CmdStan in Stan v2.10.0 questions (as used in Julia / Stan.jl)

[Rob J. Goedman]

Hi,

I’ve started testing bit with v2.10.0 and ran into a few issues.

The output of the diagnose method:

# stan_version_major = 2

# stan_version_minor = 9

# stan_version_patch = 0

# model = bernoulli_model

# method = diagnose

#   diagnose

#     test = gradient (Default)

#       gradient

#         epsilon = 9.9999999999999995e-07 (Default)

#         error = 9.9999999999999995e-07 (Default)

# id = 1

# data

#   file = bernoulli_1.data.R

# init = 2 (Default)

# random

#   seed = 2073302974

# output

#   file = bernoulli_diagnose_1.csv

#   diagnostic_file =  (Default)

#   refresh = 100 (Default)

# 

#  Log probability=-7.81905

# 

#  param idx           value           model     finite diff           error

#          0       -0.331304        -1.01508        -1.01508    -3.54424e-10

Issue 1: Minor version incorrect? Looking at the link output, e.g. boost_1.60.0 and linking the sundials_cvodes library, I think it is v2.10.0

--- Translating Stan model to C++ code ---

bin/stanc /Users/rob/.julia/v0.4/Stan/Examples/Bernoulli/tmp/bernoulli.stan --o=/Users/rob/.julia/v0.4/Stan/Examples/Bernoulli/tmp/bernoulli.hpp

Model name=bernoulli_model

Input file=/Users/rob/.julia/v0.4/Stan/Examples/Bernoulli/tmp/bernoulli.stan

Output file=/Users/rob/.julia/v0.4/Stan/Examples/Bernoulli/tmp/bernoulli.hpp

--- Linking C++ model ---

clang++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.8 -isystem stan/lib/stan_math/lib/boost_1.60.0 -isystem stan/lib/stan_math/lib/cvodes_2.8.2/include -Wall -DEIGEN_NO_DEBUG  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe  -Wno-unused-function -Wno-tautological-compare -Wno-c++11-long-long -ftemplate-depth=256    -O3 -o /Users/rob/.julia/v0.4/Stan/Examples/Bernoulli/tmp/bernoulli src/cmdstan/main.cpp -include /Users/rob/.julia/v0.4/Stan/Examples/Bernoulli/tmp/bernoulli.hpp stan/lib/stan_math/lib/cvodes_2.8.2/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/cvodes_2.8.2/lib/libsundials_cvodes.a 

Issue 2: It seems the last 4 lines of the output files are now commented out, is that intended?

Issue 3: I have not looked in detail what is happening here, but for some reason the dyes and kids examples no longer sample properly. In the case of the kids example, in fact 1 chain does sample somewhat, 3 others are constant. In the case of te dyes example, all are constant. Not sure what changed here. E.g.:

[Daniel Lee]

CmdStan v2.10 isn't out yet.

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Switching back to v2.9.0 fixes both examples.

Regards,

Rob

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[Rob J. Goedman]

Thanks Daniel,

I took your earlier message (6/18, below) as a request to start testing.

I’ll hold off for now.

Regards,

Rob

--------------------------------------------------

Hi all,

I got it tagged and released this morning.

Math: https://github.com/stan-dev/math/releases/tag/v2.10.0

Stan: https://github.com/stan-dev/stan/releases/tag/v2.10.0

If you're working on an interface, use the tagged versions.

Daniel

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[Daniel Lee]

Ah... no, not yet. Maybe in a day or two.

Daniel