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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