Issue/upgrade sundials 510 2

[wds15]

Summary

This upgrades Sundials to version 5.1.0

Tests

Any tests which use the Sundials libraries. For example

./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

No

Checklist

• Math issue sundials 5.1.0 #1553

• 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)
  • 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

[wds15]

@rok-cesnovar is this the windows fail you saw already:

g++ -std=c++1y -m64 -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs      -I lib/tbb_2019_U8/include -O3  -I . -I lib/eigen_3.3.3 -I lib/boost_1.72.0 -I lib/sundials_5.1.0/include -I lib/gtest_1.8.1/include -I lib/gtest_1.8.1   -D_USE_MATH_DEFINES  -DBOOST_DISABLE_ASSERTS       -c -MT test/unit/math/prim/fun/gamma_q_test.o -M -E -MG -MP -MF test/unit/math/prim/fun/gamma_q_test.d test/unit/math/prim/fun/gamma_q_test.cpp
Cannot contact gelman-group-win2: hudson.remoting.RequestAbortedException: java.nio.channels.ClosedChannelException
process_begin: CreateProcess(c:\Rtools\mingw_64\bin\mingw32-make.exe, mingw32-make -j16 test/unit/math/prim/fun/gamma_q_test.exe test/unit/math/prim/fun/get_base1_lhs_test.exe test/unit/math/prim/fun/get_base1_test.exe test/unit/math/prim/fun/get_lp_test.exe test/unit/math/prim/fun/gp_dot_prod_cov_test.exe test/unit/math/prim/fun/gp_exponential_cov_test.exe test/unit/math/prim/fun/gp_exp_quad_cov_test.exe test/unit/math/prim/fun/gp_matern32_cov_test.exe test/unit/math/prim/fun/gp_matern52_cov_test.exe test/unit/math/prim/fun/gp_periodic_cov_test.exe test/unit/math/prim/fun/grad_2F1_test.exe test/unit/math/prim/fun/grad_F32_test.exe test/unit/math/prim/fun/grad_reg_inc_beta_test.exe test/unit/math/prim/fun/grad_reg_inc_gamma_test.exe test/unit/math/prim/fun/grad_reg_lower_inc_gamma_test.exe test/unit/math/prim/fun/head_test.exe test/unit/math/prim/fun/hypot_test.exe test/unit/math/prim/fun/identity_transform_test.exe test/unit/math/prim/fun/if_else_test.exe test/unit/math/prim/fun/inc_beta_dda_test.exe, ...) failed.
make (e=6, rc=19): The handle is invalid.

fun/col_test.exe test/unit/math/prim/fun/constants_test.exe test/unit/math/prim/fun/containers_conversion_test.exe test/unit/math/prim/fun/corr_matrix_transform_test.exe test/unit/math/prim/fun/corr_transform_test.exe test/unit/math/prim/fun/cos_test.exe test/unit/math/prim/fun/cov_exp_quad_test.exe test/unit/math/prim/fun/cov_matrix_transform_test.exe test/unit/math/prim/fun/crossprod_test.exe
------------------------------------------------------------
mingw32-make -j16 test/unit/math/prim/fun/csr_extract_u_test.exe test/unit/math/prim/fun/csr_extract_v_test.exe test/unit/math/prim/fun/csr_extract_w_test.exe test/unit/math/prim/fun/csr_matrix_times_vector_test.exe test/unit/math/prim/fun/csr_to_dense_matrix_test.exe test/unit/math/prim/fun/csr_u_to_z_test.exe test/unit/math/prim/fun/cumulative_sum_test.exe test/unit/math/prim/fun/determinant_test.exe test/unit/math/prim/fun/diagonal_test.exe test/unit/math/prim/fun/diag_matrix_test.exe test/unit/math/prim/fun/diag_post_multiply_test.exe test/unit/math/prim/fun/diag_pre_multiply_test.exe test/unit/math/prim/fun/digamma_test.exe test/unit/math/prim/fun/dims_test.exe test/unit/math/prim/fun/distance_test.exe test/unit/math/prim/fun/divide_columns_test.exe test/unit/math/prim/fun/divide_test.exe test/unit/math/prim/fun/dot_self_test.exe test/unit/math/prim/fun/dot_test.exe test/unit/math/prim/fun/eigenvalues_sym_test.exe
------------------------------------------------------------
mingw32-make -j16 test/unit/math/prim/fun/eigenvectors_sym_test.exe test/unit/math/prim/fun/elt_divide_test.exe test/unit/math/prim/fun/elt_multiply_test.exe test/unit/math/prim/fun/erfc_test.exe test/unit/math/prim/fun/erf_test.exe test/unit/math/prim/fun/exp2_test.exe test/unit/math/prim/fun/expm1_test.exe test/unit/math/prim/fun/exp_test.exe test/unit/math/prim/fun/F32_test.exe test/unit/math/prim/fun/fabs_test.exe test/unit/math/prim/fun/factor_cov_matrix_transform_test.exe test/unit/math/prim/fun/falling_factorial_test.exe test/unit/math/prim/fun/fdim_test.exe test/unit/math/prim/fun/fill_test.exe test/unit/math/prim/fun/finite_diff_stepsize_test.exe test/unit/math/prim/fun/floor_test.exe test/unit/math/prim/fun/fmax_test.exe test/unit/math/prim/fun/fma_test.exe test/unit/math/prim/fun/fmin_test.exe test/unit/math/prim/fun/gamma_p_test.exe
------------------------------------------------------------
mingw32-make -j16 test/unit/math/prim/fun/gamma_q_test.exe test/unit/math/prim/fun/get_base1_lhs_test.exe test/unit/math/prim/fun/get_base1_test.exe test/unit/math/prim/fun/get_lp_test.exe test/unit/math/prim/fun/gp_dot_prod_cov_test.exe test/unit/math/prim/fun/gp_exponential_cov_test.exe test/unit/math/prim/fun/gp_exp_quad_cov_test.exe test/unit/math/prim/fun/gp_matern32_cov_test.exe test/unit/math/prim/fun/gp_matern52_cov_test.exe test/unit/math/prim/fun/gp_periodic_cov_test.exe test/unit/math/prim/fun/grad_2F1_test.exe test/unit/math/prim/fun/grad_F32_test.exe test/unit/math/prim/fun/grad_reg_inc_beta_test.exe test/unit/math/prim/fun/grad_reg_inc_gamma_test.exe test/unit/math/prim/fun/grad_reg_lower_inc_gamma_test.exe test/unit/math/prim/fun/head_test.exe test/unit/math/prim/fun/hypot_test.exe test/unit/math/prim/fun/identity_transform_test.exe test/unit/math/prim/fun/if_else_test.exe test/unit/math/prim/fun/inc_beta_dda_test.exe
mingw32-make -j16 test/unit/math/prim/fun/gamma_q_test.exe test/unit/math/prim/fun/get_base1_lhs_test.exe test/unit/math/prim/fun/get_base1_test.exe test/unit/math/prim/fun/get_lp_test.exe test/unit/math/prim/fun/gp_dot_prod_cov_test.exe test/unit/math/prim/fun/gp_exponential_cov_test.exe test/unit/math/prim/fun/gp_exp_quad_cov_test.exe test/unit/math/prim/fun/gp_matern32_cov_test.exe test/unit/math/prim/fun/gp_matern52_cov_test.exe test/unit/math/prim/fun/gp_periodic_cov_test.exe test/unit/math/prim/fun/grad_2F1_test.exe test/unit/math/prim/fun/grad_F32_test.exe test/unit/math/prim/fun/grad_reg_inc_beta_test.exe test/unit/math/prim/fun/grad_reg_inc_gamma_test.exe test/unit/math/prim/fun/grad_reg_lower_inc_gamma_test.exe test/unit/math/prim/fun/head_test.exe test/unit/math/prim/fun/hypot_test.exe test/unit/math/prim/fun/identity_transform_test.exe test/unit/math/prim/fun/if_else_test.exe test/unit/math/prim/fun/inc_beta_dda_test.exe failed
exit now (01/15/20 14:32:14 Eastern Standard Time)
script returned exit code 19

[rok-cesnovar]

No, this one is new, but based on the error, the connection to the machine errored-out. Just restart the tests I guess. The reason why the machine errored out could be related to #1615

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	5.01	4.95	1.01	1.24% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.97	-3.35% slower
eight_schools/eight_schools.stan	0.09	0.09	0.99	-1.11% slower
gp_regr/gp_regr.stan	0.22	0.22	0.99	-0.77% slower
irt_2pl/irt_2pl.stan	6.13	6.07	1.01	1.05% faster
performance.compilation	87.96	86.78	1.01	1.34% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.31	7.34	1.0	-0.47% slower
pkpd/one_comp_mm_elim_abs.stan	20.31	20.95	0.97	-3.15% slower
sir/sir.stan	105.01	107.37	0.98	-2.24% slower
gp_regr/gen_gp_data.stan	0.05	0.04	1.01	1.3% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.96	2.98	0.99	-0.58% slower
pkpd/sim_one_comp_mm_elim_abs.stan	0.32	0.33	0.97	-3.11% slower
arK/arK.stan	1.75	1.75	1.0	0.3% faster
arma/arma.stan	0.8	0.8	1.01	0.81% faster
garch/garch.stan	0.59	0.58	1.0	0.3% faster
Mean result: 0.994662601481

---

Jenkins Console Log
Blue Ocean
Commit hash: 926a016

---

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

[wds15]

This sundials upgrade can and definitely should wait for merge with develop until the release 2.22 of Stan / Stan-Math 3.1 .

[rok-cesnovar]

Will approve and merge on Sunday/Monday then. Looks good to me otherwise.

[wds15]

Great. Note the changes to the update script. Somehow kinsol got removed from the script, but we use that in the meantime.

[rok-cesnovar]

Release done, LGTM