[Rcpp-devel] segmentation fault when wrapping a big Eigen 2-d array

Wasey, Jack O jack at jackwasey.com
Mon Apr 9 13:22:53 CEST 2018

Dear Rcpp developers,

I'm having trouble with a reproducible error when wrapping a big Eigen dense matrix.

Rcpp::LogicalMatrix mat_out_bool = Rcpp::wrap(result);

Thread 1 "R" received signal SIGSEGV, Segmentation fault.
coerceToLogical (v=0x7fffa1a1c010) at coerce.c:441

Where 'result' is an Eigen::MatrixXi of size 472132x30, which is the result of a sparse x dense matrix multiplication.
DenseMap result = visit_codes_sparse * map;

The backtrace begins:
#0  coerceToLogical (v=0x7fffa1a1c010) at coerce.c:441
#1  Rf_coerceVector (v=<optimized out>, type=<optimized out>) at coerce.c:1243
#2  0x00007fffdc660515 in Rcpp::internal::basic_cast<10> (x=0x7fffa1a1c010) at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r_cast.h:66
#3  0x00007fffdc65edc5 in Rcpp::internal::r_true_cast<10> (x=0x7fffa1a1c010) at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r_cast.h:95
#4  0x00007fffdc664a9d in Rcpp::r_cast<10> (x=0x7fffa1a1c010) at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r_cast.h:163
#5  0x00007fffdc666f99 in Rcpp::Matrix<10, Rcpp::PreserveStorage>::Matrix (this=0x7fffffff23a0, x=0x7fffa1a1c010)
    at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/vector/Matrix.h:53
#6  0x00007fffdc68603e in icd9Comorbid_alt_MatMul (icd9df=..., icd9Mapping=..., visitId="visit_id", icd9Field="code", threads=8, chunk_size=256, omp_chunk_size=1)
    at comorbid_alt_MatMul.cpp:271
#7  0x00007fffdc64a597 in _icd_icd9Comorbid_alt_MatMul_try (icd9dfSEXP=0x555558590cd8, icd9MappingSEXP=0x55555839d9d0, visitIdSEXP=0x55555a25e2b8, icd9FieldSEXP=0x55555c066298,
    threadsSEXP=0x5555623279f8, chunk_sizeSEXP=0x5555586122e8, omp_chunk_sizeSEXP=0x555558612258) at RcppExports.cpp:347

I would love to give a small reproducible example, but at this point, I can only trigger the problem with a big data set (which makes valgrind unreasonably slow), and only by repeating the computation, as sometimes it does succeed. The code is in the eigen-sparse branch of https://github.com/jackwasey/icd . I do not expect anyone to download and debug my code (which FWIW compiles without any warnings), but I would like to know whether, in principle, I am doing something wrong with the integer to logical 'cast' when wrapping, or if this is possibly an Rcpp or RcppEigen bug. I can induce the crash on a server with huge amounts of RAM, and on Mac and Linux platforms, with and without OpenMP enabled.


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