Add model compile information to stdout and csv

[rok-cesnovar]

Submisison Checklist

• Run tests: ./runCmdStanTests.py src/test
• Declare copyright holder and open-source license: see below

Summary:

Addresses a part of #887

Add models compile information (stanc version and flags used) to the stdout and CSV.

Example:

data
  file = examples/bernoulli/bernoulli.data.json
init = 2 (Default)
random
  seed = 21139381 (Default)
output
  file = output.csv (Default)
  diagnostic_file =  (Default)
  refresh = 100 (Default)
stanc_version = stanc3 66c38187 (Unix)
stancflags = --warn-pedantic

# init = 2 (Default)
# random
#   seed = 21139381 (Default)
# output
#   file = output.csv (Default)
#   diagnostic_file =  (Default)
#   refresh = 100 (Default)
# stanc_version = stanc3 66c38187 (Unix)
# stancflags = --warn-pedantic

This should be included to make reproducing easier, especially with stanc optimization flag now available.

The tests will fail until stan-dev/stanc3#598 and stan-dev/stan#2932 are merged

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):
Rok Češnovar, Univ. of Ljubljana

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

[mitzimorris]

for version

bin/stanc --version
stanc3 8b086da (Unix)

these are the compiler options:

  --debug-lex                      For debugging purposes: print the lexer actions
  --debug-parse                    For debugging purposes: print the parser actions
  --debug-ast                      For debugging purposes: print the undecorated AST, before semantic checking
  --debug-decorated-ast            For debugging purposes: print the decorated AST, after semantic checking
  --debug-generate-data            For debugging purposes: generate a mock dataset to run the model on
  --debug-mir                      For debugging purposes: print the MIR as an S-expression.
  --debug-mir-pretty               For debugging purposes: pretty-print the MIR.
  --debug-optimized-mir            For debugging purposes: print the MIR after it's been optimized. Only has an effect when optimizations are turned on.
  --debug-optimized-mir-pretty     For debugging purposes: pretty print the MIR after it's been optimized. Only has an effect when optimizations are turned on.
  --debug-transformed-mir          For debugging purposes: print the MIR after the backend has transformed it.
  --debug-transformed-mir-pretty   For debugging purposes: pretty print the MIR after the backend has transformed it.
  --dump-stan-math-signatures Dump out the list of supported type signatures for Stan Math backend.
  --warn-uninitialized             Emit warnings about uninitialized variables to stderr. Currently an experimental feature.
  --warn-pedantic                  Emit warnings about common mistakes in Stan programs.
  --auto-format                    Pretty prints the program to the console
  --print-canonical                Prints the canonicalized program to the console
  --version                        Display stanc version number
  --name                           Take a string to set the model name (default = "$model_filename_model")
  --O Allow                        the compiler to apply all optimizations to the Stan code.
  --o                              Take the path to an output file for generated C++ code (default = "$name.hpp")
  --print-cpp                      If set, output the generated C++ Stan model class to stdout.
  --allow_undefined                Do not fail if a function is declared but not defined
  --include_paths                  Takes a comma-separated list of directories that may contain a file in an #include directive (default = "")
  --use-opencl                     If set, try to use matrix_cl signatures.

not sure that all of these options will result in there being an output csv file - for the ones that make sense, we need to make sure that this doesn't break any CSV header parsing that exists.

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.03	4.0	1.01	0.8% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.97	-2.68% slower
eight_schools/eight_schools.stan	0.09	0.09	1.03	2.48% faster
gp_regr/gp_regr.stan	0.19	0.19	1.0	0.39% faster
irt_2pl/irt_2pl.stan	5.28	5.37	0.98	-1.72% slower
performance.compilation	87.33	85.07	1.03	2.59% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.69	7.72	1.0	-0.44% slower
pkpd/one_comp_mm_elim_abs.stan	20.49	21.55	0.95	-5.16% slower
sir/sir.stan	93.14	97.63	0.95	-4.82% slower
gp_regr/gen_gp_data.stan	0.04	0.04	0.99	-1.41% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	3.13	3.03	1.03	3.3% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.32	0.32	0.98	-1.94% slower
arK/arK.stan	1.79	1.79	1.0	-0.05% slower
arma/arma.stan	0.69	0.59	1.16	13.78% faster
garch/garch.stan	0.53	0.52	1.02	1.98% faster
Mean result: 1.00682847769

---

Jenkins Console Log
Blue Ocean
Commit hash: 8c5ef35

---

Machine information

ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.03	4.08	0.99	-1.07% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	1.0	0.02% faster
eight_schools/eight_schools.stan	0.09	0.09	1.0	-0.0% slower
gp_regr/gp_regr.stan	0.19	0.19	0.98	-1.85% slower
irt_2pl/irt_2pl.stan	5.33	5.33	1.0	-0.15% slower
performance.compilation	85.9	85.0	1.01	1.05% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.69	7.74	0.99	-0.55% slower
pkpd/one_comp_mm_elim_abs.stan	23.26	22.66	1.03	2.56% faster
sir/sir.stan	92.18	98.31	0.94	-6.64% slower
gp_regr/gen_gp_data.stan	0.04	0.04	1.0	-0.47% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	3.01	3.1	0.97	-3.07% slower
pkpd/sim_one_comp_mm_elim_abs.stan	0.32	0.33	0.97	-2.81% slower
arK/arK.stan	1.78	1.78	1.0	0.2% faster
arma/arma.stan	0.66	0.59	1.12	10.43% faster
garch/garch.stan	0.54	0.52	1.04	3.91% faster
Mean result: 1.00241562789

---

Jenkins Console Log
Blue Ocean
Commit hash: 8c5ef35

---

Machine information

ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

[mitzimorris]

is this ready for review?
or does this have to wait on stan-dev/stan#2932 ?

[rok-cesnovar]

Waiting for that PR

[SteveBronder]

lcbtm!

[rok-cesnovar]

Thanks! This has to wait for 2932 in Stan, so this will not go in this release.

[mitzimorris]

LGTM!