Problem writing python with Lammps to output

LAMMPS LAMMPS Mailing List Mirror
1

Hi Lammps community,

I have a quick question while running Lammps with Python in our HPC system. I in stalled Lammps via conda cloud.

This is supposed to be a very simple question but I really don’t know anything about Lammps code.

I have a code with running Lammps in Python: let say a.py.

If I run the code using command:

$ python a.py

This code works fine and write the output to screen

However if I want to write the output to a file, for example output.txt, I run the command:

$ python a.py > output.txt

I have an error:

Traceback (most recent call last):

File “a.py”, line 10, in

a0 = L.eval(“a”)

File “usr/.conda/envs/LammpsPy/lib/python3.7/site-packages/lammps.py”, line 931, in eval

value = self.lmp_print(’"$(s)"' expr).strip()

AttributeError: ‘NoneType’ object has no attribute ‘strip’

2

It would be useful to know, which version of LAMMPS this is with (the date printed when you launch LAMMPS).
it also would be helpful, if you would provide a simple and complete example that demonstrates the issue reliably and quickly.

there are some known difficulties with line-buffering vs block-buffering when redirecting output, since PyLammps captures and interprets LAMMPS output and thus is dependent on line-buffering as far as i know.
if you want to play it safe, use the more low-level “lammps” python class, which is not affected by this.
i am copying richard berger, the author of the PyLammps class, who might be able to comment further.

axel.

3

This is related to the following issues:

https://github.com/lammps/lammps/issues/666

and

https://github.com/lammps/lammps/issues/871

Redirecting the output of LAMMPS when using PyLammps is problematic. The solution is to use stdbuf, using python3 or setting the environment variable PYTHONUNBUFFERED=1

stdbuf -oL python3 bug.py > lmp.log

Best,

Richard

4

Hi Richard,

Thanks for jumping in to help.

That’s perfect answer.

I know there is something wrong in writing the Lammps output but I could not figure it out.

I am able to run the program now.

Regards,

Tue