[Bioc-devel] R version-dependent segfault
Martin Morgan
martin.morgan at roswellpark.org
Thu Jan 5 20:32:16 CET 2017
On 01/05/2017 11:10 AM, Vladimir Kiselev wrote:
> 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 <http://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;
>
I don't think #include <armadillo> is required. I also don't know C++
well enough to know how conflicting symbols in different namespaces are
resolved. My suggestion would be to remove #include <armadillo> and and
to fully qualify symbols arma::colvec, etc in norm_laplacian.
I should have added --vanilla to the incantation
$ R --vanilla -d valgrind -f norm_laplacian.R
Using gdb seems more intimidating than it actually is. One would need to
make sure ~/.R/Makevars had lines
CFLAGS = -g -O0
CXXFLAGS = -g -O0
install RcppArmadillo and SC3 (the compiler should report flags -g -O0)
and to confirm that the segfault still occurs (it might not -- it could
be the result of a subtle bug introduced by optimization). One would then
R --vanilla -d gdb
(gdb) r
> library(SC3)
> SC3::norm_laplacian(matrix(runif(100), nrow = 10))
probably ending up in the debugger where you could do
(gdb) up
to go up the call stack unitil you see something like
(gdb) up
#1 0x00007fffe4118ac5 in arma::Mat<double>::max (this=0x7fffffffb490)
at
/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-3.5/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:6801
6801 return op_max::direct_max(memptr(), n_elem);
then down to the line that fails
(gdb) do
#0 arma::op_max::direct_max<double> (X=0xfc73dc0, n_elem=100)
at
/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-3.5/RcppArmadillo/include/armadillo_bits/op_max_meat.hpp:362
362 const eT X_i = X[i];
then take a peak at the source code
(gdb) l
357 eT max_val = priv::most_neg<eT>();
358
359 uword i,j;
360 for(i=0, j=1; j<n_elem; i+=2, j+=2)
361 {
362 const eT X_i = X[i];
363 const eT X_j = X[j];
364
365 if(X_i > max_val) { max_val = X_i; }
366 if(X_j > max_val) { max_val = X_j; }
and check out things to make sure that they make sense
(gdb) p n_elem
$1 = 100
(gdb) p i
$2 = 0
(gdb) p j
$3 = 1
(gdb) call X[i]
$4 = 0.90036606369540095
etc. One might go up the call stack, verifying along the way
(gdb) up
#1 0x00007fffe4118ac5 in arma::Mat<double>::max (this=0x7fffffffb490)
at
/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-3.5/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:6801
6801 return op_max::direct_max(memptr(), n_elem);
(gdb)
#2 0x00007fffe4116cae in norm_laplacian (A=...) at cppFunctions.cpp:86
86 A = exp(-A/A.max());
(gdb) print A
$6 = {<arma::Base<double, arma::Mat<double> >> =
{<arma::Base_inv_yes<arma::Mat<double> >> = {<No data fields>},
<arma::Base_eval_Mat<double, arma::Mat<double> >> = {<No data fields>},
<arma::Base_trans_default<arma::Mat<double> >> = {<No data fields>}, <No
data fields>}, n_rows = 10, n_cols = 10, n_elem = 100,
vec_state = 0, mem_state = 0, mem = 0xfc73dc0, mem_local = {
6.9533484229745318e-310, 6.9533490667683032e-310,
6.8279872255260272e-321,
6.9533484229745318e-310, 6.9533491664832504e-310,
6.9533558068923271e-310,
6.9533558068921294e-310, 6.9533490666871776e-310,
4.9406564584124654e-324,
-3.9321179452085543e+234, 6.9533480320859982e-310,
1.1680649801909133e-315, 6.9533558069148565e-310,
6.9533487849390297e-310,
1.1680649801909133e-315, 6.0259171035421809e-317},
static is_col = <optimized out>, static is_row = <optimized out>}
My next stop would be the Rcpp mailing list
http://lists.r-forge.r-project.org/mailman/listinfo/rcpp-devel. They
will likely either have something useful to say or be reluctant to
install the 80+ packages that SC3 depends on.
Hope that helps somehow...
Martin
>
> Many thanks in advance,
> Kind regards,
> Vladimir
>
> On Thu, Jan 5, 2017 at 12:19 PM Martin Morgan
> <martin.morgan at roswellpark.org <mailto:martin.morgan at 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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