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I've tracked it down to this issue pytorch/pytorch#27971 and the workaround of setting LRU_CACHE_CAPACITY=1 seems to do the trick -
$ export LRU_CACHE_CAPACITY=1
$ /usr/bin/time -v bonito basecaller dna_r9.4.1 read --device cpu > /dev/null
...
Maximum resident set size (kbytes): 1196220
Note: the basecaller will be very slow on CPU as PyTorch won't taking advantage of all the cores, using a different runtime like ONNX or PlaidML might be worth a look for CPU.
iiSeymour
changed the title
mem issues ?
[bug] memory leak with CPU basecalling
Feb 20, 2020
Hi,
thanks for this, interesting project.
I may have found a mem leak while testing:
Server Ubuntu 1604 48 GB RAM CPU only
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