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Quad/octree building for FMMs in Python and OpenCL
Specifically, this code here:
boxtree/boxtree/pyfmmlib_integration.py
Lines 379 to 394 in d48fcdf
should not exist.
cc @gaohao95
Following inducer/loopy#220
After installing boxtree, I tried running the included example (demo.py), and got the following error during compilation of an OpenCL kernel:
Traceback (most recent call last):
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/pytools-2014.3.5-py3.4.egg/pytools/__init__.py", line 467, in wrapper
return getattr(self, cache_dict_name)[key]
AttributeError: 'TreeBuilder' object has no attribute '_memoize_dic_get_kernel_info'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "demo.py", line 29, in <module>
tree, _ = tb(queue, particles, max_particles_in_box=30)
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/boxtree-2013.1-py3.4.egg/boxtree/tree_build.py", line 170, in __call__
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/pytools-2014.3.5-py3.4.egg/pytools/__init__.py", line 469, in wrapper
result = method(self, *args, **kwargs)
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/boxtree-2013.1-py3.4.egg/boxtree/tree_build.py", line 71, in get_kernel_info
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/boxtree-2013.1-py3.4.egg/boxtree/tree_build_kernels.py", line 1218, in get_tree_build_kernel_info
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/pyopencl-2015.1-py3.4-linux-x86_64.egg/pyopencl/scan.py", line 1036, in __init__
self.finish_setup()
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/pyopencl-2015.1-py3.4-linux-x86_64.egg/pyopencl/scan.py", line 1125, in finish_setup
use_bank_conflict_avoidance=use_bank_conflict_avoidance)
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/pyopencl-2015.1-py3.4-linux-x86_64.egg/pyopencl/scan.py", line 1277, in build_scan_kernel
prg = cl.Program(self.context, scan_src).build(self.options)
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/pyopencl-2015.1-py3.4-linux-x86_64.egg/pyopencl/__init__.py", line 218, in build
options=options, source=self._source)
File "/home/lee8rx/anaconda/envs/py34/lib/python3.4/site-packages/pyopencl-2015.1-py3.4-linux-x86_64.egg/pyopencl/__init__.py", line 258, in _build_and_catch_errors
raise err
pyopencl.RuntimeError: clBuildProgram failed: invalid binary -
Build on <pyopencl.Device 'GeForce GTX 670' on 'NVIDIA CUDA' at 0x132bc80>:
ptxas error : Entry function 'scan_scan_intervals_lev1' uses too much shared data (0xc0bc bytes, 0xc000 max)
It appears that the kernel requires slightly more than the 48k shared memory limit on my GPU (Nvidia GTX 670). Is there any relatively simple way to help limit the shared memory usage of the kernel in this case? I am not entirely certain whether the error is the fault of boxtree
or pyopencl
itself, but any feedback on how to avoid the issue would be appreciated.
If I modify the example to run with dims = 3
instead, the kernels do compile and run correctly for that case.
Because of the line
Line 919 in cacf6eb
If python <3.9, I get,
File "/home/idf2/miniconda3/envs/py38/lib/python3.8/site-packages/boxtree/tools.py", line 919, in <module>
coord_dtype: np.dtype[Any], dimensions: int) -> np.dtype[Any]:
TypeError: Type subscription requires python >= 3.9
If numpy<1.22, I get,
>>> np.dtype[Any]
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: 'numpy._DTypeMeta' object is not subscriptable
It'd be nice if we had a mechanism for automatically balancing the FMM, maybe by automatic timing runs.
The question here is effectively, "what is the biggest calculation we can fit on Titan V? (i.e. how many particles can we fit into 12 GB?)"
If that number is embarrassingly low---say below a few hundred million (@isuruf suggested as much, reporting that 100M dies in double), we should account for what the biggest memory hogs are.
Hi, using
sudo pip install boxtree
returns the following:
Downloading/unpacking boxtree
Could not find any downloads that satisfy the requirement boxtree
Cleaning up...
No distributions at all found for boxtree
Storing debug log for failure in /home/mrea1g12/.pip/pip.log
On Ubuntu 14.04, 64-bit. Any thoughts?
return DirectionalSourceDerivative(
/home/kirby/Code/firedrake-complex/src/sumpy/sumpy/kernel.py:1316: UserWarning: specified the name of the direction vector
return type(kernel)(
/home/kirby/Code/firedrake-complex/src/pytential/pytential/qbx/refinement.py:476: RefinerNotConvergedWarning: QBX layer potential source refiner did not terminate after 0 iterations (the maximum). You may call 'refine_geometry_collection()' manually and pass 'visualize=True' to see what area of the geometry is causing trouble. If the issue is disturbance of expansion disks, you may pass a slightly increased value (currently: 0.025) for 'expansion_disturbance_tolerance'. As a last resort, you may use Python's warning filtering mechanism to not treat this warning as an error. The criteria triggering refinement in each iteration were: .
warn(
/home/kirby/Code/firedrake-complex/lib/python3.8/site-packages/numpy/core/fromnumeric.py:86: VisibleDeprecationWarning: Creating an ndarray from nested sequences exceeding the maximum number of dimensions of 32 is deprecated. If you mean to do this, you must specify 'dtype=object' when creating the ndarray.
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
/home/kirby/Code/firedrake-complex/src/pytential/pytential/qbx/refinement.py:476: RefinerNotConvergedWarning: QBX layer potential source refiner did not terminate after 0 iterations (the maximum). You may call 'refine_geometry_collection()' manually and pass 'visualize=True' to see what area of the geometry is causing trouble. If the issue is disturbance of expansion disks, you may pass a slightly increased value (currently: 0.025) for 'expansion_disturbance_tolerance'. As a last resort, you may use Python's warning filtering mechanism to not treat this warning as an error. The criteria triggering refinement in each iteration were: .
warn(
/home/kirby/Code/firedrake-complex/src/loopy/loopy/target/execution.py:193: ParameterFinderWarning: Unable to generate code to automatically find 'nunit_dofs' from the shape of 'result':
division with remainder in linear solve for 'nunit_dofs'
warn("Unable to generate code to automatically "
/home/kirby/Code/firedrake-complex/src/boxtree/boxtree/tree_build.py:380: RuntimeWarning: overflow encountered in subtract
bbox["max_"+ax] - bbox["min_"+ax]
Traceback (most recent call last):
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 822, in _get_qbx_discretization
discr = self._get_discr_from_cache(geometry, discr_stage)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 782, in _get_discr_from_cache
raise KeyError(
KeyError: "cached discretization does not exist on '{geometry}'for stage '{discr_stage}'"
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/qbx/refinement.py", line 893, in _refine_for_global_qbx
discr, conn = get_from_cache(*ds)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/qbx/refinement.py", line 863, in get_from_cache
discr = places._get_discr_from_cache(geometry, to_ds)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 782, in _get_discr_from_cache
raise KeyError(
KeyError: "cached discretization does not exist on '{geometry}'for stage '{discr_stage}'"
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "mi_decoupled_nl.py", line 241, in <module>
Bctx.dlp.get_pot_and_grad(x, complex(kt))
File "/home/kirby/Documents/mibc/code/laypot.py", line 97, in get_pot_and_grad
op_grad_x = self.bound_op_and_grad(self.actx, u=density, k=kappa)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 1157, in __call__
return self.eval(kwargs, array_context=array_context)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 1131, in eval
return self.code.execute(exec_mapper)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/compiler.py", line 404, in execute
self.get_exec_function(insn, exec_mapper)(
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 313, in exec_assign
return [(name, evaluate(expr))
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 313, in <listcomp>
return [(name, evaluate(expr))
File "/home/kirby/Code/firedrake-complex/lib/python3.8/site-packages/pymbolic/mapper/__init__.py", line 129, in __call__
return method(expr, *args, **kwargs)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 279, in map_interpolation
conn = self.places.get_connection(expr.from_dd, expr.to_dd)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 853, in get_connection
return connection_from_dds(self, from_dd, to_dd)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/dof_connection.py", line 234, in connection_from_dds
to_discr = places.get_discretization(to_dd.geometry, to_dd.discr_stage)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 881, in get_discretization
return self._get_qbx_discretization(geometry, discr_stage)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/symbolic/execution.py", line 829, in _get_qbx_discretization
_refine_for_global_qbx(self, dofdesc,
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/qbx/refinement.py", line 895, in _refine_for_global_qbx
discr, conn = _refine_qbx_stage2(
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/qbx/refinement.py", line 736, in _refine_qbx_stage2
tree = wrangler.build_tree(places,
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/qbx/utils.py", line 129, in build_tree
return build_tree_with_qbx_metadata(
File "/home/kirby/Code/firedrake-complex/lib/python3.8/site-packages/pytools/__init__.py", line 2511, in wrapper
return wrapped(*args, **kwargs)
File "/home/kirby/Code/firedrake-complex/src/pytential/pytential/qbx/utils.py", line 321, in build_tree_with_qbx_metadata
tree, evt = tree_builder(queue, particles,
File "/home/kirby/Code/firedrake-complex/src/boxtree/boxtree/tree_build.py", line 461, in __call__
assert nboxes_guess > 0
AssertionError```
PYOPENCL_TEST=nvi:k40 python test_fmm.py 'test_fmm_completeness(cl._csc, 3, 50000, 40000, "", p_normal, p_normal, None)'
seems to fail somewhat reliably. Strangely, this happens with a fairly ancient set of versions: 88bdb3a for boxtree, and f999323804b6df44abf7da1181e66fed831f86f7 for pyopencl. It happens in the same fashion with newer code. The timing coincides with an Nvidia driver upgrade on those machines. I've tried rolling back to an older driver, but I can't quite reconstruct what version we were on.
cc @mattwala
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