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PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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System freezes on running mclapply #132

Open ArtPoon opened 6 years ago

ArtPoon commented 6 years ago

This has come up when running parallel analyses of BiSSE (#131) and compartmental models (issue?). The current workaround is to run R from the command line, which suggests that this problem is related to running parallel processes within RStudio.

Can someone reproduce this problem within RStudio and monitor memory usage before the crash? Then we can do the same thing for command-line execution and compare. It would be easier to diagnose memory leaks if we can run it from the command line with valgrind.

ArtPoon commented 6 years ago

@helenhe96 and @gtng92 have tried to reproduce this crash on their systems and it hasn't come up yet, which suggests that this is a stochastic problem and points to a possible memory leak/allocation bug. Please run simple tests in Valgrind.