[Rcpp-devel] RcppArmadillo Memory Leak?
Alessandro Vitale
alevitale at gmail.com
Wed Nov 20 19:24:00 CET 2013
I've done the new test (dense matrix with just Rcpp NumericMatrix, no RcppArmadillo) and in this case there is no leak.
This is the code I used
// [[Rcpp::export]]
NumericMatrix dense_numericMatrix(NumericMatrix A){
A(0,0) = 1;
A(1,0) = 2;
return A ;
}
testMatrix <- matrix(data=0,nrow=1e3*5,ncol=1e3) # 40MB Dense Matrix
for(i in 1:5){
a <- dense_numericMatrix(testMatrix)
}
and this is valgrind output
==28325== LEAK SUMMARY:
==28325== definitely lost: 36 bytes in 2 blocks
==28325== indirectly lost: 0 bytes in 0 blocks
==28325== possibly lost: 0 bytes in 0 blocks
==28325== still reachable: 74,382,445 bytes in 20,450 blocks
==28325== suppressed: 21,484 bytes in 82 blocks
==28325==
==28325== For counts of detected and suppressed errors, rerun with: -v
==28325== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 10 from 10)
Can I support in some other ways in finding what's causing the problem in RcppArmadillo sparse matrix?
Alessandro
On 20 Nov, 2013, at 18:36 , Dirk Eddelbuettel wrote:
>
> On 18 November 2013 at 18:16, Alessandro Vitale wrote:
> | Dirk, I've run the code a couple times with valgrind, one time calling sparse 5 times, the other calling sparse 10 times.
> | Below is the main code and valgrind output.
> | What do you think, could it be an Armadillo / RcppArmadillo leak?
>
> Could be. For comparison, what happens when you use a regular matrix (ie
> Rcpp::NumericMatrix) and check with valgrind?
>
> Dirk
>
>
> | testMatrix <- Matrix(data=0,nrow=1e7,ncol=1e7,sparse=TRUE)
> |
> | for(i in 1:5){
> | a <- sparse(testMatrix)
> | }
> |
> | ==22103== 160,000,032 bytes in 2 blocks are possibly lost in loss record 4,034 of 4,035
> | ==22103== at 0xC658: malloc (vg_replace_malloc.c:295)
> | ==22103== by 0x8BD503A: arma::SpMat<double>::init(unsigned long long, unsigned long long) (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/Rtmp8Krm0b/sourcecpp_565778edd300/sourceCpp_27814.so)
> | ==22103== by 0x8BD6690: Rcpp::traits::Exporter<arma::SpMat<double> >::get() (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/Rtmp8Krm0b/sourcecpp_565778edd300/sourceCpp_27814.so)
> | ==22103== by 0x8BD6B94: arma::SpMat<double> Rcpp::internal::as<arma::SpMat<double> >(SEXPREC*, Rcpp::traits::r_type_generic_tag) (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/Rtmp8Krm0b/sourcecpp_565778edd300/sourceCpp_27814.so)
> | ==22103== by 0x8BD4B37: sourceCpp_12484_sparse (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/Rtmp8Krm0b/sourcecpp_565778edd300/sourceCpp_27814.so)
> | ==22103== by 0x86D84: do_dotcall (dotcode.c:579)
> | ==22103== by 0xAEEF3: Rf_eval (eval.c:635)
> | ==22103== by 0xB8E6D: Rf_applyClosure (eval.c:1003)
> | ==22103== by 0xAEF93: Rf_eval (eval.c:654)
> | ==22103== by 0xBB1DE: do_set (eval.c:1871)
> | ==22103== by 0xAED66: Rf_eval (eval.c:607)
> | ==22103== by 0xBB53F: do_begin (eval.c:1557)
> | ==22103==
> | ==22103== 240,000,048 bytes in 3 blocks are definitely lost in loss record 4,035 of 4,035
> | ==22103== at 0xC658: malloc (vg_replace_malloc.c:295)
> | ==22103== by 0x8BD503A: arma::SpMat<double>::init(unsigned long long, unsigned long long) (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/Rtmp8Krm0b/sourcecpp_565778edd300/sourceCpp_27814.so)
> | ==22103== by 0x8BD6690: Rcpp::traits::Exporter<arma::SpMat<double> >::get() (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/Rtmp8Krm0b/sourcecpp_565778edd300/sourceCpp_27814.so)
> | ==22103== by 0x8BD6B94: arma::SpMat<double> Rcpp::internal::as<arma::SpMat<double> >(SEXPREC*, Rcpp::traits::r_type_generic_tag) (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/Rtmp8Krm0b/sourcecpp_565778edd300/sourceCpp_27814.so)
> | ==22103== by 0x8BD4B37: sourceCpp_12484_sparse (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/Rtmp8Krm0b/sourcecpp_565778edd300/sourceCpp_27814.so)
> | ==22103== by 0x86D84: do_dotcall (dotcode.c:579)
> | ==22103== by 0xAEEF3: Rf_eval (eval.c:635)
> | ==22103== by 0xB8E6D: Rf_applyClosure (eval.c:1003)
> | ==22103== by 0xAEF93: Rf_eval (eval.c:654)
> | ==22103== by 0xBB1DE: do_set (eval.c:1871)
> | ==22103== by 0xAED66: Rf_eval (eval.c:607)
> | ==22103== by 0xBB53F: do_begin (eval.c:1557)
> | ==22103==
> | ==22103== LEAK SUMMARY:
> | ==22103== definitely lost: 240,018,516 bytes in 14 blocks
> | ==22103== indirectly lost: 0 bytes in 0 blocks
> | ==22103== possibly lost: 160,010,424 bytes in 4 blocks
> | ==22103== still reachable: 210,051,491 bytes in 52,853 blocks
> | ==22103== suppressed: 25,144 bytes in 94 blocks
> | ==22103==
> | ==22103== For counts of detected and suppressed errors, rerun with: -v
> | ==22103== ERROR SUMMARY: 8 errors from 8 contexts (suppressed: 10 from 10)
> |
> |
> |
> | testMatrix <- Matrix(data=0,nrow=1e7,ncol=1e7,sparse=TRUE)
> |
> | for(i in 1:10){
> | a <- sparse(testMatrix)
> | }
> |
> | ==22148==
> | ==22148== 320,000,064 bytes in 4 blocks are possibly lost in loss record 4,039 of 4,040
> | ==22148== at 0xC658: malloc (vg_replace_malloc.c:295)
> | ==22148== by 0x8BD503A: arma::SpMat<double>::init(unsigned long long, unsigned long long) (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/RtmpLZuqjl/sourcecpp_56846fe5a651/sourceCpp_83305.so)
> | ==22148== by 0x8BD6690: Rcpp::traits::Exporter<arma::SpMat<double> >::get() (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/RtmpLZuqjl/sourcecpp_56846fe5a651/sourceCpp_83305.so)
> | ==22148== by 0x8BD6B94: arma::SpMat<double> Rcpp::internal::as<arma::SpMat<double> >(SEXPREC*, Rcpp::traits::r_type_generic_tag) (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/RtmpLZuqjl/sourcecpp_56846fe5a651/sourceCpp_83305.so)
> | ==22148== by 0x8BD4B37: sourceCpp_93626_sparse (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/RtmpLZuqjl/sourcecpp_56846fe5a651/sourceCpp_83305.so)
> | ==22148== by 0x86D84: do_dotcall (dotcode.c:579)
> | ==22148== by 0xAEEF3: Rf_eval (eval.c:635)
> | ==22148== by 0xB8E6D: Rf_applyClosure (eval.c:1003)
> | ==22148== by 0xAEF93: Rf_eval (eval.c:654)
> | ==22148== by 0xBB1DE: do_set (eval.c:1871)
> | ==22148== by 0xAED66: Rf_eval (eval.c:607)
> | ==22148== by 0xBB53F: do_begin (eval.c:1557)
> | ==22148==
> | ==22148== 480,000,096 bytes in 6 blocks are definitely lost in loss record 4,040 of 4,040
> | ==22148== at 0xC658: malloc (vg_replace_malloc.c:295)
> | ==22148== by 0x8BD503A: arma::SpMat<double>::init(unsigned long long, unsigned long long) (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/RtmpLZuqjl/sourcecpp_56846fe5a651/sourceCpp_83305.so)
> | ==22148== by 0x8BD6690: Rcpp::traits::Exporter<arma::SpMat<double> >::get() (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/RtmpLZuqjl/sourcecpp_56846fe5a651/sourceCpp_83305.so)
> | ==22148== by 0x8BD6B94: arma::SpMat<double> Rcpp::internal::as<arma::SpMat<double> >(SEXPREC*, Rcpp::traits::r_type_generic_tag) (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/RtmpLZuqjl/sourcecpp_56846fe5a651/sourceCpp_83305.so)
> | ==22148== by 0x8BD4B37: sourceCpp_93626_sparse (in /private/var/folders/2h/s9877ww97794_0fg6vrtm54c0000gn/T/RtmpLZuqjl/sourcecpp_56846fe5a651/sourceCpp_83305.so)
> | ==22148== by 0x86D84: do_dotcall (dotcode.c:579)
> | ==22148== by 0xAEEF3: Rf_eval (eval.c:635)
> | ==22148== by 0xB8E6D: Rf_applyClosure (eval.c:1003)
> | ==22148== by 0xAEF93: Rf_eval (eval.c:654)
> | ==22148== by 0xBB1DE: do_set (eval.c:1871)
> | ==22148== by 0xAED66: Rf_eval (eval.c:607)
> | ==22148== by 0xBB53F: do_begin (eval.c:1557)
> | ==22148==
> | ==22148== LEAK SUMMARY:
> | ==22148== definitely lost: 480,041,092 bytes in 28 blocks
> | ==22148== indirectly lost: 0 bytes in 0 blocks
> | ==22148== possibly lost: 320,008,408 bytes in 5 blocks
> | ==22148== still reachable: 217,092,931 bytes in 52,888 blocks
> | ==22148== suppressed: 25,144 bytes in 94 blocks
> | ==22148==
> | ==22148== For counts of detected and suppressed errors, rerun with: -v
> | ==22148== ERROR SUMMARY: 7 errors from 7 contexts (suppressed: 10 from 10)
> |
> |
> |
> |
> |
> | On 18 Nov, 2013, at 15:59 , Alessandro Vitale wrote:
> |
> | > Thanks Dirk and Hadley.
> | >
> | > Dirk, asap I will try your b) and c) suggestions. While for suggestion a), I didn't really understand how to implement it.
> | >
> | > Hadley, I am determining rsession process memory looking at osx activity monitor utility, under Real Mem column.
> | > This is what I get (I am using your own mem() function to determine r memory usage)
> | >
> | > testMatrix <- Matrix(data=0,nrow=1e7,ncol=1e7,sparse=TRUE)
> | > gc()
> | > mem() # [1] 123.3, rsession Real Mem 203.1 MB
> | > sparse(testMatrix)
> | > mem() # [1] 161.5
> | > gc()
> | > mem() # [1] 123.4, rsession Real Mem 507.8 MB
> | > sparse(testMatrix)
> | > mem() # [1] 161.5
> | > gc()
> | > mem() # [1] 123.4, rsession Real Mem 585.0 MB
> | > sparse(testMatrix)
> | > mem() # [1] 161.5
> | > gc()
> | > mem() # [1] 123.4, rsession Real Mem 661.3 MB
> | >
> | > and so on.
> | >
> | > If I call the function too many times (in fact I discovered it while using benchmark() ), it fills up the memory and the computer gets totally unresponsive.
> | >
> | >
> | >
> | >
> | >
> | > On 18 Nov, 2013, at 15:24 , Hadley Wickham wrote:
> | >
> | >>> After every call, the memory from gc() is stable, while rsession process
> | >>> memory keeps growing of around 100Mb at each call and doesn't decrease after
> | >>> the garbage collection.
> | >>
> | >> You don't mention how you're determining the size of the rsession
> | >> process, but you shouldn't necessarily expect it to decrease after
> | >> calling gc() - there may be memory fragmentation, but also the OS is
> | >> lazy about reclaiming memory from processes, so it may only be
> | >> returned to the OS when it actually needs it.
> | >>
> | >> Hadley
> | >>
> | >> --
> | >> Chief Scientist, RStudio
> | >> http://had.co.nz/
> | >
> |
> | _______________________________________________
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>
> --
> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
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