The meep module seems to be installed in the system folder
/opt/apps/intel18/impi18_0/meep/1.12.0/lib/python3.7/site-packages/meep/
but the runtime error is in simulation.py is from your local directory
in /home1/07449/pf04620/bend_flux/meep/. Perhaps there are two different
(and conflicting) PyMeep versions installed?
Try including the line "export
PYTHONPATH=/opt/apps/intel18/impi18_0/meep/1.12.0/lib/python3.7/site-packages/"
in your batch script to specify the environment variable where Python
should look to find the meep module files.
PS. The meep-discuss archives are available at:
https://www.mail-archive.com/meep-discuss@ab-initio.mit.edu/.
On 8/20/20 13:23, Patrick Flanigan wrote:
(I apologize if this has already been asked; for some reason I can't
access the discussion archives at
http://ab-initio.mit.edu/pipermail/meep-discuss/ at the moment).
I'm trying to run Python-based MEEP codes on the Stampede2 cluster
(https://portal.tacc.utexas.edu/user-guides/stampede2). I'm actually
dealing with a lot of errors, but to keep things simple for my first
post I'll just ask one question. Since I know the sample codes on the
GitHub repository work, I've been trying to run them on the cluster
before I use my own. When I take bend-flux.py
(https://github.com/NanoComp/meep/blob/master/python/examples/bend-flux.py)
and run it locally on my own Ubuntu terminal, it works fine and gives
the expected output. However, when I try to run it as batch job, I get
this error message
Traceback (most recent call last):
File "bend_flux.py", line 54, in <module>
sim.run(until_after_sources=mp.stop_when_fields_decayed(50,mp.Ez,pt,1e-3))
File "/home1/07449/pf04620/bend_flux/meep/simulation.py", line
2231, in run
self._run_sources_until(until_after_sources, step_funcs)
File "/home1/07449/pf04620/bend_flux/meep/simulation.py", line
1519, in _run_sources_until
self._run_until(new_conds, step_funcs)
File "/home1/07449/pf04620/bend_flux/meep/simulation.py", line
1495, in _run_until
self.progress.value = t0 + stop_time
UnboundLocalError: local variable 't0' referenced before assignment
This is the batch script that I've been using (it took a lot of help
from other more experienced users) :
#!/bin/bash
#SBATCH -J bend_flux
#SBATCH -o bend_flux_out.txt
#SBATCH -e bend_flux_err.txt
#SBATCH -n 1
#SBATCH -N 1
#SBATCH -p development
#SBATCH -t 0:10:00
module load python3
module load meep
ln -sf
/opt/apps/intel18/impi18_0/meep/1.12.0/lib/python3.7/site-packages/meep/
./
ibrun -np 1 python3 bend_flux.py > bend_flux_run.txt
(I just changed the - to _ in the file name because I thought it would
help avoid errors; I don't think that's the problem). I don't fully
understand it, but I think that the ln -sf line puts all the MEEP
files in the folder where the batch script is, but there's some sort
of problem with reading those files. Could it be because the cluster
is using an older version of MEEP, and this bug is fixed in more
recent versions? Or is this something I need to manually change in the
simulation.py file?
Any help would be greatly appreciated.
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