Bug#1012219: Please adjust StanHeaders to new version of (one)tbb
Hi all, On 9/3/22 22:06, Benjamin K Goodrich wrote: Sorry for the late reply. I am told that StanHeaders can be built successfully with oneTBB by setting environmental variables like TBB_INC and TBB_LIB. On CRAN, we would like to use the version of TBB that comes with the RcppParallel package [...] Thanks for the pointers, but we are able to build cppparallel and stanheaders without problems as is. But the built package is unusable as it uses "#include" statements that try to include files available in older tbb but not in new onetbb, as observed in rstan compilation. The problematic #include statment (and corresponding removed APIs) seems to be stemming from "inst/include/stan/math/prim/core/init_threadpool_tbb.hpp" On taking a deeper look, I observed that this is directly embedded from stan/math[1] The current release of stanheaders contains an older copy of the math lib. Going fwd, a patch had been added to stan/math to make it compatible with onetbb[2] On cherry-picking a couple of changes from there, I am able to get rstan to compile. I am not very sure if everything is good/works as expected (autopkgtests / CRAN tests seem to pass, so that's a good indication), but I'd be thrilled to believe so. [1]: https://github.com/stan-dev/math [2]: https://github.com/stan-dev/math/commit/6f94b2a70d11276a53e5b5bc4100d3ffa524b96c -- Best, Nilesh OpenPGP_signature Description: OpenPGP digital signature
Bug#1012219: Please adjust StanHeaders to new version of (one)tbb
Sorry for the late reply. I am told that StanHeaders can be built successfully with oneTBB by setting environmental variables like TBB_INC and TBB_LIB. On CRAN, we would like to use the version of TBB that comes with the RcppParallel package https://github.com/RcppCore/RcppParallel/pull/144 Although with the next release of StanHeaders we will not be able to achieve that because not all packages are LinkingTo RcppParallel so we have to build a similar TBB in the StanHeaders shared object. But on Debian, if r-cran-rcppparallel switches to oneTBB, then it would be fine if r-cran-stanheaders, r-cran-rstan, etc. depends on r-cran-rcppparallel.
Bug#1012219: Please adjust StanHeaders to new version of (one)tbb
Ping? Is there any place where I can open an issue about this? I've found https://github.com/cran/StanHeaders but this is readonly and has no option to report issues. Kind regards Andreas. Am Mon, Jul 18, 2022 at 10:45:14AM +0200 schrieb Andreas Tille: > Control: tags -1 upstream > Control: forwarded -1 Ben Goodrich > > Hi Ben, > > Debian is migrating from old tbb to onetbb (currently version 2021.5.0). When > trying to build rstan version 2.21.5 which includes StanHeaders we get the > error > you can find here in our CI: > >https://salsa.debian.org/r-pkg-team/r-cran-rstan/-/jobs/3011219 > > In file included from > /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/core.hpp:4, > from > /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:6, > from > /usr/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12, > from ./stan/model/log_prob_grad.hpp:4, > from ./stan/model/test_gradients.hpp:7, > from ./stan/services/diagnose/diagnose.hpp:10, > from stan_fit.cpp:33: > /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:9:10: > fatal error: tbb/task_scheduler_init.h: No such file or directory > 9 | #include > | ^~~ > compilation terminated. > > It seems StanHeaders need to be adapted to onetbb. > > There is a tbb -> onetbb transition guide: > https://oneapi-src.github.io/oneTBB/main/tbb_userguide/Migration_Guide.html > > Hope this helps > > Andreas. > > -- > http://fam-tille.de > > -- http://fam-tille.de
Bug#1012219: Please adjust StanHeaders to new version of (one)tbb
Control: tags -1 upstream Control: forwarded -1 Ben Goodrich Hi Ben, Debian is migrating from old tbb to onetbb (currently version 2021.5.0). When trying to build rstan version 2.21.5 which includes StanHeaders we get the error you can find here in our CI: https://salsa.debian.org/r-pkg-team/r-cran-rstan/-/jobs/3011219 In file included from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/core.hpp:4, from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat.hpp:6, from /usr/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:12, from ./stan/model/log_prob_grad.hpp:4, from ./stan/model/test_gradients.hpp:7, from ./stan/services/diagnose/diagnose.hpp:10, from stan_fit.cpp:33: /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:9:10: fatal error: tbb/task_scheduler_init.h: No such file or directory 9 | #include | ^~~ compilation terminated. It seems StanHeaders need to be adapted to onetbb. There is a tbb -> onetbb transition guide: https://oneapi-src.github.io/oneTBB/main/tbb_userguide/Migration_Guide.html Hope this helps Andreas. -- http://fam-tille.de
