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lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
https://dna.physics.ox.ac.uk/
GNU General Public License v3.0
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[BUG] Parallel Tempering_MPI example results (energy, trajectory ..) are not evolving #85

Closed hub-Veronika closed 3 months ago

hub-Veronika commented 6 months ago

Describe the bug After the oxDNA_mpi was built as it was suggested in README the Parallel Tempering example, I ran the example simulation as a test. I’ve gotten files mpi_i_energy.dat, mpi_i_trajactory.dat, and mpi_i_last_conf.dat with the same values as the initial condition, such as energy on all steps is -1.203504, trajectory = last_conf and all of them remains the same during simulation.

To Reproduce

  1. Build oxDNA_mpi with "make mpi=1"
  2. Run the interactive job with the command (in the folder with examples/PARALLEL_TEMPERING):

mpirun -v -n 4 /home/veronika/oxDNA/build/bin/oxDNA_mpi inputPT

where 4 is the number of MPI processes I need for that test.

Expected behavior I expected to get energy and trajectory evolution during parallel tempering VVMC simulation.

Desktop (please complete the following information):

Additional context I used different MPIs to build and run simulations, as well as I tried to run with my input, which had RNA molecule parameters. I asked our cluster support programmer, and I was told that MPI itself works correctly (the job was recognized and all 4 replicas from the example ran in parallel). I use oxDNA to rum VVMC and MD simulations of RNA molecules on CPU and GPU (MD only). I had no problem with them.

lorenzo-rovigatti commented 6 months ago

Hi! Unfortunately this is a known bug (see #15 ). I'll try to have a look, but I didn't code the backend myself so I'm not familiar with its inner workings

hub-Veronika commented 6 months ago

Dear Lorenzo Rovigatti,

Thank you for getting back to me. I saw this #15 bug, however, the last change in the example was created after the 15th issue date. That is why I assumed the prior issue had potentially been resolved, and I might have tried to build or use the program incorrectly.

Best regards.

lorenzo-rovigatti commented 6 months ago

The example now runs, but I'm not 100% sure it works (i.e. it gives sensible results).

hub-Veronika commented 6 months ago

Dear Lorenzo Rovigatti,

Thank you very much for your new commit. I will try and check as soon as possible.

Best regards.

lorenzo-rovigatti commented 3 months ago

Hey @hub-Veronika , any news on this one?

hub-Veronika commented 3 months ago

Dear Lorenzo Rovigatti,

I tried a few times and this build is working now. However, I switched before to a different type of simulation and, unfortunately, I can't say about the sensibility of the results of the Parallel Tempering simulation. I don't use the Parallel Tempering method on a daily basis, and I'm not sure when I will be using it consistently.

Best regards.

lorenzo-rovigatti commented 3 months ago

OK, thank you for the update. I'll mark this down as closed, but feel free to reopen it if you start using the backend and find more issues.