cmdstan stops working with Intel MKL

Aperta
  • Qualcosa non va?
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Valutazione

Difficoltà
4/5
Tempo stimato
3-5 giorni
Idoneità per principianti
35/100
Tipo di issue
Bug
Chiarezza
Da chiarire
Stato di attività
Ferma
Stack tecnologico
cpp
Ambito
build-system

Direzione di ricerca

Riproduci il modello allegato con cmdstan 2.28.0, le impostazioni make/local mostrate, GCC 8.2.0 e Intel MKL 2019.1.144. Inizia con il trace del compilatore in stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/ArrayWrapper.h e le chiamate attraverso stan/src/stan/io/deserializer.hpp. Il lavoro è completo quando il modello viene compilato con MKL come avveniva con cmdstan 2.21.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Summary:

The attached model used to work with previous (pre 2.28.0) MKL installations, but it fails to compile now with 2.28.0.

Description:

With the MKL being used the latest cmdstan 2.28.0 stops compiling with the model below.

make/local:

MKL_CBWR=AVX
CC = gcc
CXX = g++
C_MKL=-I ${MKLROOT}/include -march=ivybridge -DEIGEN_USE_MKL_ALL -Wno-enum-compare
LD_MKL=-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm -ldl -Wl,-rpath=${MKLROOT}/lib/intel64,--no-as-needed
# which need to be passed to compiler/linker options
CXXFLAGS += $(C_MKL)
CFLAGS += $(C_MKL)
LDFLAGS += $(LD_MKL)
STAN_THREADS=true

blrm_exnex-combo3_data_R.txt

blrm-exnex-28_stan.txt

Error message during compilation (g++ 8.2.0):

stan/lib/stan_math/stan/math/prim/fun/lb_constrain.hpp:175:49:   required from ‘auto stan::math::lb_constrain(const std::vector<T1>&, const L&, stan::return_type_t<T1, T2>&) [with T = std::vector<Eigen::Matrix<stan::math::var_value<double>, -1, 1>, std::allocator<Eigen::Matrix<stan::math::var_value<double>, -1, 1> > >; L = int; stan::require_not_std_vector_t<T_high>* <anonymous> = 0; stan::return_type_t<T1, T2> = stan::math::var_value<double>]’
stan/src/stan/io/deserializer.hpp:386:38:   required from ‘auto stan::io::deserializer<T>::read_constrain_lb(const LB&, LP&, Sizes ...) [with Ret = std::vector<std::vector<Eigen::Matrix<stan::math::var_value<double>, -1, 1>, std::allocator<Eigen::Matrix<stan::math::var_value<double>, -1, 1> > >, std::allocator<std::vector<Eigen::Matrix<stan::math::var_value<double>, -1, 1>, std::allocator<Eigen::Matrix<stan::math::var_value<double>, -1, 1> > > > >; bool Jacobian = false; LB = int; LP = stan::math::var_value<double>; Sizes = {int, int, int}; T = stan::math::var_value<double>]’
/home/weberse2/t/blrm-exnex-28.hpp:4732:24:   required from ‘stan::scalar_type_t<T2> blrm_exnex_28_model_namespace::blrm_exnex_28_model::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; VecI = Eigen::Matrix<int, -1, 1>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/weberse2/t/blrm-exnex-28.hpp:6142:77:   required from ‘T_ blrm_exnex_28_model_namespace::blrm_exnex_28_model::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stan/src/stan/model/model_base_crtp.hpp:96:77:   required from ‘stan::math::var stan::model::model_base_crtp<M>::log_prob(Eigen::Matrix<stan::math::var_value<double>, -1, 1>&, std::ostream*) const [with M = blrm_exnex_28_model_namespace::blrm_exnex_28_model; stan::math::var = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stan/src/stan/model/model_base_crtp.hpp:93:20:   required from here
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/ArrayWrapper.h:80:48: error: passing ‘const NestedExpressionType’ {aka ‘const Eigen::CwiseUnaryView<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> > >::val_Op, Eigen::Map<Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> > >’} as ‘this’ argument discards qualifiers [-fpermissive]
       return m_expression.coeffRef(rowId, colId);
                                                ^
In file included from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Core:439,
                 from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Dense:1,
                 from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22,
                 from stan/lib/stan_math/stan/math/rev.hpp:4,
                 from stan/lib/stan_math/stan/math.hpp:19,
                 from stan/src/stan/model/model_header.hpp:4,
                 from /home/weberse2/t/blrm-exnex-28.hpp:3:
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/DenseCoeffsBase.h:340:33: note:   in call to ‘Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::coeffRef(Eigen::Index, Eigen::Index) [with Derived = Eigen::CwiseUnaryView<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> > >::val_Op, Eigen::Map<Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> > >; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = double; Eigen::Index = long int]’
     EIGEN_STRONG_INLINE Scalar& coeffRef(Index row, Index col)
                                 ^~~~~~~~

This is with MKL version 2019.1.144

Reproducible Steps:
Current Output:

The current output. Knowing what is the current behavior is useful.

Expected Output:

It should just work as it did with previous versions. The last version we have tested this setup ok is cmdstan 2.21.

Additional Information:

NA

Current Version:

v2.28.0

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