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Segfault in optimizing for simple exponential model #545

NathanWycoff opened this Issue Jul 9, 2018 · 4 comments


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NathanWycoff commented Jul 9, 2018

This issue ported over from here.

Hello everyone,

I want to first thank the developers for an awesome software package that has helped me extensively in several projects.

This bug doesn't really affect me, but I felt like I should report it anyways. With a specific model/data combination and a specific random seed, I observe a segfault when invoking the optimizing function. The model is rather simple.

Steps to reproduce:

  1. Please find the model attached exp_model.txt
  2. Please find an R script attached breaks_stan.txt. Rename these if necessary (not sure why github won't accept R/stan files).
  3. Modify line 36 of the R file to point to where exp_model.stan lives on disk.
  4. Run the R file in its entirety. This is important to advance PRNG to the point of failure. This involves sampling from the posterior, but it terminates in less than half a second on my machine.

Bug Description:
Posterior sampling from the model works fine. Afterwards, when trying to find the optimum, it will print the initial loglikelihood, then R will freeze for about half a minute before this message appears (the shrug emoji is just my replacement for the standard prompt):

    ¯\_(ツ)_/¯ optimizing(mod, data = stan_dat)
    Initial log joint probability = -8.18984

     *** caught segfault ***
    address 0x256b38fff, cause 'memory not mapped'

     1: .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x7fdbf945fd70>,     dll = list(name = "Rcpp", path = "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/libs/",         dynamicLookup = TRUE, handle = <pointer: 0x7fdbf9708d90>,         info = <pointer: 0x7fdbf986aa20>), numParameters = -1L),     <pointer: 0x7fdbf97fb9b0>, <pointer: 0x7fdbf9739640>, .pointer,     ...)
     2: sampler$call_sampler(c(args, dotlist))
     3: .local(object, ...)
     4: optimizing(mod, data = stan_dat)
     5: optimizing(mod, data = stan_dat)

    Possible actions:
    1: abort (with core dump, if enabled)
    2: normal R exit
    3: exit R without saving workspace
    4: exit R saving workspace

This only seems to occur for a specific PRNG state.

Facts about the platform this was discovered on:

OS: Mac OS High Sierra 10.13.2

R: R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

rstan (Version 2.17.3, GitRev: 2e1f913)

R was executed directly from a bash terminal.


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bob-carpenter commented Jul 9, 2018


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maverickg commented Jul 9, 2018

Well, I tried on the last released version of CmdStan and had segfault for some particular seed too. So I don't think it's a RStan issue.

This is the seed I used:

./exp_model optimize data file=exp.rdump random seed=12345

And exp.rdump file has

$ more exp.rdump
alpha_l1_0 <- 0.2
alpha_l2_0 <- 0.2
beta_l1_0 <- 1
beta_l2_0 <- 1
t1 <- 0.281152420352801
t2 <- 0.164745791682175

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bob-carpenter commented Jul 9, 2018


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bob-carpenter commented Jul 9, 2018

This issue was moved to stan-dev/stan#2576

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