Thanks for the clarification. I successfully stan_rdump() the data. In installing cmdstan, I successfully completed the make build step. However, when compiling the .stan file (which I have been using with rstan without a problem), I received the errors below. In another (slower) cluster, I could complete this step and proceed to sampling without a problem.
Any idea on how to fix the compliation errors? (Are they due to the g++ version, which is g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36)?)
[sbbg070@wrds-cloud-login1-h ~/cmdstan-2.19.1]$ make ../SSM0.5.2dev
--- Translating Stan model to C++ code ---
bin/stanc --o=../SSM0.5.2dev.hpp ../SSM0.5.2dev.stan
Model name=SSM0_5_2dev_model
Input file=../SSM0.5.2dev.stan
Output file=../SSM0.5.2dev.hpp
DIAGNOSTIC(S) FROM PARSER:
Info: Comments beginning with # are deprecated. Please use // in place of # for line comments.
Info:
Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable.
If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform.
Left-hand-side of sampling statement:
err_y[j] ~ normal(...)
g++ -std=c++1y -pthread -Wno-sign-compare -O3 -I src -I stan/src -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.3 -I stan/lib/stan_math/lib/boost_1.69.0 -I stan/lib/stan_math/lib/sundials_4.1.0/include -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -c -MT ../SSM0.5.2dev.o -MT ../SSM0.5.2dev -include ../SSM0.5.2dev.hpp -include src/cmdstan/main.cpp -MM -E -MG -MP -MF ../SSM0.5.2dev.d ../SSM0.5.2dev.hpp
--- Linking C++ model ---
g++ -std=c++1y -pthread -Wno-sign-compare -O3 -I src -I stan/src -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.3 -I stan/lib/stan_math/lib/boost_1.69.0 -I stan/lib/stan_math/lib/sundials_4.1.0/include -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -include ../SSM0.5.2dev.hpp src/cmdstan/main.cpp stan/lib/stan_math/lib/sundials_4.1.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_4.1.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_4.1.0/lib/libsundials_idas.a -o ../SSM0.5.2dev
In file included from stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0,
from stan/lib/stan_math/stan/math/rev/mat.hpp:41,
from stan/lib/stan_math/stan/math.hpp:4,
from stan/src/stan/model/model_header.hpp:4,
from ./../SSM0.5.2dev.hpp:3,
from <command-line>:0:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:32: error: ‘std::index_sequence’ has not been declared
std::index_sequence<I...> i) {
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:46: error: expected ‘,’ or ‘...’ before ‘<’ token
std::index_sequence<I...> i) {
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In function ‘constexpr auto stan::math::internal::apply(const F&, const Tuple&)’:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: error: ‘make_index_sequence’ is not a member of ‘std’
return apply_impl(f, t, std::make_index_sequence<std::tuple_size<Tuple>{}>{});
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: note: suggested alternative:
In file included from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector.hpp:28:0,
from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector10.hpp:25,
from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/transform_view/transform_view.hpp:22,
from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/algorithm/transformation/transform.hpp:11,
from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/detail/begin_impl.hpp:14,
from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/zip_view.hpp:16,
from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view.hpp:12,
from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/include/zip_view.hpp:11,
from stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/resize.hpp:26,
from stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/state_wrapper.hpp:26,
from stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint.hpp:25,
from stan/lib/stan_math/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
from stan/lib/stan_math/stan/math/prim/arr.hpp:46,
from stan/lib/stan_math/stan/math/prim/mat.hpp:344,
from stan/lib/stan_math/stan/math/rev/mat.hpp:12,
from stan/lib/stan_math/stan/math.hpp:4,
from stan/src/stan/model/model_header.hpp:4,
from ./../SSM0.5.2dev.hpp:3,
from <command-line>:0:
stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/support/detail/index_sequence.hpp:59:12: note: ‘boost::fusion::detail::make_index_sequence’
struct make_index_sequence
^
In file included from stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0,
from stan/lib/stan_math/stan/math/rev/mat.hpp:41,
from stan/lib/stan_math/stan/math.hpp:4,
from stan/src/stan/model/model_header.hpp:4,
from ./../SSM0.5.2dev.hpp:3,
from <command-line>:0:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected primary-expression before ‘{’ token
return apply_impl(f, t, std::make_index_sequence<std::tuple_size<Tuple>{}>{});
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected ‘)’ before ‘{’ token
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:151:9: error: expected type-specifier
= std::result_of_t<F(decltype(is_var_), decltype(value_of(Targs()))...)>;
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:42: error: ‘FReturnType’ was not declared in this scope
std::array<int, internal::compute_dims<FReturnType>::value> M_;
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:53: error: template argument 1 is invalid
std::array<int, internal::compute_dims<FReturnType>::value> M_;
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:61: error: template argument 2 is invalid
std::array<int, internal::compute_dims<FReturnType>::value> M_;
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘std::vector<stan::math::var> stan::math::adj_jac_vari<F, Targs>::build_return_varis_and_vars(const std::vector<double>&)’:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:349:9: error: invalid types ‘int[int]’ for array subscript
M_[0] = val_y.size();
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:350:32: error: invalid types ‘int[int]’ for array subscript
std::vector<var> var_y(M_[0]);
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘Eigen::Matrix<stan::math::var, R, C> stan::math::adj_jac_vari<F, Targs>::build_return_varis_and_vars(const Eigen::Matrix<double, R, C>&)’:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:375:9: error: invalid types ‘int[int]’ for array subscript
M_[0] = val_y.rows();
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:376:9: error: invalid types ‘int[int]’ for array subscript
M_[1] = val_y.cols();
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:40: error: invalid types ‘int[int]’ for array subscript
Eigen::Matrix<var, R, C> var_y(M_[0], M_[1]);
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:47: error: invalid types ‘int[int]’ for array subscript
Eigen::Matrix<var, R, C> var_y(M_[0], M_[1]);
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘void stan::math::adj_jac_vari<F, Targs>::chain( ’:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:5: error: ‘FReturnType’ was not declared in this scope
FReturnType y_adj;
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:17: error: expected ‘;’ before ‘y_adj’
FReturnType y_adj;
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:532:38: error: ‘y_adj’ was not declared in this scope
internal::build_y_adj(y_vi_, M_, y_adj);
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:26: error: expansion pattern ‘auto&&’ contains no argument packs
[this](auto&&... args) { this->accumulate_adjoints(args...); },
^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In lambda function:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:60: error: ‘args’ was not declared in this scope
[this](auto&&... args) { this->accumulate_adjoints(args...); },
^
make: *** [../SSM0.5.2dev] Error 1