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Add /dev/shm space check before shared memory allocation in global adaptivity #217 #227

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Add /dev/shm space check before shared memory allocation in global adaptivity #217 #227

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15 changes: 15 additions & 0 deletions micro_manager/adaptivity/global_adaptivity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
Note: All ID variables used in the methods of this class are global IDs, unless they have *local* in their name.
"""
import hashlib
import shutil
from copy import deepcopy
import sys
from typing import Dict
Expand Down Expand Up @@ -90,6 +91,20 @@ def __init__(
nbytes = (
self._global_number_of_sims * self._global_number_of_sims * itemsize
)
# Check if /dev/shm has enough space before attempting allocation.
# On some systems, /dev/shm is limited to 50% of RAM, which can cause
# a cryptic MPI internal error for large simulations.
_, _, shm_free = shutil.disk_usage("/dev/shm")
if nbytes > shm_free:
raise RuntimeError(
"Not enough space in /dev/shm to allocate the similarity distance matrix "
"for global adaptivity.\n"
" Required : {} B\n"
" Available: {} B\n"
"On some systems /dev/shm is limited to 50% of RAM. "
"Consider increasing /dev/shm size (e.g. `--shm-size` in Docker, or "
"`tmpfs` remount), or use local adaptivity instead.".format(nbytes, shm_free)
)
else:
nbytes = 0

Expand Down