Can you give more detail about the data? Enzo I'm guessing? Unigrid or AMR?
How many grid patches in the output?
My first thought is that this is probably a bug, especially if it runs
within memory bounds on one core, there's probably some unnecessary
double-allocation going on.
On Fri, Feb 22, 2019 at 1:31 PM David Collins
Hi, Everybody!
I'm trying to run a parallel projection on a 1024^3 simulation, but I keep getting out-of-memory. Serial works fine. This is all on Stampede, on an interactive node. My script is direct from the website, and is below. Is there something dumb I'm doing?
Thanks!
I do
$ibrun -np 2 python parallel_test.py
and parallel_test.py contains """ from mpi4py import MPI import yt yt.enable_parallelism()
ds = yt.load("/scratch/00369/tg456484/Paper49d_moresims/ze01_M10_MA1_1024_quan/DD0095/data0095") /DD%04d/data%04d"%(22,22)) p = yt.ProjectionPlot(ds, "x", "density") p.save() """
my output then looks like:
000 yt : [INFO ] 2019-02-22 13:00:41,879 Gathering a field list (this may take a moment.) File "parallel_test.py", line 13, in <module> p = yt.ProjectionPlot(ds, "x", "density") File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/visualizati on/plot_window.py", line 1480, in __init__ max_level=max_level) File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/data_object s/construction_data_containers.py", line 270, in __init__ self.get_data(field) File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/data_object s/construction_data_containers.py", line 334, in get_data self._initialize_chunk(chunk, tree)
File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", line 271, in cached_func tr = func(self) File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", line 332, in icoords ci = np.empty((self.data_size, 3), dtype='int64') P006 yt : [ERROR ] 2019-02-22 13:03:36,145 MemoryError: File "parallel_test.py", line 13, in <module> p = yt.ProjectionPlot(ds, "x", "density") File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/visualization/plot_window.py", line 1480, in __init__ max_level=max_level) File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/data_objects/construction_data_containers.py", line 270, in __init__ self.get_data(field) File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/data_objects/construction_data_containers.py", line 334, in get_data self._initialize_chunk(chunk, tree) File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/data_objects/construction_data_containers.py", line 401, in _initialize_chunk icoords = chunk.icoords File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/data_objects/data_containers.py", line 1555, in icoords return self._current_chunk.icoords File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", line 271, in cached_func tr = func(self) File "/home1/00369/tg456484/local-yt-2019-02-22-py3/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", line 332, in icoords ci = np.empty((self.data_size, 3), dtype='int64') P007 yt : [ERROR ] 2019-02-22 13:03:36,145 MemoryError: P002 yt : [ERROR ] 2019-02-22 13:03:36,200 Error occured on rank 2. P004 yt : [ERROR ] 2019-02-22 13:03:36,200 Error occured on rank 4. P000 yt : [ERROR ] 2019-02-22 13:03:36,200 Error occured on rank 0. P001 yt : [ERROR ] 2019-02-22 13:03:36,200 Error occured on rank 1. P003 yt : [ERROR ] 2019-02-22 13:03:36,200 Error occured on rank 3. P005 yt : [ERROR ] 2019-02-22 13:03:36,200 Error occured on rank 5. P006 yt : [ERROR ] 2019-02-22 13:03:36,200 Error occured on rank 6. P007 yt : [ERROR ] 2019-02-22 13:03:36,200 Error occured on rank 7. application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 TACC: MPI job exited with code: 1 TACC: Shutdown complete. Exiting.
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