Thanks for the help. Unfortunately, that didn't work -- I tried putting export > PYTHONPATH=/opt/apps/intel18/impi18_0/meep/1.12.0/lib/python3.7/site-packages/
before, after, and in place of > ln -sf > /opt/apps/intel18/impi18_0/meep/1.12.0/lib/python3.7/site-packages/meep/ ./ > in the sbatch script but got the same error each time: Attempting to use an MPI routine before initializing MPI. Was there a different way I should have implemented that line of code? Also, when you say "Perhaps there are two different (and conflicting) PyMeep versions installed?", does that mean the issue lies within Stampede2's internal programming, and that I should ask TACC for their help again? On Thu, Aug 20, 2020 at 9:54 PM Ardavan Oskooi <ardavan.osk...@gmail.com> wrote: > 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. > > -- Patrick Flanigan Etaphase, Inc. 8201 NE 164th Avenue, Suite 200 Redmond, WA 98052 http://etaphase.com/
_______________________________________________ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
