Re: [Rcpp-devel] segmentation fault when wrapping a big Eigen 2-d array
On 9 April 2018 at 09:51, Jack Wasey wrote: | I seem to tread in unusual code paths often, which is | why I appreciate so much your guidance. I can't reproduce the error now | I've converted from integer Eigen matrix to Rcpp::IntegerMatrix, then | within Rcpp, Integer to Logical matrices. I think it is super tempting to write compact code like that. But the template magic is a little fragile, and nesting does not seem to help. So I just learned to be defensive and do it one step at time.. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
Re: [Rcpp-devel] segmentation fault when wrapping a big Eigen 2-d array
On Mon, Apr 09, 2018 at 07:09:55AM -0500, Dirk Eddelbuettel wrote: > > On 9 April 2018 at 07:22, Wasey, Jack O wrote: > | 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=, type=) at > coerce.c:1243 > | #2 0x7fffdc660515 in Rcpp::internal::basic_cast<10> (x=0x7fffa1a1c010) > at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r_cast.h:66 > | #3 0x7fffdc65edc5 in Rcpp::internal::r_true_cast<10> > (x=0x7fffa1a1c010) at > /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r_cast.h:95 > | #4 0x7fffdc664a9d in Rcpp::r_cast<10> (x=0x7fffa1a1c010) at > /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r_cast.h:163 > | #5 0x7fffdc666f99 in Rcpp::Matrix<10, Rcpp::PreserveStorage>::Matrix > (this=0x7fff23a0, x=0x7fffa1a1c010) > | at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/vector/Matrix.h:53 > | #6 0x7fffdc68603e 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 0x7fffdc64a597 in _icd_icd9Comorbid_alt_MatMul_try > (icd9dfSEXP=0x58590cd8, icd9MappingSEXP=0x5839d9d0, > visitIdSEXP=0x5a25e2b8, icd9FieldSEXP=0x5c066298, > | threadsSEXP=0x623279f8, chunk_sizeSEXP=0x586122e8, > omp_chunk_sizeSEXP=0x58612258) 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. > > From the "well then don't do it" school: can you cast _before_ you interact > with R / Rcpp / RcppEigen? What happens when you try the "big" operation > entirely in C++ / Eigen and then "merely" transfer a known object (ie an int > vector/matrix) ? If that works, try bool and then see if that maps to > Logical. > > Some code paths are simply less well trodden. Int would be first route. > > I may of course be entirely off the page. Early morning ... > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org I seem to tread in unusual code paths often, which is why I appreciate so much your guidance. I can't reproduce the error now I've converted from integer Eigen matrix to Rcpp::IntegerMatrix, then within Rcpp, Integer to Logical matrices. I naively assumed that if the compiler let me do it, it was a valid cast. Does this mean I unearthered a bug somewhere down the line of dependencies? Thanks, Jack ___ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
Re: [Rcpp-devel] segmentation fault when wrapping a big Eigen 2-d array
On 9 April 2018 at 07:22, Wasey, Jack O wrote: | 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=, type=) at coerce.c:1243 | #2 0x7fffdc660515 in Rcpp::internal::basic_cast<10> (x=0x7fffa1a1c010) at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r_cast.h:66 | #3 0x7fffdc65edc5 in Rcpp::internal::r_true_cast<10> (x=0x7fffa1a1c010) at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r_cast.h:95 | #4 0x7fffdc664a9d in Rcpp::r_cast<10> (x=0x7fffa1a1c010) at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r_cast.h:163 | #5 0x7fffdc666f99 in Rcpp::Matrix<10, Rcpp::PreserveStorage>::Matrix (this=0x7fff23a0, x=0x7fffa1a1c010) | at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/vector/Matrix.h:53 | #6 0x7fffdc68603e 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 0x7fffdc64a597 in _icd_icd9Comorbid_alt_MatMul_try (icd9dfSEXP=0x58590cd8, icd9MappingSEXP=0x5839d9d0, visitIdSEXP=0x5a25e2b8, icd9FieldSEXP=0x5c066298, | threadsSEXP=0x623279f8, chunk_sizeSEXP=0x586122e8, omp_chunk_sizeSEXP=0x58612258) 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. >From the "well then don't do it" school: can you cast _before_ you interact with R / Rcpp / RcppEigen? What happens when you try the "big" operation entirely in C++ / Eigen and then "merely" transfer a known object (ie an int vector/matrix) ? If that works, try bool and then see if that maps to Logical. Some code paths are simply less well trodden. Int would be first route. I may of course be entirely off the page. Early morning ... Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
