[R-pkg-devel] Segmentation Fault cause 'memory not mapped' on Debian only

D Z d@v|d_j_z|mmerm@nn @end|ng |rom hotm@||@com
Sat Apr 22 16:43:50 CEST 2023 

Thank you Dirk and Joshua,
Using Valgrind, I have found several memory leaks in the program that required some smaller rewrites.
Valgrind (with Makevars flags -O0 and --ggdb) now reports no "definitely" and no "indirectly" lost bytes so that's a small win already.

But two questions remain:

  1.  I have 960 bytes "possibly lost", where the callstack does not touch any of my code but seems to originate from subset.c (base R?) and libgomp, is this ok/expected, or am I misreading the output?
  2.  For all tests that I ran, there are still 105mln bytes still reachable. I read online that this can be problematic, but usually isn't. Is this something that I should invest more time in or can I ignore this?

Thank you very much!
David


To reproduce the valgrind output using bash (this is using the latest code commit https://github.com/DavZim/RITCH/commit/13ea3f478717edf24f8db709f0cac1e22b501afc)

echo "PKG_CXXFLAGS=-O0 -ggdb\nPKG_LIBS=-O0 -ggdb -lz" >> src/Makevars.win
echo "PKG_CXXFLAGS=-O0 -ggdb\nPKG_LIBS=-O0 -ggdb -lz" >> src/Makevars

R CMD build .
R CMD INSTALL RITCH_0.1.15.tar.gz

R -d "valgrind --tool=memcheck --leak-check=full" -e "tinytest::test_package('RITCH')"
# omitted for brevity...
tinytest::test_package('RITCH')
test_filename_helpers.R.......   13 tests OK 1.1s
test_filter_itch.R............   60 tests OK 30.1s
test_gz_functions.R...........    5 tests OK 6.0s
test_read_functions.R.........  122 tests OK 14.1s
test_write_itch.R.............   18 tests OK 33.0s
All ok, 218 results (1m 24.5s)
>
==1535==
==1535== HEAP SUMMARY:
==1535==     in use at exit: 105,616,149 bytes in 18,292 blocks
==1535==   total heap usage: 562,268 allocs, 543,976 frees, 6,834,040,088 bytes allocated
==1535==
==1535== 960 bytes in 3 blocks are possibly lost in loss record 199 of 2,000
==1535==    at 0x483DD99: calloc (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==1535==    by 0x40149DA: allocate_dtv (dl-tls.c:286)
==1535==    by 0x40149DA: _dl_allocate_tls (dl-tls.c:532)
==1535==    by 0x5741322: allocate_stack (allocatestack.c:622)
==1535==    by 0x5741322: pthread_create@@GLIBC_2.2.5 (pthread_create.c:660)
==1535==    by 0x5710DEA: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==1535==    by 0x57088E0: GOMP_parallel (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==1535==    by 0x10882EB9: subsetVectorRaw (subset.c:54)
==1535==    by 0x10883B50: subsetDT (subset.c:309)
==1535==    by 0x494253D: ??? (in /usr/lib/R/lib/libR.so)
==1535==    by 0x49861A6: ??? (in /usr/lib/R/lib/libR.so)
==1535==    by 0x4999D77: Rf_eval (in /usr/lib/R/lib/libR.so)
==1535==    by 0x499BC2E: ??? (in /usr/lib/R/lib/libR.so)
==1535==    by 0x499CB21: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==1535==
==1535== LEAK SUMMARY:
==1535==    definitely lost: 0 bytes in 0 blocks
==1535==    indirectly lost: 0 bytes in 0 blocks
==1535==      possibly lost: 960 bytes in 3 blocks
==1535==    still reachable: 105,615,189 bytes in 18,289 blocks
==1535==                       of which reachable via heuristic:
==1535==                         newarray           : 4,264 bytes in 1 blocks
==1535==         suppressed: 0 bytes in 0 blocks
==1535== Reachable blocks (those to which a pointer was found) are not shown.
==1535== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==1535==
==1535== For lists of detected and suppressed errors, rerun with: -s
==1535== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)

________________________________
From: Joshua Ulrich <josh.m.ulrich using gmail.com>
Sent: Friday, April 21, 2023 7:48 PM
To: Dirk Eddelbuettel <edd using debian.org>
Cc: D Z <david_j_zimmermann using hotmail.com>; r-package-devel using r-project.org <R-package-devel using r-project.org>
Subject: Re: [R-pkg-devel] Segmentation Fault cause 'memory not mapped' on Debian only

Hi David,

In addition to running under valgrind as Dirk suggests below, you
should also run under UBSAN and ASAN.

You can do all 3 (and more) using Winston Cheng's docker images:
https://github.com/wch/r-debug/

That should help you narrow down the problematic code.

Best,
Josh


On Fri, Apr 21, 2023 at 2:33 PM Dirk Eddelbuettel <edd using debian.org> wrote:
>
>
> Hi David,
>
> On 21 April 2023 at 19:17, D Z wrote:
> | Hi all,
> | I wanted to publish my RITCH package (https://github.com/DavZim/RITCH) to CRAN, which has Rcpp code.
>
> That would be great!
>
> | It has, in it’s CICD Pipeline, Tests for Macos, Windows, and Ubuntu (devel, release,, and oldrel-1), which all succeed on Github Actions.
> | When I submitted the package to CRAN, I was notified, that I got the following error on Debian (the tests on Windows throw no such bug, neither do the Github Actions tests):
> |
> |
> |    *** caught segfault ***
> |
> |   address 0x55939b7ca000, cause 'memory not mapped'
> |
> |   Segmentation fault
> |
> | The full Report is currently available here: https://win-builder.r-project.org/incoming_pretest/RITCH_0.1.14_20230420_223157/Debian/00check.log (note the error happens in the test_filter_itch.R unit tests).
> |
> | I looked for the error online but couldn’t find anything useful, and as I am not able to reproduce the segfault locally, cannot debug it.
> | Do you have any ideas or hunches what might cause this and how to resolve it?
>
> "Absence of error" on one platform does proove correctness on all, the hint
> from the segfault should be taken seriously.  I just updated my older
> checkout of your repo, built a current tarball and simply invoked
>
>    R CMD check --use-valgrind RITCH_0.1.14.tar.gz
>
> which you could do on CI too (I can help as needed, I would also pull the CI
> runners forward from Ubuntu 20.04 to 22.04). When we do the above, the
> examples output file RITCH-Ex.Rout ends in
>
>   ==2269271== LEAK SUMMARY:
>   ==2269271==    definitely lost: 1,363,969 bytes in 5,473 blocks
>   ==2269271==    indirectly lost: 177,235 bytes in 1,281 blocks
>   ==2269271==      possibly lost: 101,924,267 bytes in 148 blocks
>   ==2269271==    still reachable: 89,572,890 bytes in 17,950 blocks
>   ==2269271==         suppressed: 0 bytes in 0 blocks
>   ==2269271== Reachable blocks (those to which a pointer was found) are not shown.
>   ==2269271== To see them, rerun with: --leak-check=full --show-leak-kinds=all
>   ==2269271==
>   ==2269271== ERROR SUMMARY: 30 errors from 30 contexts (suppressed: 0 from 0)
>
> and the tests end in
>
>   ==2273761== LEAK SUMMARY:
>   ==2273761==    definitely lost: 5,223,981 bytes in 141,151 blocks
>   ==2273761==    indirectly lost: 2,241,700 bytes in 2,767 blocks
>   ==2273761==      possibly lost: 1,201,493,644 bytes in 270 blocks
>   ==2273761==    still reachable: 133,909,136 bytes in 19,110 blocks
>   ==2273761==         suppressed: 0 bytes in 0 blocks
>   ==2273761== Reachable blocks (those to which a pointer was found) are not shown.
>   ==2273761== To see them, rerun with: --leak-check=full --show-leak-kinds=all
>   ==2273761==
>   ==2273761== ERROR SUMMARY: 43 errors from 39 contexts (suppressed: 0 from 0)
>
> That probably warrants a few more close looks.
>
> Hth, Dirk
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel



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