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?
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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