Hi Pratibha, I highly doubt that the segfault is related to the optimization level. FWIW, I still cannot replicate the segfault as you described -- Ubuntu 14.04, gcc 4.8.2, and...
Kevin On Wed, Sep 3, 2014 at 12:34 PM, Pratibha Rana <pr...@vertica.com> wrote: > I think I got to the bottom of the issue. I was using the -O0 option > instead of the -O2 option while compiling the code. Including the -O2 > option resolved the issue. > > Thanks > Pratibha > > On 09/02/2014 04:49 PM, Dirk Eddelbuettel wrote: > > Hi, > > > > On 2 September 2014 at 20:16, Pratibha Rana wrote: > > | Hi Dirk, > > | > > | Yes I work for Vertica which is apparent from my email. But I do not > > | work on the distributedR project. I work on the vertica-R integration. > > > > You could tell us about that too ... > > > > | I acknowledge that it is a local issue because the same code works fine > > | in the RInside's example directory on the same machine with the same > > | libraries that I installed from sources. I verified the dll's being > > | loaded in both the cases. The back trace doesn't help either. I am out > > | of ideas as to what can be wrong. I am stumped as to why Rcpp::List > > | works fine but Rcpp::DataFrame causes a segfault. Any suggestion on > > | debugging the cause are greatly appreciated. > > > > So you may be doing something different in the build process for your > local > > directory. You need to work out what is different. > > > > Can you please post this __on the list__ for a continued thread there? > > > > Dirk > > > > | > > | Thanks > > | Pratibha > > | > Dear Pratibha, > > | > > > | > On 2 September 2014 at 19:22, Pratibha Rana wrote: > > | > | I have a custom application that uses Rcpp and Rinside to execute > R code. All > > | > > > | > [ Random thought: I might make people a bit more sympathetic for > your cause > > | > and questions if you pointed out that a) you are selling a db > solution, b) > > | > that these days Vertica is part of HP and c) the code for the R > integration > > | > is apparently on GitHub: https://github.com/vertica/DistributedR > (or at least > > | > that is where I think it may be). Why you guys never announced that > here > > | > is a bit of a mystery to me. ] > > | > > > | > | was well until I was using R-3.0.0, Rcpp 0.10.2 and RInside 0.2.10 > but now its > > | > | time to upgrade to the latest version and I can't get even the > Rinside samples > > | > | to work in place of my application. My machine has Ubuntu14.04. > The code > > | > > > | > Well, consider that > > | > > > | > a) I (and others) develop on Ubuntu 14.04. Things work on Ubuntu > 14.04 > > | > > > | > b) CRAN tests all packages on several backends, including Ubuntu, > Debian, > > | > FC, OS X and Windows and would tell me (as maintainer) in no > uncertain > > | > terms if it didn't work. > > | > > > | > c) So if it fails to work for you, maybe assume a local issue > first? > > | > > > | > | compiles fine but when I run it, I get a segfault during Rinside > > | > | initialization. I tried to troubleshoot by replacing my code by > one of the > > | > | examples rinside_sample0. The example runs fine as is but if I add > just a > > | > | single line "Rcpp::DataFrame p; " it segfaults again. Here is the > complete > > | > | code. The same code works fine inside the Rinside examples > directory. > > | > | > > | > | > > | > | #include <RInside.h> > > | > | > > | > | int main(int argc, char *argv[]) > > | > | { > > | > | > > | > | std::getchar(); > > | > > > | > That line makes little sense. I omitted it. > > | > > > | > | > > | > | RInside R(argc, argv); > > | > | > > | > | R["txt"] = "Hello, world!\n"; > > | > | Rcpp::DataFrame pf; <-------- Runs fine if I comment > out this line. > > | > | R.parseEvalQ("cat(txt)"); > > | > | > > | > | exit(0); > > | > | } > > | > > > | > Works fine here: > > | > > > | > edd@max:~/git/rinside/inst/examples/standard$ cat > rinside_vertica.cpp > > | > > > | > #include <RInside.h> > > | > > > | > int main(int argc, char *argv[]) > > | > { > > | > > > | > RInside R(argc, argv); > > | > > > | > R["txt"] = "Hello, world!\n"; > > | > Rcpp::DataFrame pf; // <-------- Runs fine if I comment > out this line. > > | > R.parseEvalQ("cat(txt)"); > > | > > > | > exit(0); > > | > } > > | > edd@max:~/git/rinside/inst/examples/standard$ make rinside_vertica > > | > ccache g++-4.8 -I/usr/share/R/include > -I/usr/local/lib/R/site-library/Rcpp/include > -I/usr/local/lib/R/site-library/RInside/include -g -O2 -fstack-protector > --param=ssp-buffer-size=4 -Wformat -Werror=format-security > -D_FORTIFY_SOURCE=2 -g -O3 -Wall -pipe -Wno-unused -pedantic -Wall > rinside_vertica.cpp -Wl,--export-dynamic -fopenmp -L/usr/lib/R/lib -lR > -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -lblas -llapack > -L/usr/local/lib/R/site-library/RInside/lib -lRInside > -Wl,-rpath,/usr/local/lib/R/site-library/RInside/lib -o rinside_vertica > > | > edd@max:~/git/rinside/inst/examples/standard$ ./rinside_vertica > > | > Hello, world! > > | > edd@max:~/git/rinside/inst/examples/standard$ > > | > > > | > > > | > I maybe running github versions of Rcpp and/or RInside, but the only > thing > > | > that may matter is that you probably should > > | > > > | > a) install Rcpp from source > > | > b) install RInside from source > > | > > > | > and then build these examples. > > | > > > | > A reproducible issue may help. This was not reproducible. Or > rather, this > > | > may not even have been a bug. > > | > > > | > Regards, Dirk > > | > > > | > > > | > | Here is the backtrace of the segfault > > | > | > > | > | > > | > | Program received signal SIGSEGV, Segmentation fault. > > | > | 0x00007ffff7597767 in reset_current_error() () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | (gdb) bt -10 > > | > | #261636 0x00007ffff7597769 in reset_current_error() () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | #261637 0x00007ffff7597769 in reset_current_error() () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | #261638 0x00007ffff7597769 in reset_current_error() () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | #261639 0x00007ffff7597769 in reset_current_error() () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | #261640 0x00007ffff7598530 in Rcpp::Rcpp_eval(SEXPREC*, SEXPREC*) > () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | #261641 0x00007ffff7599542 in > Rcpp::Language_Impl<Rcpp::PreserveStorage>::eval() const () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | #261642 0x00007ffff75969c7 in RInside::autoloads() () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | #261643 0x00007ffff7595fd3 in RInside::initialize(int, char const* > const*, bool, bool, bool) () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | #261644 0x00007ffff7595a4a in RInside::RInside(int, char const* > const*, bool, bool, bool) () from > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | #261645 0x000000000040361e in main (argc=1, argv=0x7fffffffdc88) > at rinside_sample0.cpp:14 > > | > | (gdb) > > | > | > > | > | > > | > | > > | > | > > | > | I also looked at the libraries that were being loaded at runtime > and they are > > | > | exactly the same for both the rinside examples and my app. Pasted > below for > > | > | completeness. I am out ofdebugging tricks to get this to work. Any > ideas as to > > | > | what's wrong. what am I missing? > > | > | > > | > | > > | > | > prana:trunk/third-party/install/lib/R/library/RInside/examples/standard $ > cat /proc/21915/maps | awk '{print $6}' | grep '\.so' | sort | uniq > > | > | /home/prana/trunk/third-party/install/lib/R/lib/libRblas.so > > | > | /home/prana/trunk/third-party/install/lib/R/lib/libRlapack.so > > | > | /home/prana/trunk/third-party/install/lib/R/lib/libR.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/graphics/libs/graphics.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/grDevices/libs/grDevices.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/methods/libs/methods.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/Rcpp/libs/Rcpp.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/stats/libs/stats.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/utils/libs/utils.so > > | > | /lib/x86_64-linux-gnu/ld-2.19.so > > | > | /lib/x86_64-linux-gnu/libc-2.19.so > > | > | /lib/x86_64-linux-gnu/libdl-2.19.so > > | > | /lib/x86_64-linux-gnu/libgcc_s.so.1 > > | > | /lib/x86_64-linux-gnu/libm-2.19.so > > | > | /lib/x86_64-linux-gnu/libnsl-2.19.so > > | > | /lib/x86_64-linux-gnu/libnss_compat-2.19.so > > | > | /lib/x86_64-linux-gnu/libnss_files-2.19.so > > | > | /lib/x86_64-linux-gnu/libnss_nis-2.19.so > > | > | /lib/x86_64-linux-gnu/libpthread-2.19.so > > | > | /lib/x86_64-linux-gnu/librt-2.19.so > > | > | /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0 > > | > | /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 > > | > | /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0 > > | > | /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 > > | > | > > | > | > > | > | prana:trunk/myapp $ cat /proc/21730/maps | awk '{print $6}' | grep > '\.so' | sort | uniq > > | > | /home/prana/trunk/third-party/install/lib/R/lib/libRblas.so > > | > | /home/prana/trunk/third-party/install/lib/R/lib/libRlapack.so > > | > | /home/prana/trunk/third-party/install/lib/R/lib/libR.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/graphics/libs/graphics.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/grDevices/libs/grDevices.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/methods/libs/methods.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/Rcpp/libs/Rcpp.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/stats/libs/stats.so > > | > | > /home/prana/trunk/third-party/install/lib/R/library/utils/libs/utils.so > > | > | /lib/x86_64-linux-gnu/ld-2.19.so > > | > | /lib/x86_64-linux-gnu/libc-2.19.so > > | > | /lib/x86_64-linux-gnu/libdl-2.19.so > > | > | /lib/x86_64-linux-gnu/libgcc_s.so.1 > > | > | /lib/x86_64-linux-gnu/libm-2.19.so > > | > | /lib/x86_64-linux-gnu/libnsl-2.19.so > > | > | /lib/x86_64-linux-gnu/libnss_compat-2.19.so > > | > | /lib/x86_64-linux-gnu/libnss_files-2.19.so > > | > | /lib/x86_64-linux-gnu/libnss_nis-2.19.so > > | > | /lib/x86_64-linux-gnu/libpthread-2.19.so > > | > | /lib/x86_64-linux-gnu/librt-2.19.so > > | > | /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0 > > | > | /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 > > | > | /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0 > > | > | /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 > > | > | > > | > | > > | > | > > | > | > > | > | Thanks > > | > | Pratibha > > | > | _______________________________________________ > > | > | 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 > > | > > > | > > > > _______________________________________________ > 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 >
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