de/serialization issues

[wds15]

Summary:

When using rstan 2.13 stan_rdump to serialize arrays with zero size , then these cannot be read with cmdstan 2.13

Description:

Serializing with stan_rdump and starting a cmdstan run does not work any more if the arrays has size zero. This used to work with rstan 2.12 and cmdstand 2.12.

This releated to the issue rstan#371 .

Reproducible Steps:

serialized data with rstan 2.13 which does not work with cmdstan 2.13:

N <- 0
y <- 
structure(integer(0), 
.Dim = c(0))

this data works with cmdstan 2.13 and was generated with rstan 2.12:

N <- 0
y <- 
structure(c(),
.Dim = c(0))

Here is a dummy Stan program:

data {
  int N;
  int y[N];
}
parameters {
  real mu;
}
model {
  target += normal_lpdf(mu|0, 1);
}

Current Output:

cmdstan fails to run

Expected Output:

Error from cmdstan:

[weberse2@node04:~/work/stan/misc] ./stan_int_bug sample data file=notok.R

Exception: data y value  beyond int range
Diagnostic information: 
stan_2.13.1/src/stan/io/dump.hpp(518): Throw in function bool stan::io::dump_reader::next()
Dynamic exception type: boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::invalid_argument> >
std::exception::what: data y value  beyond int range

cmdstan Stan Version:

2.13.1

Operating System:

RHEL 6.7

[bob-carpenter]

This issue was moved to stan-dev/rstan#373

[maverickg]

I will try to fix it in stan rather than rstan so all are happy.

[bob-carpenter]

OK, if you want to fix it there, it should be a Stan issue. But it should be opened as a Stan issue rather than as a comment about RStan to CmdStan translation. But why not just go back to having RStan generate the same output as before? - Bob

…

On Dec 21, 2016, at 11:08 PM, maverickg ***@***.***> wrote: I will try to fix it in stan rather than rstan so all are happy. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or mute the thread.

[maverickg]

see here for why rstan changed this function: stan-dev/rstan#366

The issue is kind of with stan/io/dump.hpp now. In the case of zero length array/matrix/vector, dump in stan depends on a technically wrong behavior of stan_rdump prior to 2.13.2, which outputs zero length array as structure(c(), .Dim = c(1,2,3)). But c() gives NULL in R. So now I think it's better that dump can read data current stan_rdump outputs (examples below).

x <- structure(integer(0), .Dim = c(2, 3, 0))
y <- structure(integer(), .Dim = c(2, 0))
z <- structure(integer(2), .Dim = c(2))
a <- integer()
b <- integer(1)

[bob-carpenter]

Got it. Thanks for re-opening. R never ceases to amaze me:

> c()
NULL

> length(c())
[1] 0