在 linux 批處理模式下運行 Rcpp 時出錯
[英]Error when running Rcpp in linux batch mode
問題描述
我正在嘗試使用 rstan 在批處理模式下運行一個非常簡單的 model 並且有一些錯誤。 當我嘗試不以批處理模式運行相同的代碼時，我沒有任何錯誤。
STAN 論壇的社區幫助我了解問題是 Rcpp 而不是 STAN 在我大學的服務器上無法正常工作。 我們通過嘗試在批處理模式而不是批處理模式下運行非常簡單的 Rcpp 代碼的測試得出了這種理解。 Rcpp 代碼是：
### Libraries
library(Rcpp)
Rcpp::sourceCpp(code='
#include <Rcpp.h>
// [[Rcpp::export]]
int fibonacci(const int x) {
if (x == 0) return(0);
if (x == 1) return(1);
return (fibonacci(x - 1)) + fibonacci(x - 2);
}',
verbose = TRUE,
rebuild = TRUE
)
結果如下。
不在批處理模式下：
Generated R functions
-------------------------------------------------------
`.sourceCpp_1_DLLInfo` <- dyn.load('/tmp/RtmpDNL6of/sourceCpp-x86_64-pc-linux-gnu-1.0.7/sourcecpp_178b21d435d91/sourceCpp_4.so')
fibonacci <- Rcpp:::sourceCppFunction(function(x) {}, FALSE, `.sourceCpp_1_DLLInfo`, 'sourceCpp_1_fibonacci')
rm(`.sourceCpp_1_DLLInfo`)
Building shared library
--------------------------------------------------------
DIR: /tmp/RtmpDNL6of/sourceCpp-x86_64-pc-linux-gnu-1.0.7/sourcecpp_178b21d435d91
/hpc/apps/R/4.1.2/lib64/R/bin/R CMD SHLIB --preclean -o 'sourceCpp_4.so' 'file178b25628f5ea.cpp'
g++ -std=gnu++14 -I"/hpc/apps/R/4.1.2/lib64/R/include" -DNDEBUG -I"/hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include" -I"/tmp/RtmpDNL6of/sourceCpp-x86_64-pc-linux-gnu-1.0.7" -I/hpc/apps/zlib/1.2.8/include -I/hpc/apps/pcre/8.38/include -I/hpc/apps/bzip2/1.0.6/include -I/hpc/apps/curl/7.54.1/include -I/hpc/apps/cairo/1.14.12/include -fpic -g -O2 -c file178b25628f5ea.cpp -o file178b25628f5ea.o
g++ -std=gnu++14 -shared -L/hpc/apps/R/4.1.2/lib64/R/lib -L/hpc/apps/zlib/1.2.8/lib -L/hpc/apps/pcre/8.38/lib -L/hpc/apps/bzip2/1.0.6/lib -L/hpc/apps/curl/7.54.1/lib -L/hpc/apps/cairo/1.14.12/lib -o sourceCpp_4.so file178b25628f5ea.o -L/hpc/apps/R/4.1.2/lib64/R/lib -lR
在批處理模式下：
Generated R functions
-------------------------------------------------------
`.sourceCpp_1_DLLInfo` <- dyn.load('/localscratch/250948.1.ragatkolab.q/RtmpDlK5Sy/sourceCpp-x86_64-pc-linux-gnu-1.0.7/sourcecpp_142bd68d660f1/sourceCpp_2.so')
fibonacci <- Rcpp:::sourceCppFunction(function(x) {}, FALSE, `.sourceCpp_1_DLLInfo`, 'sourceCpp_1_fibonacci')
rm(`.sourceCpp_1_DLLInfo`)
Building shared library
--------------------------------------------------------
DIR: /localscratch/250948.1.mylab.q/RtmpDlK5Sy/sourceCpp-x86_64-pc-linux-gnu-1.0.7/sourcecpp_142bd68d660f1
/hpc/apps/R/4.1.2/lib64/R/bin/R CMD SHLIB -o 'sourceCpp_2.so' 'file142bd64ebe902.cpp'
g++ -std=gnu++14 -I"/hpc/apps/R/4.1.2/lib64/R/include" -DNDEBUG -I"/hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include" -I"/localscratch/250948.1.ragatkolab.q/RtmpDlK5Sy/sourceCpp-x86_64-pc-linux-gnu-1.0.7" -I/hpc/apps/zlib/1.2.8/include -I/hpc/apps/pcre/8.38/include -I/hpc/apps/bzip2/1.0.6/include -I/hpc/apps/curl/7.54.1/include -I/hpc/apps/cairo/1.14.12/include -fpic -g -O2 -c file142bd64ebe902.cpp -o file142bd64ebe902.o
In file included from /hpc/apps/gcc/9.1.0/include/c++/9.1.0/x86_64-pc-linux-gnu/bits/c++config.h:524,
from /hpc/apps/gcc/9.1.0/include/c++/9.1.0/cmath:41,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/Rcpp/platform/compiler.h:100,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/Rcpp/r/headers.h:66,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/RcppCommon.h:30,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/Rcpp.h:27,
from file142bd64ebe902.cpp:2:
/hpc/apps/gcc/9.1.0/include/c++/9.1.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: fatal error: features.h: No such file or directory
39 | #include <features.h>
| ^~~~~~~~~~~~
compilation terminated.
make: *** [file142bd64ebe902.o] Error 1
Error in Rcpp::sourceCpp(code = "\n #include <Rcpp.h>\n\n // [[Rcpp::export]]\n int fibonacci(const int x) {\n if (x == 0) return(0);\n if (x == 1) return(1);\n return (fibonacci(x - 1)) + fibonacci(x - 2);\n }", :
Error 1 occurred building shared library.
WARNING: The tools required to build C++ code for R were not found.
Please install GNU development tools including a C++ compiler.
Execution halted
然后，他們要求我修改我的 makevars 文件 - 我使用 R 包usethis::edit_r_makevars()進行了修改 - 添加以下行：
CXXFLAGS += -I"/hpc/apps/gcc/9.1.0/include/c++/9.1.0/parallel/"
CXX14FLAGS += -I"/hpc/apps/gcc/9.1.0/include/c++/9.1.0/parallel/"
一旦我做了這個修改（我希望我做對了），我的錯誤信息變為：
Generated extern "C" functions
--------------------------------------------------------
#include <Rcpp.h>
#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif
// fibonacci
int fibonacci(const int x);
RcppExport SEXP sourceCpp_1_fibonacci(SEXP xSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< const int >::type x(xSEXP);
rcpp_result_gen = Rcpp::wrap(fibonacci(x));
return rcpp_result_gen;
END_RCPP
}
Generated R functions
-------------------------------------------------------
`.sourceCpp_1_DLLInfo` <- dyn.load('/localscratch/251578.1.mylablab.q/RtmpCHyEAd/sourceCpp-x86_64-pc-linux-gnu-1.0.7/sourcecpp_1e50364a03315/sourceCpp_2.so')
fibonacci <- Rcpp:::sourceCppFunction(function(x) {}, FALSE, `.sourceCpp_1_DLLInfo`, 'sourceCpp_1_fibonacci')
rm(`.sourceCpp_1_DLLInfo`)
Building shared library
--------------------------------------------------------
DIR: /localscratch/251578.1.mylablab.q/RtmpCHyEAd/sourceCpp-x86_64-pc-linux-gnu-1.0.7/sourcecpp_1e50364a03315
/hpc/apps/R/4.1.2/lib64/R/bin/R CMD SHLIB -o 'sourceCpp_2.so' 'file1e50325e7686.cpp'
g++ -std=gnu++14 -I"/hpc/apps/R/4.1.2/lib64/R/include" -DNDEBUG -I"/hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include" -I"/localscratch/251578.1.mylablab.q/RtmpCHyEAd/sourceCpp-x86_64-pc-linux-gnu-1.0.7" -I/hpc/apps/zlib/1.2.8/include -I/hpc/apps/pcre/8.38/include -I/hpc/apps/bzip2/1.0.6/include -I/hpc/apps/curl/7.54.1/include -I/hpc/apps/cairo/1.14.12/include -fpic -g -O2 -I"/hpc/apps/gcc/9.1.0/include/c++/9.1.0/parallel/" -c file1e50325e7686.cpp -o file1e50325e7686.o
In file included from /hpc/apps/gcc/11.1.0/include/c++/11.1.0/x86_64-pc-linux-gnu/bits/c++config.h:571,
from /hpc/apps/gcc/11.1.0/include/c++/11.1.0/cmath:41,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/Rcpp/platform/compiler.h:100,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/Rcpp/r/headers.h:66,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/RcppCommon.h:30,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/Rcpp.h:27,
from file1e50325e7686.cpp:2:
/hpc/apps/gcc/11.1.0/include/c++/11.1.0/x86_64-pc-linux-gnu/bits/os_defines.h:44:19: error: missing binary operator before token "("
44 | #if __GLIBC_PREREQ(2,15) && defined(_GNU_SOURCE)
| ^
/hpc/apps/gcc/11.1.0/include/c++/11.1.0/x86_64-pc-linux-gnu/bits/os_defines.h:52:19: error: missing binary operator before token "("
52 | #if __GLIBC_PREREQ(2, 27)
| ^
In file included from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/Rcpp/platform/compiler.h:100,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/Rcpp/r/headers.h:66,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/RcppCommon.h:30,
from /hpc/home/user/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include/Rcpp.h:27,
from file1e50325e7686.cpp:2:
/hpc/apps/gcc/11.1.0/include/c++/11.1.0/cmath:45:15: fatal error: math.h: No such file or directory
45 | #include_next <math.h>
| ^~~~~~~~
compilation terminated.
make: *** [file1e50325e7686.o] Error 1
Error in Rcpp::sourceCpp(code = "\n #include <Rcpp.h>\n\n // [[Rcpp::export]]\n int fibonacci(const int x) {\n if (x == 0) return(0);\n if (x == 1) return(1);\n return (fibonacci(x - 1)) + fibonacci(x - 2);\n }", :
Error 1 occurred building shared library.
WARNING: The tools required to build C++ code for R were not found.
Please install GNU development tools including a C++ compiler.
Execution halted
我在 Linux 方面的知識有限，恐怕我的問題超出了 STAN 論壇的 scope 范圍。 任何想法如何進行？
2 個解決方案
解決方案1
0 2021-12-24 16:43:37
我擔心你的問題仍然是本地的。 在您使用的計算中，有人可能已經設置了 R，使其在交互式 R 使用和您所謂的批量使用之間有所不同。
但那是非標准的，而且在你的最后。 一般來說，它只是工作。 使用您的程序的最小修改版本（我仍然覺得令人困惑：它加載doParallel ，注冊核心但是......觸發並行代碼 - 無論如何）它工作得很好：
使用腳本
edd@rob:~/git/stackoverflow/70470842(master)$ Rscript answer.R
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Fib(10) is 55
edd@rob:~/git/stackoverflow/70470842(master)$
在批處理模式下使用 R
edd@rob:~/git/stackoverflow/70470842(master)$ R -s -f answer.R
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Fib(10) is 55
edd@rob:~/git/stackoverflow/70470842(master)$
使用我們更小的前端
edd@rob:~/git/stackoverflow/70470842(master)$ r answer.R
Loading required package: foreach
Loading required package: iterators
Loading required package: utils
Loading required package: parallel
Fib(10) is 55
edd@rob:~/git/stackoverflow/70470842(master)$
修改后的源代碼
library(doParallel) # Library
ncores <- 5 # Simulation parameters
n_sim <- 5
registerDoParallel(ncores)
Rcpp::sourceCpp(code='
#include <Rcpp.h>
// [[Rcpp::export]]
int fibonacci(const int x) {
if (x == 0) return(0);
if (x == 1) return(1);
return (fibonacci(x - 1)) + fibonacci(x - 2);
}'
)
cat("Fib(10) is ", fibonacci(10), "\n")
解決方案2
0 2022-01-05 19:04:43
為了將來參考，在收到這里的反饋和 STAN 論壇后，我與我所在機構的 IT 團隊進行了互動，他們終於找到了解決方案。 用他們的話說：“計算節點通常不用於開發。因此默認情況下不安裝某些開發包。我們在計算節點上安裝了“glibc-devel”和“glibc-headers”。
運行我的C ++代碼w / Rcpp / RcppArmadillo時出現內存錯誤：用valgrind調試后無法准確識別出什么問題
[英]Memory Error when running my C++ code w/ Rcpp/RcppArmadillo : Can't identify exactly what is wrong after debugging with valgrind
Rcpp：將列表中的布爾值從R傳遞給采用Rcpp :: List的C ++函數時出錯
[英]Rcpp: error when passing a boolean value in a list from R to a C++ function that takes an Rcpp::List
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