[Rcpp-devel] Rstudio crashes with repeated calls to sourceCpp with Xptr export

Helske, Jouni jouni.helske at jyu.fi
Tue Sep 5 12:12:57 CEST 2017 

It looks like the issue has something to do with the cache from the previous sourceCpp calls: If inside of the segfaulting loop (with index i) I set Rcpp::sourceCpp("sde_functions1.cpp", rebuild = TRUE, cacheDir = paste0("dir", i)) everything works fine. Note that by just using cleanupCacheDir = TRUE does not help, which I though would do essentially the same thing.


Best,

Jouni



________________________________
Lähettäjä: rcpp-devel-bounces at r-forge.wu-wien.ac.at <rcpp-devel-bounces at r-forge.wu-wien.ac.at> käyttäjän Helske, Jouni <jouni.helske at jyu.fi> puolesta
Lähetetty: tiistai 5. syyskuuta 2017 12.32.05
Vastaanottaja: Dirk Eddelbuettel
Kopio: Rcpp-devel at lists.r-forge.r-project.org
Aihe: Re: [Rcpp-devel] Rstudio crashes with repeated calls to sourceCpp with Xptr export


Oops, forgot the link to the repo: https://github.com/helske/crashtest/issues/1


Best,

Jouni

________________________________
Lähettäjä: Helske, Jouni
Lähetetty: tiistai 5. syyskuuta 2017 12.31.15
Vastaanottaja: Dirk Eddelbuettel
Kopio: Rcpp-devel at lists.r-forge.r-project.org
Aihe: VS: [Rcpp-devel] Rstudio crashes with repeated calls to sourceCpp with Xptr export



I was finally able to get reproducible, although likely not minimal segfault even without Rstudio.  I built a new package and running a weird loop with rebuilding of the source files and doing some other random stuff as well, I was able to get a segfault. valgrind output looks like this:

==26398== Jump to the invalid address stated on the next line
==26398==    at 0x1DD75010: ???
==26398==    by 0x4F7D026: R_RunWeakRefFinalizer (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F7D213: ??? (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F4A679: Rf_eval (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F4EA11: ??? (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F4AB99: Rf_eval (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F4D723: ??? (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F4AA9F: Rf_eval (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F4CABE: ??? (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F42F67: ??? (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F50D55: ??? (in /usr/lib/R/lib/libR.so)
==26398==    by 0x4F512FF: ??? (in /usr/lib/R/lib/libR.so)
==26398==  Address 0x1dd75010 is not stack'd, malloc'd or (recently) free'd
==26398==

 *** caught segfault ***
address 0x1dd75010, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
==26398==
==26398== Process terminating with default action of signal 11 (SIGSEGV)
==26398==    at 0x547451D: raise (raise.c:53)
==26398==    by 0x547466F: ??? (in /lib/x86_64-linux-gnu/libpthread-2.24.so)
==26398==    by 0x1DD7500F: ???
==26398==
==26398== HEAP SUMMARY:
==26398==     in use at exit: 259,162,338 bytes in 28,465 blocks
==26398==   total heap usage: 315,728 allocs, 287,263 frees, 1,311,929,706 bytes allocated
==26398==
==26398== LEAK SUMMARY:
==26398==    definitely lost: 0 bytes in 0 blocks
==26398==    indirectly lost: 0 bytes in 0 blocks
==26398==      possibly lost: 0 bytes in 0 blocks
==26398==    still reachable: 259,162,338 bytes in 28,465 blocks
==26398==                       of which reachable via heuristic:
==26398==                         newarray           : 4,264 bytes in 1 blocks
==26398==         suppressed: 0 bytes in 0 blocks
==26398== Reachable blocks (those to which a pointer was found) are not shown.
==26398== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==26398==
==26398== For counts of detected and suppressed errors, rerun with: -v
==26398== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)
Segmentation fault (core dumped)


What is super weird is that currently I have this extra C++ function which is not even used at all:

double log_prior_pdf(const arma::vec& theta) {

  double log_pdf = 0.0;
  double infinite = -arma::datum::inf; //comment out this line and everything works??
  return log_pdf;
}

If I remove the middle line, I seem to get rid of the segfault. However, I also have some extra stuff on the R script (crash.R) as well which looks to be necessary for the segfault to trigger at certain point (third iteration of the outer loop).



Jouni

________________________________
Lähettäjä: Dirk Eddelbuettel <dirk.eddelbuettel at gmail.com> käyttäjän Dirk Eddelbuettel <edd at debian.org> puolesta
Lähetetty: maanantai 4. syyskuuta 2017 15.32.13
Vastaanottaja: Helske, Jouni
Kopio: Rcpp-devel at lists.r-forge.r-project.org
Aihe: Re: [Rcpp-devel] Rstudio crashes with repeated calls to sourceCpp with Xptr export


Hi Jouni,

On 4 September 2017 at 08:22, Helske, Jouni wrote:
| In the bssm package (https://github.com/helske/bssm), I let the users
| define a state space model via own C++ functions which are then exported as
| Xptr to R side, and passed back to C++ function for SMC/MCMC etc. Normally
| this works fine, but when user repeatedly modifies the model functions and
| re-exports them via repeated calls sourceCpp, sometimes whole Rstudio
| crashes.

Which version of RStudio?  See Help -> About

| I haven't been able to pinpoint the reason or minimal example. Have anyone else experienced similar issues or is it just me i.e. error in my own implementations?

There are a lot of dependencies here [re-indented by me]:

  Suggests: KFAS (>= 1.2.1), knitr (>= 1.11), rmarkdown (>= 0.8.1), testthat,
     bayesplot
  Imports: coda (>= 0.18-1), diagis, ggplot2 (>= 2.0.0), Rcpp (>= 0.12.3)
  LinkingTo: BH, Rcpp, RcppArmadillo, ramcmc, sitmo

We do know Boost interactions (between code compiled 'by us' as R extensions
using Boost, and RStudio itself also using an older version of Boost) had
thrown spanners in the past. A while back Kevin updated RStudio internals and
shielded "their" Boost better.

I happen to run RStudio "Daily" builds on all my machines -- those have the
fix and "behave". Maybe worth a try for you.

| Simplest case of this is the discretized SDE models, this is the function
| which user modifies:
| https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp,
[https://avatars2.githubusercontent.com/u/1560448?v=4&s=400]<https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp>

bssm/sde_functions.cpp at master · helske/bssm · GitHub<https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp>
github.com
bssm - Bayesian Inference of State Space Models


| <https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp>
[https://avatars2.githubusercontent.com/u/1560448?v=4&s=400]<https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp>

bssm/sde_functions.cpp at master · helske/bssm · GitHub<https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp>
github.com
bssm - Bayesian Inference of State Space Models


| and the relevant parts of the package codes are in src/function_pointers.h,
| src/sde_ssm.cpp and src/R_sde.cpp (I don't really expect anyone to read
| through all of these).

We'd probably need a reproducible example to really help.

Dirk

--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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