Python PETSc Example BP1 #1806
Python PETSc Example BP1 #1806
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examples/python/bpsraw.py
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| matrix = PETSc.Mat().createAIJ([num_dofs, num_dofs], comm=PETSc.COMM_WORLD) | ||
| matrix.setFromOptions() | ||
| matrix.setUp() | ||
| for i in range(num_dofs): | ||
| e_vec = ceed.Vector(num_dofs) | ||
| r_vec = ceed.Vector(num_dofs) | ||
| e_vec.set_value(0.0) | ||
| r_vec.set_value(0.0) | ||
| with e_vec.array_write() as arr: | ||
| arr[i] = 1.0 | ||
| op.apply(e_vec, r_vec) | ||
| with r_vec.array_read() as r_arr: | ||
| matrix.setValues(range(num_dofs), [i], r_arr) | ||
| matrix.assemble() |
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You'll want a MatShell, not a MatAIJ
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Apologies for leaving this a bit stale. Addressing this led to a lot of other changes. I had trouble setting the matrix type to "shell" and applying context, kept getting segmentation faults. So, instead of using the "shell" type, I used the "python" type and set the context through a python class. Pulled that implementation from the petsc4py 2DPoisson example (about half way down) --> link. I'll tidy up what I have a submit an update soon.
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Overall this is looking like the right approach. The big thing is to try to avoid copying around data during frequent operations, like the matrix application
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Thank you for all the suggestions! Definitely, keeping the data in place would mean less overhead and better efficiency
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@tylercollins5737 , thank you for your work. Are you able to address the reviewer's comments? |
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@valeriabarra I was able to get it working using the "python" matrix type, MatAIJ was not the best. I believe the "python" type and MatCreateShell can achieve the same thing. |
| with self.v.array_read() as va: | ||
| y.setValues(range(lo, hi), va[lo:hi]) | ||
| y.assemble() |
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Ideally, you'd set v to use y's array before you apply the libCEED operator
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That makes more sense, thank you!
| def CreateRestriction(ceed, mesh_elem, P, num_comp, ndofs, offsets): | ||
| return ceed.ElemRestriction(mesh_elem, P, num_comp, 1, ndofs, offsets, cmode=libceed.USE_POINTER) |
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If this just wraps another function call, I think its clearer to use the function call itself
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Totally agree, I have another CreateRestriction function that reflects C but its a WIP
Co-authored-by: Jeremy L Thompson <[email protected]>
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Hey @tylercollins5737 , how are you? I was wondering if you intended to complete this PR or if there were any impeding issues that you encountered. There are a couple of other potential contributors that are eyeing this project and I was wondering if there was a missing interface for which this BP could not be completed or if it was just for personal reasons. Thank you! |
Hey @valeriabarra hope you are doing well! In short, progress didn't stop because of any major limitations in the libceed or petsc libraries. But the qfunction for building the RHS "SetupMassRHS" and "Error" I believe aren't available so a workaround would have to be implemented which could be very slow, or an addition to the gallery of qfunctions, or someway to use the qfunctions used by the BPs, or a way to define a custom one in python. If there are interested contributors they're more than welcome to work on it. If no one picks it up, I'll start on it again and get the development environment setup on a computer I actually own. Cheers! |
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Yeah, since there are QFunctions that are not available via the gallery, you'd have to use the technique shown in this folder for |
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@jeremylt Cool, yeah that should do the trick. |
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Hello!
This is a Python implementation of bpsraw.c for BP1 and was initially discussed in #1774 . I'm aiming to recreate the benchmark behavior using libceed and petsc4py. I appreciate any feedback or indications I'm headed in the right direction!
It does run, but this is a work in progress. Remaining tasks: