Dear Martin,
Many thanks for your reply, it was really helpful. My collaborator ran the
commands you suggested and got the following output:
*****
$ Rscript norm_laplacian.R
/home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
'norm_laplacian.cpp'
g++ -I/home/jake/miniconda3/lib/R/include -DNDEBUG
-I/home/jake/miniconda3/include
-I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/RcppArmadillo/include"
-I"/home/jake/Documents" -fpic -I/home/jake/miniconda3/include -c
norm_laplacian.cpp -o norm_laplacian.o
g++ -shared -L/home/jake/miniconda3/lib/R/lib -L/home/jake/miniconda3/lib
-lgfortran -o sourceCpp_2.so norm_laplacian.o
-L/home/jake/miniconda3/lib/R/lib -lRlapack
-L/home/jake/miniconda3/lib/R/lib -lRblas -lgfortran -lm -lquadmath
-L/home/jake/miniconda3/lib/R/lib -lR
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.10
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets base
other attached packages:
[1] Rcpp_0.12.8
loaded via a namespace (and not attached):
[1] tools_3.3.2 RcppArmadillo_0.7.600.1.0
$ g++ --version|head -n1
g++ (Ubuntu 6.2.0-5ubuntu12) 6.2.0 20161005
*****
So running the simplified code did not produce a segfault and suggested
that the problem was in SC3::norm_laplacian(). And indeed, running valgrind
with SC3::norm_laplacian(matrix(runif(100), nrow = 10)) did catch the error:
*****
$ R -d valgrind -f norm_laplacian.R
==7046== Memcheck, a memory error detector
==7046== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==7046== Using Valgrind-3.12.0.SVN and LibVEX; rerun with -h for copyright
info
==7046== Command: /home/jake/miniconda3/lib/R/bin/exec/R -f norm_laplacian.R
==7046==
R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
> library(Rcpp)
> sourceCpp("norm_laplacian.cpp", showOutput=TRUE)
/home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
'norm_laplacian.cpp'
g++ -I/home/jake/miniconda3/lib/R/include -DNDEBUG
-I/home/jake/miniconda3/include
-I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/RcppArmadillo/include"
-I"/home/jake/Documents" -fpic -I/home/jake/miniconda3/include -c
norm_laplacian.cpp -o norm_laplacian.o
g++ -shared -L/home/jake/miniconda3/lib/R/lib -L/home/jake/miniconda3/lib
-lgfortran -o sourceCpp_2.so norm_laplacian.o
-L/home/jake/miniconda3/lib/R/lib -lRlapack
-L/home/jake/miniconda3/lib/R/lib -lRblas -lgfortran -lm -lquadmath
-L/home/jake/miniconda3/lib/R/lib -lR
> xx <- norm_laplacian(matrix(runif(100), nrow = 10))
> SC3::norm_laplacian(matrix(runif(100), nrow = 10))
==7046== Use of uninitialised value of size 8
==7046== at 0x213645B8: direct_max<double> (op_max_meat.hpp:362)
==7046== by 0x213645B8: max (Mat_meat.hpp:6801)
==7046== by 0x213645B8: norm_laplacian(arma::Mat<double>)
(cppFunctions.cpp:87)
==7046== by 0x21360E8C: SC3_norm_laplacian (RcppExports.cpp:49)
==7046== by 0x521DE81: R_doDotCall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x522BD99: do_dotcall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x5267AAC: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x526B0A7: do_begin (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x526789E: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x5268B8C: Rf_applyClosure (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x5267BBF: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x52A6C1E: Rf_ReplIteration (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x52A6DD1: R_ReplConsole (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x52A8758: run_Rmainloop (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==
==7046== Invalid read of size 8
==7046== at 0x213645B8: direct_max<double> (op_max_meat.hpp:362)
==7046== by 0x213645B8: max (Mat_meat.hpp:6801)
==7046== by 0x213645B8: norm_laplacian(arma::Mat<double>)
(cppFunctions.cpp:87)
==7046== by 0x21360E8C: SC3_norm_laplacian (RcppExports.cpp:49)
==7046== by 0x521DE81: R_doDotCall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x522BD99: do_dotcall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x5267AAC: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x526B0A7: do_begin (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x526789E: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x5268B8C: Rf_applyClosure (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x5267BBF: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x52A6C1E: Rf_ReplIteration (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x52A6DD1: R_ReplConsole (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x52A8758: run_Rmainloop (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== Address 0xa0000000a is not stack'd, malloc'd or (recently) free'd
==7046==
*** caught segfault ***
address 0xa0000000a, cause 'memory not mapped'
Traceback:
1: .Call("SC3_norm_laplacian", PACKAGE = "SC3", A)
2: SC3::norm_laplacian(matrix(runif(100), nrow = 10))
An irrecoverable exception occurred. R is aborting now ...
==7046==
==7046== Process terminating with default action of signal 11 (SIGSEGV)
==7046== at 0x5C4C4DD: raise (raise.c:53)
==7046== by 0x52A76C4: sigactionSegv (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046== by 0x5C4C62F: ??? (in /lib/x86_64-linux-gnu/libpthread-2.24.so)
==7046== by 0x213645B7: direct_max<double> (op_max_meat.hpp:360)
==7046== by 0x213645B7: max (Mat_meat.hpp:6801)
==7046== by 0x213645B7: norm_laplacian(arma::Mat<double>)
(cppFunctions.cpp:87)
==7046==
==7046== HEAP SUMMARY:
==7046== in use at exit: 149,681,035 bytes in 81,447 blocks
==7046== total heap usage: 275,293 allocs, 193,846 frees, 410,601,938
bytes allocated
==7046==
==7046== LEAK SUMMARY:
==7046== definitely lost: 0 bytes in 0 blocks
==7046== indirectly lost: 0 bytes in 0 blocks
==7046== possibly lost: 0 bytes in 0 blocks
==7046== still reachable: 149,681,035 bytes in 81,447 blocks
==7046== of which reachable via heuristic:
==7046== newarray : 7,152 bytes in 1
blocks
==7046== suppressed: 0 bytes in 0 blocks
==7046== Rerun with --leak-check=full to see details of leaked memory
==7046==
==7046== For counts of detected and suppressed errors, rerun with: -v
==7046== Use --track-origins=yes to see where uninitialised values come from
==7046== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 0 from 0)
Segmentation fault (core dumped)
*****
So, it looks like the problem is in finding the max of the input matrix A,
specifically in the direct_max() function of Armadillo library. But the
segfault only appears when running SC3::norm_laplacian() and not the
simplified code. Does it suggest that I have some linking or exporting
problems in the package? Can you think of any solution to this problem?
In case this can help, the SC3::norm_laplacian() function is stored in the
file with the following header:
#include <armadillo>
#include <RcppArmadillo.h>
using namespace arma;
using namespace Rcpp;
Many thanks in advance,
Kind regards,
Vladimir
On Thu, Jan 5, 2017 at 12:19 PM Martin Morgan <martin.mor...@roswellpark.org>
wrote:
> On 01/05/2017 06:41 AM, Vladimir Kiselev wrote:
> > My package (SC3 -
> http://bioconductor.org/packages/3.4/bioc/html/SC3.html)
> > has a function that causes R version/platform-dependent seqfault. Here is
> > the function (it's in C++ using RccpArmadillo):
> >
> > arma::mat norm_laplacian(arma::mat A) {
> > A = exp(-A/A.max());
> > arma::rowvec D_row = pow(sum(A), -0.5);
> > A.each_row() %= D_row;
> > colvec D_col = conv_to< colvec >::from(D_row);
> > A.each_col() %= D_col;
> > arma::mat res = eye(A.n_cols, A.n_cols) - A;
> > return(res);
> > }
> >
> > The test code that provides a segfault on some R versions/platforms:
> > SC3::norm_laplacian(matrix(runif(100), nrow = 10))
>
> The first line of attack is to simplify the problem as much as possible.
> I did this by writing a C++ file norm_laplacian.cpp
>
> #include <RcppArmadillo.h>
>
> using namespace arma;
>
> // [[Rcpp::depends(RcppArmadillo)]]
>
> // [[Rcpp::export]]
> arma::mat norm_laplacian(arma::mat A) {
> A = exp(-A/A.max());
> arma::rowvec D_row = pow(sum(A), -0.5);
> A.each_row() %= D_row;
> colvec D_col = conv_to< colvec >::from(D_row);
> A.each_col() %= D_col;
> arma::mat res = eye(A.n_cols, A.n_cols) - A;
> return(res);
> }
>
> and then in R, e.g., norm_laplacian.R
>
> library(Rcpp)
> sourceCpp("norm_laplacian.cpp", showOutput=TRUE)
> xx <- norm_laplacian(matrix(runif(100), nrow = 10))
> sessionInfo()
>
> It would be helpful to use set.seed() to make the example more
> reproducible. One would hope that
>
> R -f norm_laplacian.R
>
> would produce a segfault. Unfortunately not for me. My next step was to
> run this code under valgrind to look for invalid memory access
>
> R -d valgrind -f norm_laplacian.R
>
> again hoping for a report of 'invalid write' or 'invalid read', but
> again no luck for me.
>
> You could see if your collaborators are able to generate segfaults with
> this simpler code. If R -f norm_laplacian.R is sufficient, the next step
> would be to run it under a C-level debugger like gdb, with some hints at
> http://bioconductor.org/developers/how-to/c-debugging/
>
> Here's my output; it's also useful to know information about the
> compiler, and to pay attention to the compiler options (especially
> optimization level -O0 for me)
>
> $ g++ --version|head -n1
> g++ (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
>
> $ R --vanilla -f norm_laplacian.R
> > library(Rcpp)
> > sourceCpp("norm_laplacian.cpp", showOutput=TRUE)
> /home/mtmorgan/bin/R-devel/bin/R CMD SHLIB -o 'sourceCpp_2.so'
> 'norm_laplacian.cpp'
> g++ -I/home/mtmorgan/bin/R-devel/include -DNDEBUG -I/usr/local/include
>
> -I"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-3.5/Rcpp/include"
>
> -I"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-3.5/RcppArmadillo/include"
> -I"/tmp" -fpic -g -O0 -c norm_laplacian.cpp -o norm_laplacian.o
> g++ -shared -L/home/mtmorgan/bin/R-devel/lib -L/usr/local/lib -o
> sourceCpp_2.so norm_laplacian.o -L/home/mtmorgan/bin/R-devel/lib
> -lRlapack -L/home/mtmorgan/bin/R-devel/lib -lRblas -lgfortran -lm
> -lquadmath -L/home/mtmorgan/bin/R-devel/lib -lR
> > xx <- norm_laplacian(matrix(runif(100), nrow = 10))
> > sessionInfo()
> R Under development (unstable) (2016-12-20 r71827)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.1 LTS
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] Rcpp_0.12.8.3
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0 tools_3.4.0
> [3] RcppArmadillo_0.7.600.1.0
> >
>
>
> if the segfault does not occur with the simpler code, then one could try
> gdb / valgrind with SC3::norm_laplacian(matrix(runif(100), nrow = 10))
>
> Martin
>
> >
> > The segfault usually looks like this:
> > *** caught segfault ***
> > address 0x7ffdc981e000, cause 'memory not mapped'
> >
> > (where address can be a different sequence)
> >
> > So far by a collaborative effort (me and some users of the package) we
> > figured out configurations that cause or do not cause a segfault:
> >
> > * Configurations causing a segfault:
> >
> > R version 3.3.2 (2016-10-31)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Arch Linux
> >
> > R version 3.3.2 (2016-10-31)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 16.10
> >
> > * Configurations causing no segfault:
> >
> > R version 3.3.2 (2016-10-31)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 16.04.1 LTS
> >
> > R version 3.3.1 (2016-06-21)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 14.04.5 LTS
> >
> > R version 3.3.0 (2016-05-03)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu precise (12.04.5 LTS)
> >
> > R Under development (unstable) (2016-10-20 r71540)
> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
> > Running under: OS X Yosemite 10.10.5
> >
> > More details on our discussion can be found here:
> > https://github.com/hemberg-lab/SC3/issues/33
> >
> > Has anybody had a similar issue? Do you have any suggestions on how to
> fix
> > this, except rewriting the function in R? Or maybe there already exists a
> > normalised Laplacian function written in C++?
> >
> > Many thanks,
> > Cheers,
> > Vladimir
> >
>
>
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