaces/kepler16b-using-imce-vocabulary (feat/6-prototype-for-integration-of-orbital-analysis) $ find / -name "libstdc++.so.6"
find: ‘/etc/ssl/private’: Permission denied
/usr/lib/x86_64-linux-gnu/libstdc++.so.6
find: ‘/proc/tty/driver’: Permission denied
find: ‘/proc/1/task/1/fd’: Permission denied
find: ‘/proc/1/task/1/fdinfo’: Permission denied
find: ‘/proc/1/task/1/ns’: Permission denied
find: ‘/proc/1/fd’: Permission denied
find: ‘/proc/1/map_files’: Permission denied
find: ‘/proc/1/fdinfo’: Permission denied
find: ‘/proc/1/ns’: Permission denied
find: ‘/proc/323/task/323/fd’: Permission denied
find: ‘/proc/323/task/323/fdinfo’: Permission denied
find: ‘/proc/323/task/323/ns’: Permission denied
find: ‘/proc/323/fd’: Permission denied
find: ‘/proc/323/map_files’: Permission denied
find: ‘/proc/323/fdinfo’: Permission denied
find: ‘/proc/323/ns’: Permission denied
find: ‘/proc/1226/task/1226/fd’: Permission denied
find: ‘/proc/1226/task/1226/fdinfo’: Permission denied
find: ‘/proc/1226/task/1226/ns’: Permission denied
find: ‘/proc/1226/fd’: Permission denied
find: ‘/proc/1226/map_files’: Permission denied
find: ‘/proc/1226/fdinfo’: Permission denied
find: ‘/proc/1226/ns’: Permission denied
find: ‘/proc/23234/task/23234/fd’: Permission denied
find: ‘/proc/23234/task/23234/fdinfo’: Permission denied
find: ‘/proc/23234/task/23234/ns’: Permission denied
find: ‘/proc/23234/fd’: Permission denied
find: ‘/proc/23234/map_files’: Permission denied
find: ‘/proc/23234/fdinfo’: Permission denied
find: ‘/proc/23234/ns’: Permission denied
/opt/conda/lib/libstdc++.so.6
/opt/conda/envs/py39/lib/libstdc++.so.6
/opt/conda/pkgs/libstdcxx-ng-13.2.0-hc0a3c3a_7/lib/libstdc++.so.6
find: ‘/var/lib/apt/lists/partial’: Permission denied
find: ‘/var/cache/ldconfig’: Permission denied
find: ‘/var/cache/apt/archives/partial’: Permission denied
find: ‘/root’: Permission denied
/workspaces/.codespaces/shared/editors/jetbrains/pycharm-2023.1.1/plugins/remote-dev-server/selfcontained/lib/libstdc++.so.6
/workspaces/.codespaces/shared/editors/jetbrains/JetBrainsRider-2023.1/plugins/remote-dev-server/selfcontained/lib/libstdc++.so.6
/workspaces/.codespaces/shared/editors/jetbrains/RubyMine-2023.1.1/plugins/remote-dev-server/selfcontained/lib/libstdc++.so.6
/workspaces/.codespaces/shared/editors/jetbrains/idea-IU-231.8770.65/plugins/remote-dev-server/selfcontained/lib/libstdc++.so.6
In Quarto + reticulate package, "/usr/lib/x86_64-linux-gnu/libstdc++.so.6:" is used because the error logs said "OSError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found " "/usr/lib/x86_64-linux-gnu/libstdc++.so.6" doesn't contain GLIBCXX_3.4.29 as shown in below.
@UTNAK ➜ /workspaces/kepler16b-using-imce-vocabulary (feat/6-prototype-for-integration-of-orbital-analysis) $ strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX_3.4
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28
In python interpreter at conda environment, it seems conda uses "/opt/conda/envs/py39/lib/libstdc++.so.6" However, "/opt/conda/envs/py39/lib/libstdc++.so.6" contains "GLIBCXX_3.4.29" and after.
(py39) @UTNAK ➜ /workspaces/kepler16b-using-imce-vocabulary (feat/6-prototype-for-integration-of-orbital-analysis) $ strings /opt/conda/envs/py39/lib/libstdc++.so.6 | grep GLIBCXX_3.4
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28
GLIBCXX_3.4.29
GLIBCXX_3.4.30
GLIBCXX_3.4.31
GLIBCXX_3.4.32
Below commands enable updating the libstdc++.so.6 for quarto + reticulate I think this is not recommended because this manually copy a libstdc++.so.6 file.
cd /opt/conda/envs/py39/lib/
sudo cp libstdc++.so.6 /usr/lib/x86_64-linux-gnu/libstdc++.so.6
Checklist before submitting a merge request
Description of contribution
Using the quarto notebook as an analysis engine, this PR demonstrate the integration of mathematical analysis using Python and R with OML Descriptive models.
Close #6
Testing performed
Prepare Environment
Before you run simulations on your local computer, you need to setup simulation environments.
Testing
In VSCODE,