Output file

[MathXCruz]

Hello,

I tried to run an example case, like

ctwrap run freeflame freeflame.yaml --parallel --strategy sequence

and I got some warnings, with this error message:

RuntimeWarning: Output of metadata failed with error message:
Unable to open file (unable to open file: name = 'freeflame.h5', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2)

Do I need to create an empty freeflame.h5 file beforehand? If so, where should it be created? Also, can i choose csv instead of h5 in the YAML configuration file?

[ischoegl]

Shouldn't be necessary. Could you let me know what operating system this is running on? (also, what python version)

[MathXCruz]

I don't have pip installed outside conda, so it doesn't work.

Running which ctwrap, I get

/home/matheus/anaconda3/envs/ctwrap/bin/ctwrap

and the output from running, with the extra -v, is below.

################################################################################
Running simulations: module ctwrap.modules.freeflame
Conditions specified in freeflame.yaml
################################################################################
Simulations for entry upstream.phi with values: [0.4, 0.6, 0.8, 1.0, 1.2, 1.4,
1.6, 1.8, 2.0, 2.2, 2.4, 2.6]

• Starting serial batch simulation
• running case_00 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_00' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_01 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_01' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_02 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_02' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_03 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_03' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_04 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_04' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_05 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_05' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_06 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_06' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_07 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_07' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_08 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_08' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_09 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_09' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_10 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_10' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
• running case_11 (main)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/handler.py:522: RuntimeWarning: Simulation of 'Freeflame' for 'case_11' failed with error message:
  Cannot construct 'Parser' object from freeflame.yaml with type '<class 'str'>'
  warnings.warn(msg, RuntimeWarning)
  /home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/ctwrap/output.py:349: RuntimeWarning: Output of metadata failed with error message:
  Unable to open file (unable to open file: name = 'freeflame.h5', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2)
  warnings.warn(msg, RuntimeWarning)

[ischoegl]

Alright. I think we're getting closer as it looks like there's something amiss with the parser. Could you run

pytest tests/test_parser.py

from the root folder? (this is the test suite for the parser)

If it runs without errors, also try pytest for everything.

[MathXCruz]

I ran it an this is the output.
After that, I tried searching for the tests folder and found out there is another ctwrap folder which is in my home folder and contains the tests folder, is that OK?

==================================== test session starts =====================================
platform linux -- Python 3.7.10, pytest-6.2.2, py-1.10.0, pluggy-0.13.1
rootdir: /
plugins: cov-2.11.1
collected 0 items

====================================== warnings summary ======================================
home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/_pytest/cacheprovider.py:428
/home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/_pytest/cacheprovider.py:428: PytestCacheWarning: could not create cache path /.pytest_cache/v/cache/nodeids
config.cache.set("cache/nodeids", sorted(self.cached_nodeids))

home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/_pytest/stepwise.py:49
/home/matheus/anaconda3/envs/ctwrap/lib/python3.7/site-packages/_pytest/stepwise.py:49: PytestCacheWarning: could not create cache path /.pytest_cache/v/cache/stepwise
session.config.cache.set(STEPWISE_CACHE_DIR, [])

-- Docs: https://docs.pytest.org/en/stable/warnings.html
==================================== 2 warnings in 0.01s =====================================
ERROR: file or directory not found: tests/test_parser.py

[ischoegl]

Just to make sure: please run it from the same folder where you ran the setup for conda etc.. The conda environment also has to be activated for this to work. I’ll probably push an update that allows to troubleshoot it further over the weekend

[MathXCruz]

When running it from the installation folder I get

ERROR: usage: pytest [options] [file_or_dir] [file_or_dir] [...]
pytest: error: unrecognized arguments: --cov=ctwrap
inifile: /home/matheus/ctwrap/pytest.ini
rootdir: /home/matheus/ctwrap

[ischoegl]

Per your other comment: CSV output currently doesn't appear to work, but that's likely not a big issue to fix (see #86). The advantage of H5 is that you can re-import a solution into a cantera FreeFlame object at a later point.

[ischoegl]

@MathXCruz ... one thing I just remembered is that MultiProcessing really messes with error outputs. Could you run the same job sequentially (non-parallel):

ctwrap run freeflame freeflame.yaml --strategy sequence -v

(I am throwing the 'v' flag in here so you see more output)

[ischoegl]

@MathXCruz ... I pushed an update to the repository that should help diagnose the issue (I believe there is something not quite right about the conda environment). From the installation folder, run

git pull
python setup.py develop

to update to the newest version, and then run

ctwrap test freeflame

which should give the actual error stack. (I added this option as the package converts errors to warnings for batch jobs, which loses important information that I need to diagnose the issue).

[MathXCruz]

Here is the message I get by following these steps.

usage: ctwrap [-h] {list,run} ...
ctwrap: error: argument command: invalid choice: 'test' (choose from 'list', 'run')

[ischoegl]

Looks like it didn’t update. Could you run pip uninstall ctwrap followed by pip install . -e?

[MathXCruz]

pip install . -e doesn't work, I tried pip install . -e ctwrap and the result is:

ERROR: File "setup.py" not found. Directory cannot be installed in editable mode: /home/matheus/ctwrap/ctwrap

The weird thing is I can see setup.py in the ctwrap folder.

[ischoegl]

Ok. Did you activate the conda environment?

[MathXCruz]

I did. I cannot use pip without activating it.

[ischoegl]

Alright. I believe there's something awry with the conda environment. Could you start over, and make sure that the old environment is completely removed? I.e. start with a deactivated environment in the installation folder (below, I am assuming that your conda environment is 'ctwrap'). Start by removing the old version

conda remove --name ctwrap --all

and then reinstall as follows:

conda env create -f environment.yml
conda activate ctwrap
git pull
pip install -e .

After this, test it by running

ctwrap test freeflame

[MathXCruz]

It works! I also tested

ctwrap run freeflame freeflame.yaml --parallel --strategy sequence

and it works just fine. Thank you very much!

[ischoegl]

There may have been some remnants from a previous conda environment. Really happy that this is resolved!