options for mclapply
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Description
Summary:
Fitting a large model (1.4m rows, 1m ranefs) and saving ranefs in parallel on a scientific computing cluster leads to the error "long vectors not supported yet" in fork.c. I might be able to fix this by turning off prescheduling in mclapply, but I cannot set options for it from outside rstan.
Description:
It seems to be this issue: http://stackoverflow.com/questions/23231183/mclapply-long-vectors-not-supported-yet?rq=1
Reproducible Steps:
Fit very large model, save ranefs (more than 1m ranefs).
Current Output:
Chain 4, Iteration: 1500 / 1500 [100%] (Sampling)
Elapsed Time: 197373 seconds (Warm-up)
30336.8 seconds (Sampling)
227710 seconds (Total)Error in sendMaster(try(eval(expr, env), silent = TRUE)) :
long vectors not supported yet: fork.c:376
RStan Version:
2.14.1
R Version:
"R version 3.3.1 (2016-06-21)"
Operating System:
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux 7.2 (Nitrogen)
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the ranef-saving path that invokes mclapply and inspect how its arguments are currently selected. Determine how callers could supply mclapply options, then reproduce the large-ranef workload and confirm the configured scheduling avoids the reported fork.c error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- distributed-systems
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100