Feature/issue 1818 upgrade sundials 520

[wds15]

Summary

Bump to Sundials 5.2.0. Upgrade handled with update-sundials.sh script without any hiccups.

Tests

No new tests. These tests link against the new sundials:

test/unit/math/rev/functor/cvodes_ode_data_rev_test.cpp
test/unit/math/rev/functor/integrate_ode_cvodes_grad_rev_test.cpp
test/unit/math/rev/functor/cvodes_ode_data_prim_test.cpp

Side Effects

None

Release notes

Upgrade Sundials to version 5.2.0

Checklist

• Math issue Upgrade to Sundials 5.2.0 #1818

• Copyright holder: Sebastian Weber

  The copyright holder is typically you or your assignee, such as a university or company. By submitting this pull request, the copyright holder is agreeing to the 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/)

• the basic tests are passing

  • unit tests pass (to run, use: ./runTests.py test/unit)
  • header checks pass, (make test-headers)
  • dependencies checks pass, (make test-math-dependencies)
  • docs build, (make doxygen)
  • code passes the built in C++ standards checks (make cpplint)

• the code is written in idiomatic C++ and changes are documented in the doxygen

• the new changes are tested

[rok-cesnovar]

Looks good. Merge when/if tests pass

[wds15]

looks like upstream failure due to pow, right?

[rok-cesnovar]

Network issue on a worker. This needs a conflict resolve now anyways.

[wds15]

Here we go again.

[rok-cesnovar]

Thanks

[wds15]

Hä? This is stopped by clang-format on Stan upstream? Odd.

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.84	4.84	1.0	-0.01% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.99	-0.9% slower
eight_schools/eight_schools.stan	0.09	0.09	0.97	-2.58% slower
gp_regr/gp_regr.stan	0.22	0.22	1.0	0.47% faster
irt_2pl/irt_2pl.stan	6.44	6.44	1.0	0.05% faster
performance.compilation	89.43	87.37	1.02	2.31% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.56	7.53	1.0	0.37% faster
pkpd/one_comp_mm_elim_abs.stan	20.5	20.51	1.0	-0.02% slower
sir/sir.stan	92.55	94.94	0.97	-2.59% slower
gp_regr/gen_gp_data.stan	0.05	0.05	0.99	-1.26% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.95	2.95	1.0	-0.08% slower
pkpd/sim_one_comp_mm_elim_abs.stan	0.31	0.3	1.03	2.54% faster
arK/arK.stan	1.76	1.74	1.01	0.92% faster
arma/arma.stan	0.66	0.66	0.99	-0.84% slower
garch/garch.stan	0.52	0.51	1.01	0.55% faster
Mean result: 0.999488695589

---

Jenkins Console Log
Blue Ocean
Commit hash: 5edd97b

---

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