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Fix memory allocation on MPI gather_abundance() #69

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richardreeve opened this issue Jul 21, 2021 · 0 comments
Open

Fix memory allocation on MPI gather_abundance() #69

richardreeve opened this issue Jul 21, 2021 · 0 comments

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@richardreeve
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Trying to fix some MPI problems in #66 has led to an issue with gather_abundance() doing a lot of allocation while trying to collect the abundance data sensibly onto one node. It seems to be non-trivial to fix, but doesn't get done very often, so this issue just notes it needs fixed when possible. This might involve one or many of:

  1. Some kind of custom view into the full abundance array on the root process where the abundances are gathered to
  2. Some kind of custom view into the process-specific abundance array on every process
  3. Distributed calculation instead of whatever is being done on the root process

I suspect 1 may be the easiest to accomplish, then the array can be copied as is from the other processes, but 3 might be the ideal solution in many cases.

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