Я следовал решению, предложенному здесь для обработки ошибок, возникающих внутри блоков OpenMP в C++. Очевидно, это не работает при использовании Rcpp, но это только в Fedora, с Clang-11 и с libc++ (без libc++ работает нормально). Рассмотрим следующий файл C++:
// openmp-exception-issue.cpp
#ifdef _OPENMP
#include <omp.h>
#endif
#include <exception>
#include <stdexcept>
#include <iostream>
// from https://github.com/boennecd/mdgc/blob/b749ef33e0b324fa5f07d3d528097b8c22fb586c/src/openmp-exception_ptr.h#L10-L43
class openmp_exception_ptr {
std::exception_ptr Ptr = nullptr;
bool is_set = false;
public:
inline void rethrow_if_error(){
#ifdef _OPENMP
if(this->Ptr)
std::rethrow_exception(this->Ptr);
#endif
}
template <typename Function, typename... Parameters>
void run(Function f, Parameters... params)
{
#ifdef _OPENMP
try
{
f(params...);
}
catch (...)
{
#pragma omp critical(openmp_exception_ptr)
{
if(!is_set){
this->Ptr = std::current_exception();
is_set = true;
}
}
}
#else
f(params...);
#endif
}
};
int do_work(int const x){
if(x > -1)
throw std::runtime_error("boh :(");
return x;
}
// [[Rcpp::plugins(openmp)]]
#include <Rcpp.h>
// [[Rcpp::export()]]
double that_cpp_func(int const n_it){
openmp_exception_ptr obj;
double out(0.);
#pragma omp parallel num_threads(4)
{
#pragma omp for schedule(static) reduction(+:out) nowait
for(int i = 0; i < n_it; ++i){
obj.run([&]() -> void {
out += do_work(i);
});
}
}
try
{
obj.rethrow_if_error();
}
catch(...)
{
Rcpp::Rcout << "Caught an error\n" << out << '\n';
}
return out;
}
Затем используйте Rcpp с настройкой R, как описано для CRAN's r-devel-linux-x86_64-fedora-clang с использованием Docker, начиная с rhub/fedora-clang, я получаю следующую ошибку:
R -d valgrind -e "Rcpp::sourceCpp('openmp-exception-issue.cpp'); that_cpp_func(100)"
# ==2897== Memcheck, a memory error detector
# ==2897== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
# ==2897== Using Valgrind-3.16.1 and LibVEX; rerun with -h for copyright info
# ==2897== Command: /root/R-devel/bin/exec/R -e Rcpp::sourceCpp('openmp-exception-issue.cpp');~+~that_cpp_func(100)
# ==2897==
#
# R Under development (unstable) (2021-02-22 r80031) -- "Unsuffered Consequences"
# Copyright (C) 2021 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.
#
# Natural language support but running in an English locale
#
# 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.
#
# > Rcpp::sourceCpp('openmp-exception-issue.cpp'); that_cpp_func(100)
# In file included from openmp-exception-issue.cpp:52:
# In file included from /root/R-devel/library/Rcpp/include/Rcpp.h:57:
# /root/R-devel/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
# SEXP data = Parent::get__();
# ^
# 1 warning generated.
# ==2897== Syscall param sched_setaffinity(mask) points to unaddressable byte(s)
# ==2897== at 0x550F55D: syscall (in /usr/lib64/libc-2.32.so)
# ==2897== by 0x539AD1C: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x536AAE9: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x535774A: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x5357B8C: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x10B0FB77: that_cpp_func(int) (openmp-exception-issue.cpp:55)
# ==2897== by 0x10B0FF7A: sourceCpp_1_that_cpp_func (openmp-exception-issue.cpp:89)
# ==2897== by 0x49DA3A: R_doDotCall (dotcode.c:598)
# ==2897== by 0x4A0510: do_dotcall (dotcode.c:1281)
# ==2897== by 0x4D50BC: Rf_eval (eval.c:830)
# ==2897== by 0x4EED11: R_execClosure (eval.c:0)
# ==2897== by 0x4EE288: Rf_applyClosure (eval.c:1823)
# ==2897== Address 0x0 is not stack'd, malloc'd or (recently) free'd
# ==2897==
# ==2897== Invalid read of size 8
# ==2897== at 0x71EC2DF: __cxa_end_catch (in /usr/lib64/libstdc++.so.6.0.28)
# ==2897== by 0x10B0FEED: run<(lambda at openmp-exception-issue.cpp:62:13)> (openmp-exception-issue.cpp:38)
# ==2897== by 0x10B0FEED: .omp_outlined._debug__ (openmp-exception-issue.cpp:62)
# ==2897== by 0x10B0FEED: .omp_outlined. (openmp-exception-issue.cpp:58)
# ==2897== by 0x53B27C2: __kmp_invoke_microtask (in /usr/lib64/libomp.so)
# ==2897== by 0x5358068: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x535BFF2: __kmp_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x534A740: __kmpc_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x10B0FBCA: that_cpp_func(int) (openmp-exception-issue.cpp:58)
# ==2897== by 0x10B0FF7A: sourceCpp_1_that_cpp_func (openmp-exception-issue.cpp:89)
# ==2897== by 0x49DA3A: R_doDotCall (dotcode.c:598)
# ==2897== by 0x4A0510: do_dotcall (dotcode.c:1281)
# ==2897== by 0x4D50BC: Rf_eval (eval.c:830)
# ==2897== by 0x4EED11: R_execClosure (eval.c:0)
# ==2897== Address 0x9d69a30 is 96 bytes inside a block of size 144 free'd
# ==2897== at 0x483A9F5: free (vg_replace_malloc.c:538)
# ==2897== by 0xB6AE48A: __cxa_decrement_exception_refcount (in /usr/lib64/libc++abi.so.1.0)
# ==2897== by 0x10B0FECB: run<(lambda at openmp-exception-issue.cpp:62:13)> (openmp-exception-issue.cpp:34)
# ==2897== by 0x10B0FECB: .omp_outlined._debug__ (openmp-exception-issue.cpp:62)
# ==2897== by 0x10B0FECB: .omp_outlined. (openmp-exception-issue.cpp:58)
# ==2897== by 0x53B27C2: __kmp_invoke_microtask (in /usr/lib64/libomp.so)
# ==2897== by 0x5358068: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x535BFF2: __kmp_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x534A740: __kmpc_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x10B0FBCA: that_cpp_func(int) (openmp-exception-issue.cpp:58)
# ==2897== by 0x10B0FF7A: sourceCpp_1_that_cpp_func (openmp-exception-issue.cpp:89)
# ==2897== by 0x49DA3A: R_doDotCall (dotcode.c:598)
# ==2897== by 0x4A0510: do_dotcall (dotcode.c:1281)
# ==2897== by 0x4D50BC: Rf_eval (eval.c:830)
# ==2897== Block was alloc'd at
# ==2897== at 0x4839809: malloc (vg_replace_malloc.c:307)
# ==2897== by 0x71EC0C3: __cxa_allocate_exception (in /usr/lib64/libstdc++.so.6.0.28)
# ==2897== by 0x10B0FE41: do_work (openmp-exception-issue.cpp:47)
# ==2897== by 0x10B0FE41: operator() (openmp-exception-issue.cpp:63)
# ==2897== by 0x10B0FE41: run<(lambda at openmp-exception-issue.cpp:62:13)> (openmp-exception-issue.cpp:27)
# ==2897== by 0x10B0FE41: .omp_outlined._debug__ (openmp-exception-issue.cpp:62)
# ==2897== by 0x10B0FE41: .omp_outlined. (openmp-exception-issue.cpp:58)
# ==2897== by 0x53B27C2: __kmp_invoke_microtask (in /usr/lib64/libomp.so)
# ==2897== by 0x5358068: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x535BFF2: __kmp_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x534A740: __kmpc_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x10B0FBCA: that_cpp_func(int) (openmp-exception-issue.cpp:58)
# ==2897== by 0x10B0FF7A: sourceCpp_1_that_cpp_func (openmp-exception-issue.cpp:89)
# ==2897== by 0x49DA3A: R_doDotCall (dotcode.c:598)
# ==2897== by 0x4A0510: do_dotcall (dotcode.c:1281)
# ==2897== by 0x4D50BC: Rf_eval (eval.c:830)
# ==2897==
# ==2897== Invalid read of size 4
# ==2897== at 0x71EC2E9: __cxa_end_catch (in /usr/lib64/libstdc++.so.6.0.28)
# ==2897== by 0x10B0FEED: run<(lambda at openmp-exception-issue.cpp:62:13)> (openmp-exception-issue.cpp:38)
# ==2897== by 0x10B0FEED: .omp_outlined._debug__ (openmp-exception-issue.cpp:62)
# ==2897== by 0x10B0FEED: .omp_outlined. (openmp-exception-issue.cpp:58)
# ==2897== by 0x53B27C2: __kmp_invoke_microtask (in /usr/lib64/libomp.so)
# ==2897== by 0x5358068: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x535BFF2: __kmp_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x534A740: __kmpc_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x10B0FBCA: that_cpp_func(int) (openmp-exception-issue.cpp:58)
# ==2897== by 0x10B0FF7A: sourceCpp_1_that_cpp_func (openmp-exception-issue.cpp:89)
# ==2897== by 0x49DA3A: R_doDotCall (dotcode.c:598)
# ==2897== by 0x4A0510: do_dotcall (dotcode.c:1281)
# ==2897== by 0x4D50BC: Rf_eval (eval.c:830)
# ==2897== by 0x4EED11: R_execClosure (eval.c:0)
# ==2897== Address 0x9d69a08 is 56 bytes inside a block of size 144 free'd
# ==2897== at 0x483A9F5: free (vg_replace_malloc.c:538)
# ==2897== by 0xB6AE48A: __cxa_decrement_exception_refcount (in /usr/lib64/libc++abi.so.1.0)
# ==2897== by 0x10B0FECB: run<(lambda at openmp-exception-issue.cpp:62:13)> (openmp-exception-issue.cpp:34)
# ==2897== by 0x10B0FECB: .omp_outlined._debug__ (openmp-exception-issue.cpp:62)
# ==2897== by 0x10B0FECB: .omp_outlined. (openmp-exception-issue.cpp:58)
# ==2897== by 0x53B27C2: __kmp_invoke_microtask (in /usr/lib64/libomp.so)
# ==2897== by 0x5358068: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x535BFF2: __kmp_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x534A740: __kmpc_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x10B0FBCA: that_cpp_func(int) (openmp-exception-issue.cpp:58)
# ==2897== by 0x10B0FF7A: sourceCpp_1_that_cpp_func (openmp-exception-issue.cpp:89)
# ==2897== by 0x49DA3A: R_doDotCall (dotcode.c:598)
# ==2897== by 0x4A0510: do_dotcall (dotcode.c:1281)
# ==2897== by 0x4D50BC: Rf_eval (eval.c:830)
# ==2897== Block was alloc'd at
# ==2897== at 0x4839809: malloc (vg_replace_malloc.c:307)
# ==2897== by 0x71EC0C3: __cxa_allocate_exception (in /usr/lib64/libstdc++.so.6.0.28)
# ==2897== by 0x10B0FE41: do_work (openmp-exception-issue.cpp:47)
# ==2897== by 0x10B0FE41: operator() (openmp-exception-issue.cpp:63)
# ==2897== by 0x10B0FE41: run<(lambda at openmp-exception-issue.cpp:62:13)> (openmp-exception-issue.cpp:27)
# ==2897== by 0x10B0FE41: .omp_outlined._debug__ (openmp-exception-issue.cpp:62)
# ==2897== by 0x10B0FE41: .omp_outlined. (openmp-exception-issue.cpp:58)
# ==2897== by 0x53B27C2: __kmp_invoke_microtask (in /usr/lib64/libomp.so)
# ==2897== by 0x5358068: ??? (in /usr/lib64/libomp.so)
# ==2897== by 0x535BFF2: __kmp_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x534A740: __kmpc_fork_call (in /usr/lib64/libomp.so)
# ==2897== by 0x10B0FBCA: that_cpp_func(int) (openmp-exception-issue.cpp:58)
# ==2897== by 0x10B0FF7A: sourceCpp_1_that_cpp_func (openmp-exception-issue.cpp:89)
# ==2897== by 0x49DA3A: R_doDotCall (dotcode.c:598)
# ==2897== by 0x4A0510: do_dotcall (dotcode.c:1281)
# ==2897== by 0x4D50BC: Rf_eval (eval.c:830)
# ==2897==
# 29 more errors...
# ==2897== For lists of detected and suppressed errors, rerun with: -s
# ==2897== ERROR SUMMARY: 32 errors from 18 contexts (suppressed: 0 from 0)
Я не уверен, почему это происходит и почему это происходит только с Clang-11, использующим libc++. Глядя на первую ошибку, память выделяется в throw std::runtime_error("boh :(");, освобождается в this->Ptr = std::current_exception(); и впоследствии читается в конце блока catch в openmp_exception_ptr.run.
Простой код
Этот код также вызывает аналогичные (но меньше) ошибки:
// openmp-exception-issue.cpp
#include <omp.h>
#include <exception>
#include <stdexcept>
// [[Rcpp::plugins(openmp)]]
#include <Rcpp.h>
// [[Rcpp::export()]]
double that_cpp_func(int const n_it){
std::exception_ptr Ptr = nullptr;
bool is_set = false;
double out(0.);
#pragma omp parallel for num_threads(4) reduction(+:out)
for(int i = 0; i < n_it; ++i)
try
{
if(i > -1)
throw std::runtime_error("boh :(");
out += i;
}
catch (...)
{
#pragma omp critical
if(!is_set){
Ptr = std::current_exception();
is_set = true;
}
}
if(Ptr)
Rcpp::Rcout << "Caught an error\n" << out << '\n';
return out;
}
Оригинальный вопрос
Я следовал решению, предложенному здесь для обработки ошибок, возникающих внутри блоков OpenMP в C++. В качестве примера рассмотрим следующий код:
// openmp-exception-issue.cpp
#ifdef _OPENMP
#include <omp.h>
#endif
#include <exception>
#include <stdexcept>
#include <iostream>
// from https://github.com/boennecd/mdgc/blob/b749ef33e0b324fa5f07d3d528097b8c22fb586c/src/openmp-exception_ptr.h#L10-L43
class openmp_exception_ptr {
std::exception_ptr Ptr = nullptr;
bool is_set = false;
public:
inline void rethrow_if_error(){
#ifdef _OPENMP
if(this->Ptr)
std::rethrow_exception(this->Ptr);
#endif
}
template <typename Function, typename... Parameters>
void run(Function f, Parameters... params)
{
#ifdef _OPENMP
try
{
f(params...);
}
catch (...)
{
#pragma omp critical(openmp_exception_ptr)
{
if(!is_set){
this->Ptr = std::current_exception();
is_set = true;
}
}
}
#else
f(params...);
#endif
}
};
int main(){
openmp_exception_ptr obj;
#ifdef _OPENMP
#pragma omp parallel for num_threads(4)
#endif
for(int i = 0; i < 10000; ++i){
obj.run([&]() -> void {
throw std::runtime_error("boh :(");
});
}
try
{
obj.rethrow_if_error();
}
catch(...)
{
std::cout << "Caught an error\n";
}
}
Кажется, это отлично работает с версией Clang Fedora 11.0.0-2.fc33 в Fedora:
clang++-11 -stdlib=libc++ -std=gnu++14 -DNDEBUG -O3 -o issue-example openmp-exception-issue.cpp -fopenmp
valgrind ./issue-example
# ==1844== Memcheck, a memory error detector
# ...
# ==1844== Syscall param sched_setaffinity(mask) points to unaddressable byte(s)
# ==1844== at 0x4CA755D: syscall (in /usr/lib64/libc-2.32.so)
# ==1844== by 0x4B30D1C: ??? (in /usr/lib64/libomp.so)
# ==1844== by 0x4B00AE9: ??? (in /usr/lib64/libomp.so)
# ==1844== by 0x4AED74A: ??? (in /usr/lib64/libomp.so)
# ==1844== by 0x4AEDB8C: ??? (in /usr/lib64/libomp.so)
# ==1844== by 0x40132E: main (in /sdir/issue-example)
# ==1844== Address 0x0 is not stack'd, malloc'd or (recently) free'd
# ==1844==
# Caught an error
# ...
#
# ==1844== LEAK SUMMARY:
# ==1844== definitely lost: 0 bytes in 0 blocks
# ==1844== indirectly lost: 0 bytes in 0 blocks
# ==1844== possibly lost: 0 bytes in 0 blocks
# ==1844== still reachable: 81,248 bytes in 12 blocks
# ==1844== suppressed: 0 bytes in 0 blocks
# ==1844== Rerun with --leak-check=full to see details of leaked memory
# ==1844==
# ==1844== For lists of detected and suppressed errors, rerun with: -s
# ==1844== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)
где я полагаю, что ошибка является ложным срабатыванием.
Проблемы, которые мне не удалось воспроизвести на небольшом примере, связаны с моим пакетом R здесь , только в Fedora, с Clang-11 и с libc++ (отлично работает без libc++). Он также работает с Ubuntu (clang 6 и GCC 10), Windows, macOS и Solaris.
Если я запускаю R CMD check --use-valgrind --as-cran --no-stop-on-test-error --run-donttest mdgc_0.1.2.tar.gz в файле tar.gz из R CMD build, я получаю указанные ниже ошибки в файле mdgc.Rcheck/tests/testthat.Rout.
#...
==1370==
==1370== Invalid read of size 8
==1370== at 0x71EC2DF: __cxa_end_catch (in /usr/lib64/libstdc++.so.6.0.28)
==1370== by 0x1095A26D: run<(lambda at cpp-to-R.cpp:192:23)> (openmp-exception_ptr.h:38)
==1370== by 0x1095A26D: .omp_outlined._debug__ (cpp-to-R.cpp:192)
==1370== by 0x1095A26D: .omp_outlined. (cpp-to-R.cpp:179)
==1370== by 0x53B27C2: __kmp_invoke_microtask (in /usr/lib64/libomp.so)
==1370== by 0x5358068: ??? (in /usr/lib64/libomp.so)
==1370== by 0x535BFF2: __kmp_fork_call (in /usr/lib64/libomp.so)
==1370== by 0x534A740: __kmpc_fork_call (in /usr/lib64/libomp.so)
==1370== by 0x10959813: eval_log_lm_terms(SEXPREC*, arma::Col<int> const&, arma::Mat<double> const&, arma::Col<double> const&, int, double, double, int, bool, unsigned int, bool, bool) (cpp-to-R.cpp:179)
# ...
==1370== Address 0x7d76800 is 96 bytes inside a block of size 144 free'd
==1370== at 0x483A9F5: free (vg_replace_malloc.c:538)
==1370== by 0xFC7E48A: __cxa_decrement_exception_refcount (in /usr/lib64/libc++abi.so.1.0)
==1370== by 0x1095A24A: run<(lambda at cpp-to-R.cpp:192:23)> (openmp-exception_ptr.h:34)
==1370== by 0x1095A24A: .omp_outlined._debug__ (cpp-to-R.cpp:192)
==1370== by 0x1095A24A: .omp_outlined. (cpp-to-R.cpp:179)
==1370== by 0x53B27C2: __kmp_invoke_microtask (in /usr/lib64/libomp.so)
==1370== by 0x5358068: ??? (in /usr/lib64/libomp.so)
==1370== by 0x535BFF2: __kmp_fork_call (in /usr/lib64/libomp.so)
==1370== by 0x534A740: __kmpc_fork_call (in /usr/lib64/libomp.so)
==1370== by 0x10959813: eval_log_lm_terms(SEXPREC*, arma::Col<int> const&, arma::Mat<double> const&, arma::Col<double> const&, int, double, double, int, bool, unsigned int, bool, bool) (cpp-to-R.cpp:179)
# ...
==1370== Block was alloc'd at
==1370== at 0x4839809: malloc (vg_replace_malloc.c:307)
==1370== by 0x71EC0C3: __cxa_allocate_exception (in /usr/lib64/libstdc++.so.6.0.28)
==1370== by 0x109696CE: restrictcdf::cdf<restrictcdf::likelihood, restrictcdf::likelihood::out_type>::cdf(restrictcdf::likelihood&, arma::Col<double> const&, arma::Col<double> const&, arma::Col<double> const&, arma::Mat<double> const&, bool, bool) (restrict-cdf.h:235)
==1370== by 0x10987D8B: mdgc::log_ml_term::approximate(arma::Mat<double> const&, arma::Col<double> const&, arma::Mat<double>&, arma::Col<double>&, int, double, double, bool, bool, unsigned long, bool) const (logLik.cpp:266)
==1370== by 0x1095A1EC: operator() (cpp-to-R.cpp:193)
==1370== by 0x1095A1EC: run<(lambda at cpp-to-R.cpp:192:23)> (openmp-exception_ptr.h:27)
# ...
# 31 more related errors ...
==1370==
==1370== For lists of detected and suppressed errors, rerun with: -s
==1370== ERROR SUMMARY: 32 errors from 18 contexts (suppressed: 0 from 0)
Однако я не понимаю, почему это не работает. Проходим первую ошибку:
- ошибка возникает из-за конца области
catchвopenmp_exception_ptrздесь. - он пытается прочитать выделенную память, когда возникает ошибка < /a> в лямбда-функции передал
openmp_exception_ptr.runв эти строки. - эта память была освобождена после
std::current_exception.
