Example run using updated torsten

[yendls]

@sundav05 According to error msg you've likely downloaded an old version of Torsten. To use cmdstanr as Torsten's R interface, you need the latest version. You can either re-download

git clone -b develop git@github.com:metrumresearchgroup/Torsten.git; cd Torsten

or update

cd Torsten
git checkout develop
git pull

It may also help if you can share the platform & compiler information.

Guessing that you are providing a customized cmdstan wrapper that uses libraries from a system installation of cmdstan?

cmdstanr is Stan's to-be-released R interface, and yes it's a light-weight wrapper of cmdstan. Torsten provides customized version of the following libraries in the Stan family:

• Stan Math: math kernel
• Stan: sampler
• cmdstan: command line interface
• stanc3: Stan-to-c++ transpiler.

User will be able to find these components in Torsten folder after download. cmdstanr is installed from official Stan repo. So if a Torsten can be built by cmdstan, so should it be by cmdstanr.

Originally posted by @yizhang-yiz in https://github.com/metrumresearchgroup/Torsten/issues/26#issuecomment-739063235

[yendls]

Hi Yi,

We have tried updating the torsten to the latest commit in the "develop" branch and below you can see the R Session.

[root@45bdf2658655 /]# cd Torsten/ [root@45bdf2658655 Torsten]# git checkout develop Already on 'develop' [root@45bdf2658655 Torsten]# git pull Already up-to-date. [root@45bdf2658655 Torsten]# R

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

[Previously saved workspace restored]

library("cmdstanr") This is cmdstanr version 0.2.2

• Online documentation and vignettes at mc-stan.org/cmdstanr
• Use set_cmdstan_path() to set the path to CmdStan
• Use install_cmdstan() to install CmdStan set_cmdstan_path("cmdstan") CmdStan path set to: /Torsten/cmdstan file <- file.path("/Torsten/example-models/pk2cpt/pk2cpt.stan") mod <- cmdstan_model(file) Compiling Stan program... ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 637 100 637 0 0 2746 0 --:--:-- --:--:-- --:--:-- 2769 100 16.6M 100 16.6M 0 0 33.5M 0 --:--:-- --:--:-- --:--:-- 33.5M /Torsten/cmdstan/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=linux runtime=cc4.9.2_libc2.17_kernel3.10.0 In file included from stan/lib/stan_math/stan/math/torsten/ev_manager.hpp:5:0, from stan/lib/stan_math/stan/math/torsten/pmx_solve_bdf.hpp:7, from stan/lib/stan_math/stan/math/torsten/torsten.hpp:4, from stan/lib/stan_math/stan/math.hpp:21, from stan/src/stan/model/model_header.hpp:4: stan/lib/stan_math/stan/math/torsten/ev_history.hpp: In instantiation of 'torsten::NonEventParameters<T0, T4, theta_container, std::tuple<ContainerOperands ...>, Ts ...>::NonEventParameters(int, const rec_t&, const std::vector<theta_container >&, const std::vector<std::vector >& ..., const std::vector<std::vector >& ...) [with rec_t = torsten::NONMENEventsRecord<double, double, double, double>; T0 = double; T4 = double; theta_container = std::vector; tuple_pars_t = {}; Ts = {}]': stan/lib/stan_math/stan/math/torsten/ev_manager.hpp:68:0: required from 'torsten::EventsManager<torsten::NONMENEventsRecord<T0, T1, T2, T3>, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<tuple_pars_t ...>, Ts ...> >::EventsManager(int, const ER&, const std::vector<theta_container >&, const std::vector<std::vector >& ...) [with Tss = {}; T0 = double; T1 = double; T2 = double; T3 = double; T4 = double; theta_container = std::vector; tuple_pars_t = {}; Ts = {}; torsten::EventsManager<torsten::NONMENEventsRecord<T0, T1, T2, T3>, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<tuple_pars_t ...>, Ts ...> >::ER = torsten::NONMENEventsRecord<double, double, double, double>]' stan/lib/stan_math/stan/math/torsten/ev_solver.hpp:131:78: required from 'void torsten::EventSolver<T_model, torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> > >::pred(int, const T_event_record&, Eigen::Matrix<typename torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> >::T_scalar, -1, -1>&, torsten::PMXOdeIntegrator, const std::vector<theta_container >&, const std::vector<std::vector >& ..., const std::vector<std::vector >& ..., const scalar_pars_type ...) [with torsten::PMXOdeIntegratorId It = (torsten::PMXOdeIntegratorId)0u; scalar_pars_type = {}; T_model = torsten::PMXTwoCptModel; T_event_record = torsten::NONMENEventsRecord<double, double, double, double>; T0 = double; T4 = double; theta_container = std::vector; array_2d_tuple_pars_value_type = {}; array_2d_pars_value_type = {}; typename torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> >::T_scalar = double]' stan/lib/stan_math/stan/math/torsten/pmx_solve_cpt.hpp:120:7: required from 'static Eigen::Matrix<typename stan::return_type<T0, T1, T2, T3, T4, Ts ...>::type, -1, -1> torsten::PMXSolveCPT::solve(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector<std::vector >&, const std::vector<std::vector >& ...) [with T0 = double; T1 = double; T2 = double; T3 = double; T4 = double; Ts = {}; model_t = torsten::PMXTwoCptModel; typename stan::return_type<T0, T1, T2, T3, T4, Ts ...>::type = double]' stan/lib/stan_math/stan/math/torsten/pmx_solve_cpt.hpp:178:91: required from 'static Eigen::Matrix<typename stan::return_type<T0, T1, T2, T3, typename torsten::value_type::type>::type, -1, -1> torsten::PMXSolveCPT::solve(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&) [with T0 = double; T1 = double; T2 = double; T3 = double; T_par = double; std::enable_if_t<(!(torsten::is_std_vector::value))> = 0u; model_t = torsten::PMXTwoCptModel; typename stan::return_type<T0, T1, T2, T3, typename torsten::value_type::type>::type = double]' stan/lib/stan_math/stan/math/torsten/pmx_solve_twocpt.hpp:32:54: required from 'auto torsten::pmx_solve_twocpt(Ts ...) [with Ts = {std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<double, std::allocator >}]' /tmp/RtmpY89mpW/model-1dd7461592c.hpp:503:0: required from 'T__ pk2cpt_model_namespace::pk2cpt_model::log_prob(std::vector&, std::vector&, std::ostream) const [with bool propto = false; bool jacobian = false; T = double; std::ostream = std::basic_ostream]' stan/src/stan/model/model_base_crtp.hpp:147:29: required from 'double stan::model::model_base_crtp::log_prob(std::vector&, std::vector&, std::ostream) const [with M = pk2cpt_model_namespace::pk2cpt_model; std::ostream = std::basic_ostream]' /tmp/RtmpY89mpW/model-1dd7461592c.hpp:1034:0: required from here stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for 'const std::tuple<>' model_array_2d_params{std::tie(model_array_2d_params0...)} { ^ stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for 'const std::tuple<>' stan/lib/stan_math/stan/math/torsten/ev_history.hpp: In instantiation of 'torsten::NonEventParameters<T0, T4, theta_container, std::tuple<ContainerOperands ...>, Ts ...>::NonEventParameters(int, const rec_t&, const std::vector<theta_container >&, const std::vector<std::vector >& ..., const std::vector<std::vector >& ...) [with rec_t = torsten::NONMENEventsRecord<double, double, double, double>; T0 = double; T4 = stan::math::var_value; theta_container = std::vector; tuple_pars_t = {}; Ts = {}]': stan/lib/stan_math/stan/math/torsten/ev_manager.hpp:68:0: required from 'torsten::EventsManager<torsten::NONMENEventsRecord<T0, T1, T2, T3>, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<tuple_pars_t ...>, Ts ...> >::EventsManager(int, const ER&, const std::vector<theta_container >&, const std::vector<std::vector >& ...) [with Tss = {}; T0 = double; T1 = double; T2 = double; T3 = double; T4 = stan::math::var_value; theta_container = std::vector; tuple_pars_t = {}; Ts = {}; torsten::EventsManager<torsten::NONMENEventsRecord<T0, T1, T2, T3>, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<tuple_pars_t ...>, Ts ...> >::ER = torsten::NONMENEventsRecord<double, double, double, double>]' stan/lib/stan_math/stan/math/torsten/ev_solver.hpp:131:78: required from 'void torsten::EventSolver<T_model, torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> > >::pred(int, const T_event_record&, Eigen::Matrix<typename torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> >::T_scalar, -1, -1>&, torsten::PMXOdeIntegrator, const std::vector<theta_container >&, const std::vector<std::vector >& ..., const std::vector<std::vector >& ..., const scalar_pars_type ...) [with torsten::PMXOdeIntegratorId It = (torsten::PMXOdeIntegratorId)0u; scalar_pars_type = {}; T_model = torsten::PMXTwoCptModel<stan::math::var_value >; T_event_record = torsten::NONMENEventsRecord<double, double, double, double>; T0 = double; T4 = stan::math::var_value; theta_container = std::vector; array_2d_tuple_pars_value_type = {}; array_2d_pars_value_type = {}; typename torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> >::T_scalar = stan::math::var_value]' stan/lib/stan_math/stan/math/torsten/pmx_solve_cpt.hpp:120:7: required from 'static Eigen::Matrix<typename stan::return_type<T0, T1, T2, T3, T4, Ts ...>::type, -1, -1> torsten::PMXSolveCPT::solve(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector<std::vector >&, const std::vector<std::vector >& ...) [with T0 = double; T1 = double; T2 = double; T3 = double; T4 = stan::math::var_value; Ts = {}; model_t = torsten::PMXTwoCptModel; typename stan::return_type<T0, T1, T2, T3, T4, Ts ...>::type = stan::math::var_value]' stan/lib/stan_math/stan/math/torsten/pmx_solve_cpt.hpp:178:91: required from 'static Eigen::Matrix<typename stan::return_type<T0, T1, T2, T3, typename torsten::value_type::type>::type, -1, -1> torsten::PMXSolveCPT::solve(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&) [with T0 = double; T1 = double; T2 = double; T3 = double; T_par = stan::math::var_value; std::enable_if_t<(!(torsten::is_std_vector::value))> = 0u; model_t = torsten::PMXTwoCptModel; typename stan::return_type<T0, T1, T2, T3, typename torsten::value_type::type>::type = stan::math::var_value]' stan/lib/stan_math/stan/math/torsten/pmx_solve_twocpt.hpp:32:54: required from 'auto torsten::pmx_solve_twocpt(Ts ...) [with Ts = {std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<stan::math::var_value<double, void>, std::allocator<stan::math::var_value<double, void> > >}]' /tmp/RtmpY89mpW/model-1dd7461592c.hpp:503:0: required from 'T__ pk2cpt_model_namespace::pk2cpt_model::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto = false; bool jacobian = false; T = stan::math::var_value; std::ostream = std::basic_ostream]' stan/src/stan/model/model_base_crtp.hpp:153:29: required from 'stan::math::var stan::model::model_base_crtp::log_prob(std::vector<stan::math::var_value, std::allocator<stan::math::var_value > >&, std::vector&, std::ostream*) const [with M = pk2cpt_model_namespace::pk2cpt_model; stan::math::var = stan::math::var_value; std::ostream = std::basic_ostream]' /tmp/RtmpY89mpW/model-1dd7461592c.hpp:1034:0: required from here stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for 'const std::tuple<>' stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for 'const std::tuple<>' cc1plus: warning: unrecognized command line option "-Wno-ignored-attributes" cc1plus: warning: unrecognized command line option "-Wno-ignored-attributes" make: *** [/tmp/RtmpY89mpW/model-1dd7461592c] Error 1 Error: An error occured during compilation! See the message above for more information. fit <- mod$sample(...) Error: object 'mod' not found

[yizhang-yiz]

I'm confused as I thought you were able to build on cmdstan. Could you do the following in shell and let me know the outcome?

cd Torsten/cmdstan
make clean-all
make -j4 build
make Torsten/example-models/pk2cpt/pk2cpt

Thank you.

[yendls]

Here is the output:

[root@45bdf2658655 Torsten]# cd /Torsten/cmdstan [root@45bdf2658655 cmdstan]# make clean-all rm -f -r test rm -f rm -f rm -f rm -f removing dependency files rm -f src/cmdstan/main.d stan//src/stan/model/model_header.d rm -f rm -f cleaning sundials targets rm -f stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o cleaning Intel TBB targets rm -f -rf stan/lib/stan_math/lib/tbb rm -f bin/stanc bin/stanc2 bin/stansummary bin/print bin/diagnose rm -f -r src/cmdstan/main*.o bin/cmdstan rm -f stan/src/stan/model/model_header.hpp.gch rm -f examples/bernoulli/bernoulli examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.d examples/bernoulli/bernoulli.hpp rm -f -r [root@45bdf2658655 cmdstan]# make -j4 build curl -L https://github.com/metrumresearchgroup/stanc3/releases/download/torsten_v0.88/linux-stanc -o bin/stanc --retry 5 --retry-delay 10 cd stan/lib/stan_math/lib/boost_1.72.0; ./bootstrap.sh g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/stansummary.o src/cmdstan/stansummary.cpp g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/print.o src/cmdstan/print.cpp % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 637 100 637 0 0 2258 0 --:--:-- --:--:-- --:--:-- 2275Building Boost.Build engine with toolset gcc... 100 16.6M 100 16.6M 0 0 23.8M 0 --:--:-- --:--:-- --:--:-- 71.5M chmod +x bin/stanc g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/diagnose.o src/cmdstan/diagnose.cpp tools/build/src/engine/b2 Detecting Python version... 3.6 Detecting Python root... /opt/rh/rh-python36/root/usr Unicode/ICU support for Boost.Regex?... /usr Generating Boost.Build configuration in project-config.jam for gcc...

Bootstrapping is done. To build, run:

./b2

To generate header files, run:

./b2 headers

To adjust configuration, edit 'project-config.jam'. Further information:

• Command line help: ./b2 --help

• Getting started guide: http://www.boost.org/more/getting_started/unix-variants.html

• Boost.Build documentation: http://www.boost.org/build/

cd stan/lib/stan_math/lib/boost_1.72.0; ./b2 --visibility=hidden --with-program_options cxxstd=11 variant=release link=static Performing configuration checks

- default address-model    : 64-bit
- default architecture     : x86

Building the Boost C++ Libraries.

Component configuration:

- atomic                   : not building
- chrono                   : not building
- container                : not building
- context                  : not building
- contract                 : not building
- coroutine                : not building
- date_time                : not building
- exception                : not building
- fiber                    : not building
- filesystem               : not building
- graph                    : not building
- graph_parallel           : not building
- headers                  : not building
- iostreams                : not building
- locale                   : not building
- log                      : not building
- math                     : not building
- mpi                      : not building
- program_options          : building
- python                   : not building
- random                   : not building
- regex                    : not building
- serialization            : not building
- stacktrace               : not building
- system                   : not building
- test                     : not building
- thread                   : not building
- timer                    : not building
- type_erasure             : not building
- wave                     : not building

...patience... ...found 1069 targets... ...updating 48 targets... common.copy /Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib/cmake/BoostDetectToolset-1.72.0.cmake common.copy /Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib/cmake/Boost-1.72.0/BoostConfig.cmake boost-install.generate-cmake-config-version- bin.v2/tools/boost_install/BoostConfigVersion.cmake common.copy /Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib/cmake/Boost-1.72.0/BoostConfigVersion.cmake boost-install.generate-cmake-config- bin.v2/libs/headers/build/stage/boost_headers-config.cmake boost-install.generate-cmake-config-version- bin.v2/libs/headers/build/stage/boost_headers-config-version.cmake boost-install.generate-cmake-config- bin.v2/libs/program_options/build/stage/boost_program_options-config.cmake boost-install.generate-cmake-config-version- bin.v2/libs/program_options/build/stage/boost_program_options-config-version.cmake common.copy /Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib/cmake/boost_headers-1.72.0/boost_headers-config.cmake common.copy /Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib/cmake/boost_program_options-1.72.0/boost_program_options-config.cmake common.copy /Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib/cmake/boost_headers-1.72.0/boost_headers-config-version.cmake common.copy /Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib/cmake/boost_program_options-1.72.0/boost_program_options-config-version.cmake gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/positional_options.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/utf8_codecvt_facet.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/convert.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/config_file.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/winmain.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/variables_map.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/value_semantic.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/split.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/options_description.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/cmdline.o gcc.compile.c++ bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/parsers.o gcc.archive bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/libboost_program_options.a boost-install.generate-cmake-variant- bin.v2/libs/program_options/build/gcc-4.9.2/release/cxxstd-11-iso/link-static/threading-multi/visibility-hidden/libboost_program_options-variant-static.cmake common.copy /Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options.a common.copy /Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib/cmake/boost_program_options-1.72.0/libboost_program_options-variant-static.cmake ...updated 48 targets...

The Boost C++ Libraries were successfully built!

The following directory should be added to compiler include paths:

/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0

The following directory should be added to linker library paths:

/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.72.0/stage/lib

g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.o g++ -pipe -pthread -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_5.2.0/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.c -o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.o touch stan/lib/stan_math/lib/tbb/tbb-make-check

--- Compiling the main object file. This might take up to a minute. --- g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -c -o src/cmdstan/main.o src/cmdstan/main.cpp

--- Compiling pre-compiled header. This might take a few seconds. --- g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -c stan/src/stan/model/model_header.hpp -o stan/src/stan/model/model_header.hpp.gch g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -Wl,-L,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" bin/cmdstan/print.o stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options.a stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options.a -o bin/print g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -Wl,-L,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" bin/cmdstan/diagnose.o stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options.a stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options.a -o bin/diagnose ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_diag.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_bandpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodea_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/cvodes/cvodes_nls_stg1.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ic.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idaa_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_stg.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/idas/idas_nls_sim.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a ar -rs stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_bbdpre.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_ls.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_spils.o stan/lib/stan_math/lib/sundials_5.2.0/src/kinsol/kinsol_io.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.2.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o stan/lib/stan_math/lib/sundials_5.2.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o ar: creating stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a tbb_root="../tbb_2019_U8" CXX="g++" CC="gcc" LDFLAGS='-Wl,-L,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" ' 'make' -C "stan/lib/stan_math/lib/tbb" -r -f "/Torsten/cmdstan/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbbmalloc" compiler=gcc cfg=release stdver=c++1y malloc CXXFLAGS="-Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation " make[1]: Entering directory /Torsten/cmdstan/stan/lib/stan_math/lib/tbb' g++ -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -fPIC -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/backend.cpp g++ -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -fPIC -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/large_objects.cpp g++ -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -fPIC -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/backref.cpp g++ -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -fPIC -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/tbbmalloc.cpp g++ -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -fPIC -o itt_notify_malloc.o -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/itt_notify.cpp sh ../tbb_2019_U8/build/version_info_linux.sh g++ -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include >version_string.ver echo "INPUT (libtbbmalloc.so.2)" > libtbbmalloc.so g++ -E -x c++ ../tbb_2019_U8/src/tbbmalloc/lin64-tbbmalloc-export.def -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include > tbbmalloc.def g++ -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -Wno-parentheses -fPIC -D__TBBMALLOC_BUILD=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/proxy.cpp g++ -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -Wno-parentheses -fPIC -D__TBBMALLOC_BUILD=1 -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc ../tbb_2019_U8/src/tbbmalloc/tbb_function_replacement.cpp echo "INPUT (libtbbmalloc_proxy.so.2)" > libtbbmalloc_proxy.so g++ -E -x c++ ../tbb_2019_U8/src/tbbmalloc/lin64-proxy-export.def -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wall -Wextra -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -Wno-parentheses -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include > tbbmallocproxy.def g++ -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -fPIC -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I../tbb_2019_U8/src/tbbmalloc -I../tbb_2019_U8/src/tbbmalloc -I. ../tbb_2019_U8/src/tbbmalloc/frontend.cpp g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -Wl,-L,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" bin/cmdstan/stansummary.o stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options.a stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options.a -o bin/stansummary gcc -fPIC -o libtbbmalloc.so.2 backend.o large_objects.o backref.o tbbmalloc.o itt_notify_malloc.o frontend.o -ldl -lpthread -lrt -shared -Wl,-soname=libtbbmalloc.so.2 -m64 -Wl,-L,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,--version-script,tbbmalloc.def g++ -fPIC -o libtbbmalloc_proxy.so.2 proxy.o tbb_function_replacement.o -ldl -lpthread -lrt libtbbmalloc.so -shared -Wl,-soname=libtbbmalloc_proxy.so.2 -m64 -Wl,-L,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,--version-script,tbbmallocproxy.def make[1]: Leaving directory/Torsten/cmdstan/stan/lib/stan_math/lib/tbb' touch stan/lib/stan_math/lib/tbb/version_tbb_2019_U8 tbb_root="../tbb_2019_U8" CXX="g++" CC="gcc" LDFLAGS='-Wl,-L,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" ' 'make' -C "stan/lib/stan_math/lib/tbb" -r -f "/Torsten/cmdstan/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbb" compiler=gcc cfg=release stdver=c++1y CXXFLAGS="-Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation " make[1]: Entering directory /Torsten/cmdstan/stan/lib/stan_math/lib/tbb' /Torsten/cmdstan/stan/lib/stan_math/lib/tbb_2019_U8/build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=linux runtime=cc4.9.2_libc2.17_kernel3.10.0 g++ -o concurrent_hash_map.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_hash_map.cpp g++ -o concurrent_queue.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_queue.cpp g++ -o concurrent_vector.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_vector.cpp g++ -o dynamic_link.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/dynamic_link.cpp g++ -o itt_notify.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/itt_notify.cpp g++ -o cache_aligned_allocator.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/cache_aligned_allocator.cpp g++ -o pipeline.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/pipeline.cpp g++ -o queuing_mutex.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/queuing_mutex.cpp g++ -o queuing_rw_mutex.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/queuing_rw_mutex.cpp g++ -o reader_writer_lock.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/reader_writer_lock.cpp g++ -o spin_rw_mutex.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/spin_rw_mutex.cpp g++ -o x86_rtm_rw_mutex.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/x86_rtm_rw_mutex.cpp g++ -o spin_mutex.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/spin_mutex.cpp g++ -o critical_section.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/critical_section.cpp g++ -o mutex.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/mutex.cpp g++ -o recursive_mutex.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/recursive_mutex.cpp g++ -o condition_variable.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/condition_variable.cpp g++ -o tbb_thread.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_thread.cpp g++ -o concurrent_monitor.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/concurrent_monitor.cpp g++ -o semaphore.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/semaphore.cpp g++ -o private_server.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/private_server.cpp g++ -o rml_tbb.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/rml/client/rml_tbb.cpp g++ -o tbb_misc.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include -I. ../tbb_2019_U8/src/tbb/tbb_misc.cpp g++ -o tbb_misc_ex.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_misc_ex.cpp g++ -o task.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/task.cpp g++ -o task_group_context.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/task_group_context.cpp g++ -o governor.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/governor.cpp g++ -o market.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/market.cpp g++ -o arena.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/arena.cpp g++ -o scheduler.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/scheduler.cpp g++ -o observer_proxy.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/observer_proxy.cpp g++ -o tbb_statistics.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_statistics.cpp g++ -o tbb_main.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/tbb/tbb_main.cpp g++ -o concurrent_vector_v2.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/concurrent_vector_v2.cpp g++ -o concurrent_queue_v2.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/concurrent_queue_v2.cpp g++ -o spin_rw_mutex_v2.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/spin_rw_mutex_v2.cpp g++ -o task_v2.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -std=c++1y -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include ../tbb_2019_U8/src/old/task_v2.cpp sh ../tbb_2019_U8/build/generate_tbbvars.sh echo "INPUT (libtbb.so.2)" > libtbb.so g++ -E -x c++ ../tbb_2019_U8/src/tbb/lin64-tbb-export.def -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fPIC -D__TBB_BUILD=1 -Wall -Wextra -Wno-parentheses -Wno-unknown-warning-option -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -I../tbb_2019_U8/src -I../tbb_2019_U8/src/rml/include -I../tbb_2019_U8/include > tbb.def g++ -fPIC -o libtbb.so.2 concurrent_hash_map.o concurrent_queue.o concurrent_vector.o dynamic_link.o itt_notify.o cache_aligned_allocator.o pipeline.o queuing_mutex.o queuing_rw_mutex.o reader_writer_lock.o spin_rw_mutex.o x86_rtm_rw_mutex.o spin_mutex.o critical_section.o mutex.o recursive_mutex.o condition_variable.o tbb_thread.o concurrent_monitor.o semaphore.o private_server.o rml_tbb.o tbb_misc.o tbb_misc_ex.o task.o task_group_context.o governor.o market.o arena.o scheduler.o observer_proxy.o tbb_statistics.o tbb_main.o concurrent_vector_v2.o concurrent_queue_v2.o spin_rw_mutex_v2.o task_v2.o -ldl -lpthread -lrt -shared -Wl,-soname=libtbb.so.2 -m64 -Wl,-L,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,--version-script,tbb.def make[1]: Leaving directory/Torsten/cmdstan/stan/lib/stan_math/lib/tbb'

--- CmdStan v2.25.0 built --- [root@45bdf2658655 cmdstan]# make /Torsten/example-models/pk2cpt/pk2cpt g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -c -MT stan/src/stan/model/model_header.hpp.gch -MT stan/src/stan/model/model_header.d -MM -E -MG -MP -MF stan/src/stan/model/model_header.d stan/src/stan/model/model_header.hpp g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -c -MT src/cmdstan/main.o -MM -E -MG -MP -MF src/cmdstan/main.d src/cmdstan/main.cpp

--- Translating Stan model to C++ code --- bin/stanc --o=/Torsten/example-models/pk2cpt/pk2cpt.hpp /Torsten/example-models/pk2cpt/pk2cpt.stan

--- Compiling, linking C++ code --- g++ -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30 -DBOOST_DISABLE_ASSERTS -c -Wno-ignored-attributes -x c++ -o /Torsten/example-models/pk2cpt/pk2cpt.o /Torsten/example-models/pk2cpt/pk2cpt.hpp In file included from stan/lib/stan_math/stan/math/torsten/ev_manager.hpp:5:0, from stan/lib/stan_math/stan/math/torsten/pmx_solve_bdf.hpp:7, from stan/lib/stan_math/stan/math/torsten/torsten.hpp:4, from stan/lib/stan_math/stan/math.hpp:21, from stan/src/stan/model/model_header.hpp:4: stan/lib/stan_math/stan/math/torsten/ev_history.hpp: In instantiation of 'torsten::NonEventParameters<T0, T4, theta_container, std::tuple<ContainerOperands ...>, Ts ...>::NonEventParameters(int, const rec_t&, const std::vector<theta_container >&, const std::vector<std::vector >& ..., const std::vector<std::vector >& ...) [with rec_t = torsten::NONMENEventsRecord<double, double, double, double>; T0 = double; T4 = double; theta_container = std::vector; tuple_pars_t = {}; Ts = {}]': stan/lib/stan_math/stan/math/torsten/ev_manager.hpp:68:0: required from 'torsten::EventsManager<torsten::NONMENEventsRecord<T0, T1, T2, T3>, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<tuple_pars_t ...>, Ts ...> >::EventsManager(int, const ER&, const std::vector<theta_container >&, const std::vector<std::vector >& ...) [with Tss = {}; T0 = double; T1 = double; T2 = double; T3 = double; T4 = double; theta_container = std::vector; tuple_pars_t = {}; Ts = {}; torsten::EventsManager<torsten::NONMENEventsRecord<T0, T1, T2, T3>, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<tuple_pars_t ...>, Ts ...> >::ER = torsten::NONMENEventsRecord<double, double, double, double>]' stan/lib/stan_math/stan/math/torsten/ev_solver.hpp:131:78: required from 'void torsten::EventSolver<T_model, torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> > >::pred(int, const T_event_record&, Eigen::Matrix<typename torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> >::T_scalar, -1, -1>&, torsten::PMXOdeIntegrator, const std::vector<theta_container >&, const std::vector<std::vector >& ..., const std::vector<std::vector >& ..., const scalar_pars_type ...) [with torsten::PMXOdeIntegratorId It = (torsten::PMXOdeIntegratorId)0u; scalar_pars_type = {}; T_model = torsten::PMXTwoCptModel; T_event_record = torsten::NONMENEventsRecord<double, double, double, double>; T0 = double; T4 = double; theta_container = std::vector; array_2d_tuple_pars_value_type = {}; array_2d_pars_value_type = {}; typename torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> >::T_scalar = double]' stan/lib/stan_math/stan/math/torsten/pmx_solve_cpt.hpp:120:7: required from 'static Eigen::Matrix<typename stan::return_type<T0, T1, T2, T3, T4, Ts ...>::type, -1, -1> torsten::PMXSolveCPT::solve(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector<std::vector >&, const std::vector<std::vector >& ...) [with T0 = double; T1 = double; T2 = double; T3 = double; T4 = double; Ts = {}; model_t = torsten::PMXTwoCptModel; typename stan::return_type<T0, T1, T2, T3, T4, Ts ...>::type = double]' stan/lib/stan_math/stan/math/torsten/pmx_solve_cpt.hpp:178:91: required from 'static Eigen::Matrix<typename stan::return_type<T0, T1, T2, T3, typename torsten::value_type::type>::type, -1, -1> torsten::PMXSolveCPT::solve(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&) [with T0 = double; T1 = double; T2 = double; T3 = double; T_par = double; std::enable_if_t<(!(torsten::is_std_vector::value))> = 0u; model_t = torsten::PMXTwoCptModel; typename stan::return_type<T0, T1, T2, T3, typename torsten::value_type::type>::type = double]' stan/lib/stan_math/stan/math/torsten/pmx_solve_twocpt.hpp:32:54: required from 'auto torsten::pmx_solve_twocpt(Ts ...) [with Ts = {std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<double, std::allocator >}]' /Torsten/example-models/pk2cpt/pk2cpt.hpp:503:0: required from 'T__ pk2cpt_model_namespace::pk2cpt_model::log_prob(std::vector&, std::vector&, std::ostream) const [with bool propto = false; bool jacobian = false; T = double; std::ostream = std::basic_ostream]' stan/src/stan/model/model_base_crtp.hpp:147:29: required from 'double stan::model::model_base_crtp::log_prob(std::vector&, std::vector&, std::ostream) const [with M = pk2cpt_model_namespace::pk2cpt_model; std::ostream = std::basic_ostream]' /Torsten/example-models/pk2cpt/pk2cpt.hpp:1034:0: required from here stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for 'const std::tuple<>' model_array_2d_params{std::tie(model_array_2d_params0...)} { ^ stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for 'const std::tuple<>' stan/lib/stan_math/stan/math/torsten/ev_history.hpp: In instantiation of 'torsten::NonEventParameters<T0, T4, theta_container, std::tuple<ContainerOperands ...>, Ts ...>::NonEventParameters(int, const rec_t&, const std::vector<theta_container >&, const std::vector<std::vector >& ..., const std::vector<std::vector >& ...) [with rec_t = torsten::NONMENEventsRecord<double, double, double, double>; T0 = double; T4 = stan::math::var_value; theta_container = std::vector; tuple_pars_t = {}; Ts = {}]': stan/lib/stan_math/stan/math/torsten/ev_manager.hpp:68:0: required from 'torsten::EventsManager<torsten::NONMENEventsRecord<T0, T1, T2, T3>, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<tuple_pars_t ...>, Ts ...> >::EventsManager(int, const ER&, const std::vector<theta_container >&, const std::vector<std::vector >& ...) [with Tss = {}; T0 = double; T1 = double; T2 = double; T3 = double; T4 = stan::math::var_value; theta_container = std::vector; tuple_pars_t = {}; Ts = {}; torsten::EventsManager<torsten::NONMENEventsRecord<T0, T1, T2, T3>, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<tuple_pars_t ...>, Ts ...> >::ER = torsten::NONMENEventsRecord<double, double, double, double>]' stan/lib/stan_math/stan/math/torsten/ev_solver.hpp:131:78: required from 'void torsten::EventSolver<T_model, torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> > >::pred(int, const T_event_record&, Eigen::Matrix<typename torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> >::T_scalar, -1, -1>&, torsten::PMXOdeIntegrator, const std::vector<theta_container >&, const std::vector<std::vector >& ..., const std::vector<std::vector >& ..., const scalar_pars_type ...) [with torsten::PMXOdeIntegratorId It = (torsten::PMXOdeIntegratorId)0u; scalar_pars_type = {}; T_model = torsten::PMXTwoCptModel<stan::math::var_value >; T_event_record = torsten::NONMENEventsRecord<double, double, double, double>; T0 = double; T4 = stan::math::var_value; theta_container = std::vector; array_2d_tuple_pars_value_type = {}; array_2d_pars_value_type = {}; typename torsten::EventsManager<T_event_record, torsten::NonEventParameters<T0, T4, theta_container, std::tuple<array_2d_tuple_pars_value_type ...>, array_2d_pars_value_type ...> >::T_scalar = stan::math::var_value]' stan/lib/stan_math/stan/math/torsten/pmx_solve_cpt.hpp:120:7: required from 'static Eigen::Matrix<typename stan::return_type<T0, T1, T2, T3, T4, Ts ...>::type, -1, -1> torsten::PMXSolveCPT::solve(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector<std::vector >&, const std::vector<std::vector >& ...) [with T0 = double; T1 = double; T2 = double; T3 = double; T4 = stan::math::var_value; Ts = {}; model_t = torsten::PMXTwoCptModel; typename stan::return_type<T0, T1, T2, T3, T4, Ts ...>::type = stan::math::var_value]' stan/lib/stan_math/stan/math/torsten/pmx_solve_cpt.hpp:178:91: required from 'static Eigen::Matrix<typename stan::return_type<T0, T1, T2, T3, typename torsten::value_type::type>::type, -1, -1> torsten::PMXSolveCPT::solve(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&) [with T0 = double; T1 = double; T2 = double; T3 = double; T_par = stan::math::var_value; std::enable_if_t<(!(torsten::is_std_vector::value))> = 0u; model_t = torsten::PMXTwoCptModel; typename stan::return_type<T0, T1, T2, T3, typename torsten::value_type::type>::type = stan::math::var_value]' stan/lib/stan_math/stan/math/torsten/pmx_solve_twocpt.hpp:32:54: required from 'auto torsten::pmx_solve_twocpt(Ts ...) [with Ts = {std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<double, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<int, std::allocator >, std::vector<stan::math::var_value<double, void>, std::allocator<stan::math::var_value<double, void> > >}]' /Torsten/example-models/pk2cpt/pk2cpt.hpp:503:0: required from 'T__ pk2cpt_model_namespace::pk2cpt_model::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto = false; bool jacobian = false; T = stan::math::var_value; std::ostream = std::basic_ostream]' stan/src/stan/model/model_base_crtp.hpp:153:29: required from 'stan::math::var stan::model::model_base_crtp::log_prob(std::vector<stan::math::var_value, std::allocator<stan::math::var_value > >&, std::vector&, std::ostream*) const [with M = pk2cpt_model_namespace::pk2cpt_model; stan::math::var = stan::math::var_value; std::ostream = std::basic_ostream]' /Torsten/example-models/pk2cpt/pk2cpt.hpp:1034:0: required from here stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for 'const std::tuple<>' stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for 'const std::tuple<>' cc1plus: warning: unrecognized command line option "-Wno-ignored-attributes" cc1plus: warning: unrecognized command line option "-Wno-ignored-attributes" make: *** [/Torsten/example-models/pk2cpt/pk2cpt] Error 1

---

Platform: NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"

Compilers: [root@45bdf2658655 cmdstan]# yum list installed | grep -i --color gcc devtoolset-3-gcc.x86_64 4.9.2-6.el7 @Centos-Local devtoolset-3-gcc-c++.x86_64 4.9.2-6.el7 @Centos-Local devtoolset-3-gcc-gfortran.x86_64 4.9.2-6.el7 @Centos-Local gcc.x86_64 4.8.5-39.el7 @Centos-Local gcc-c++.x86_64 4.8.5-39.el7 @Centos-Local gcc-gfortran.x86_64 4.8.5-39.el7 @Centos-Local libgcc.x86_64 4.8.5-39.el7 @CentOS [root@45bdf2658655 cmdstan]# yum list installed | grep -i --color java java-1.8.0-openjdk.x86_64 1:1.8.0.222.b10-0.el7_6 @Centos-Local java-1.8.0-openjdk-devel.x86_64 1:1.8.0.222.b10-0.el7_6 @Centos-Local java-1.8.0-openjdk-headless.x86_64 1:1.8.0.222.b10-0.el7_6 @Centos-Local javapackages-tools.noarch 3.4.1-11.el7 @Centos-Local python-javapackages.noarch 3.4.1-11.el7 @Centos-Local tzdata-java.noarch 2019c-1.el7 @Centos-Local [root@45bdf2658655 cmdstan]# yum list installed | grep -i --color python audit-libs-python.x86_64 2.8.5-4.el7 @Centos-Local dbus-python.x86_64 1.1.1-9.el7 @CentOS libselinux-python.x86_64 2.5-14.1.el7 @Centos-Local libsemanage-python.x86_64 2.5-14.el7 @Centos-Local libxml2-python.x86_64 2.9.1-6.el7_2.3 @CentOS policycoreutils-python.x86_64 2.5-33.el7 @Centos-Local python.x86_64 2.7.5-86.el7 @CentOS python-IPy.noarch 0.75-6.el7 @Centos-Local python-backports.x86_64 1.0-8.el7 @Centos-Local python-backports-ssl_match_hostname.noarch python-chardet.noarch 2.2.1-3.el7 @CentOS python-deltarpm.x86_64 3.6-3.el7 @Centos-Local python-devel.x86_64 2.7.5-86.el7 @Centos-Local python-gobject-base.x86_64 3.22.0-1.el7_4.1 @CentOS python-iniparse.noarch 0.4-9.el7 @CentOS python-ipaddress.noarch 1.0.16-2.el7 @Centos-Local python-javapackages.noarch 3.4.1-11.el7 @Centos-Local python-kitchen.noarch 1.1.1-5.el7 @CentOS python-libs.x86_64 2.7.5-86.el7 @CentOS python-lxml.x86_64 3.2.1-4.el7 @Centos-Local python-meld3.x86_64 0.6.10-1.el7 @Centos-Local python-nose.noarch 1.3.7-1.el7 @Centos-Local python-pycurl.x86_64 7.19.0-19.el7 @CentOS python-rpm-macros.noarch 3-32.el7 @Centos-Local python-setuptools.noarch 0.9.8-7.el7 @Centos-Local python-six.noarch 1.9.0-2.el7 @Centos-Local python-srpm-macros.noarch 3-32.el7 @Centos-Local python-urlgrabber.noarch 3.10-9.el7 @CentOS python2-rpm-macros.noarch 3-32.el7 @Centos-Local rh-python36.x86_64 2.0-1.el7 @Centos-Local rh-python36-python.x86_64 3.6.9-2.el7 @Centos-Local rh-python36-python-devel.x86_64 3.6.9-2.el7 @Centos-Local rh-python36-python-libs.x86_64 3.6.9-2.el7 @Centos-Local rh-python36-python-pip.noarch 9.0.1-2.el7 @Centos-Local rh-python36-python-setuptools.noarch 36.5.0-1.el7 @Centos-Local rh-python36-python-virtualenv.noarch 15.1.0-2.el7 @Centos-Local rh-python36-runtime.x86_64 2.0-1.el7 @Centos-Local rpm-python.x86_64 4.11.3-40.el7 @CentOS

[yizhang-yiz]

Thanks for providing compiler information, as it helped me reproduce the issue with gcc 4.9.3 on metworx' ubuntu 18.05:

tan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >&, std::vector<int>&, std::ostream*) const [with M = pk2cpt_model_namespace::pk2cpt_model; stan::math::var = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
../example-models/pk2cpt/pk2cpt.hpp:1034:0:   required from here
stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for ‘const std::tuple<>’
stan/lib/stan_math/stan/math/torsten/ev_history.hpp:149:64: error: too many initializers for ‘const std::tuple<>’
cc1plus: warning: unrecognized command line option "-Wno-ignored-attributes"
cc1plus: warning: unrecognized command line option "-Wno-ignored-attributes"
make/program:59: recipe for target '../example-models/pk2cpt/pk2cpt' failed

On the other hand, the issue is removed using gcc 6.5.0:

--- Compiling, linking C++ code ---
g++-6 -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30    -DBOOST_DISABLE_ASSERTS        -c -Wno-ignored-attributes   -x c++ -o ../example-models/pk2cpt/pk2cpt.o ../example-models/pk2cpt/pk2cpt.hpp
g++-6 -std=c++1y -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30    -DBOOST_DISABLE_ASSERTS              -Wl,-L,"/data/Torsten/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/data/Torsten/cmdstan/stan/lib/stan_math/lib/tbb"      ../example-models/pk2cpt/pk2cpt.o src/cmdstan/main.o         stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.2.0/lib/libsundials_kinsol.a  stan/lib/stan_math/lib/tbb/libtbb.so.2  -o ../example-models/pk2cpt/pk2cpt
rm -f ../example-models/pk2cpt/pk2cpt.o

So it seems the failure can be resolved by upgrading gcc to >6.

[yizhang-yiz]

@sundav05 @yendls please let me know if you were able to resolve the issue with a newer version of gcc, or if there are any other issues.

[yendls]

Working after installing gcc > 6.5