Cmdstan installation fails on linux - issue with tbb?

Unlearned5341 · April 19, 2023, 4:50pm

I wish my first post would not be about an installation issue… but here I am! Yesterday, I upgraded my linux system from Fedora 37 to Fedora 38 and noticed I could not compile Stan models with cmdstanr anymore. I have tried to reinstall cmdstan multiple ways (through cmdstanr in R, or using make on github downloads of v2.31.0 and v2.32.0-rc1) but it keeps failing. According to cmdstanr::check_cmdstan_toolchain(), my C++ toolchain is setup properly. The problem seems to be related with “tbb”.

example of error message with cmdstanr::install_cmdstan():

../tbb_2020.3/include/tbb/task.h:300:20: error: declaration of ‘tbb::task& tbb::internal::task_prefix::task()’ changes meaning of ‘task’ [-Wchanges-meaning]

and the installation stops with:

make[1]: *** [../tbb_2020.3/build/common_rules.inc:80: pipeline.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/home/username/.cmdstan/cmdstan-2.31.0/stan/lib/stan_math/lib/tbb'
make: *** [stan/lib/stan_math/make/libraries:169: stan/lib/stan_math/lib/tbb/tbb.def] Error 2
make: *** Waiting for unfinished jobs....
make: *** [make/command:5: bin/cmdstan/print.o] Error 1
make: *** [make/command:5: bin/cmdstan/stansummary.o] Error 1
make: *** [make/command:5: bin/cmdstan/diagnose.o] Error 1
make: *** [make/program:14: src/cmdstan/main.o] Error 1
make: *** [make/program:27: stan/src/stan/model/model_header.hpp.gch] Error 1

example of error message using make on v2.32.0-rc1:

stan/lib/stan_math/lib/tbb_2020.3/include/tbb/task.h:300:20: error: declaration of ‘tbb::task& tbb::internal::task_prefix::task()’ changes meaning of ‘task’ [-Wchanges-meaning]

Any hint of what could be wrong on my side?

WardBrian · April 19, 2023, 5:33pm

Fedora 38 seems to have updated to GCC 13, which is the source of this error. TBB themselves fixed it here:

github.com/oneapi-src/oneTBB

tbb_2020: fix build on gcc-13

oneapi-src:tbb_2020 ← trofi:tbb_2020-fix-for-gcc-13

opened 06:51AM - 20 May 22 UTC

trofi

+1 -1

On gcc-13 build started failing due to 'task' identifier collision as: ..…/../include/tbb/task.h:300:20: error: declaration of 'tbb::task& tbb::internal::task_prefix::task()' changes meaning of 'task' [-fpermissive] 300 | tbb::task& task() {return *reinterpret_cast<tbb::task*>(this+1);} | ^~~~ ../../include/tbb/task.h:252:9: note: used here to mean 'class tbb::task' 252 | task* next_offloaded; | ^~~~ ../../include/tbb/task.h:43:7: note: declared here 43 | class task; | ^~~~ The change adds explicit qualifier to class name to avoid ambiguity with method name. ### Description _Add a comprehensive description of proposed changes_ Fixes # - _issue number(s) if exists_ - [x] - git commit message contains an appropriate signed-off-by string _(see [CONTRIBUTING.md](https://github.com/oneapi-src/oneTBB/blob/master/CONTRIBUTING.md#pull-requests) for details)_ ### Type of change _Choose one or multiple, leave empty if none of the other choices apply_ _Add a respective label(s) to PR if you have permissions_ - [x] bug fix - _change that fixes an issue_ - [ ] new feature - _change that adds functionality_ - [ ] tests - _change in tests_ - [ ] infrastructure - _change in infrastructure and CI_ - [ ] documentation - _documentation update_ ### Tests - [ ] added - _required for new features and some bug fixes_ - [x] not needed ### Documentation - [ ] updated in # - _add PR number_ - [ ] needs to be updated - [x] not needed ### Breaks backward compatibility - [ ] Yes - [x] No - [ ] Unknown ### Notify the following users _List users with `@` to send notifications_ ### Other information

The fix was to change this line:

github.com

stan-dev/math/blob/6cd15b88d16dbace9ee4ce9d27997901159c44e7/lib/tbb_2020.3/include/tbb/task.h#L252


      
                  union {
          #endif /* __TBB_TASK_PRIORITY */
                  //! Obsolete. The scheduler that owns the task.
                  /** Retained only for the sake of backward binary compatibility.
                      Still used by inline methods in the task.h header. **/
                  scheduler* owner;
          
          
#if __TBB_TASK_PRIORITY
                  //! Pointer to the next offloaded lower priority task.
                  /** Used to maintain a list of offloaded tasks inside the scheduler. **/
                  task* next_offloaded;
          #endif
          
          
#if __TBB_PREVIEW_RESUMABLE_TASKS
                  //! Pointer to the abandoned scheduler where the current task is waited for.
                  scheduler* abandoned_scheduler;
          #endif
          #if __TBB_TASK_PRIORITY || __TBB_PREVIEW_RESUMABLE_TASKS
                  };
          #endif /* __TBB_TASK_PRIORITY || __TBB_PREVIEW_RESUMABLE_TASKS */

to tbb::task* next_offloaded;

We should consider either applying this patch ourselves in the math library or updating our vendored copy of TBB. (pinging @andrjohns @rok_cesnovar @wds15 - how would we like to handle this?)

For now, if it’s acceptable to you, making this change to your downloaded copy should allow the build to succeed @Unlearned5341

Unlearned5341 · April 19, 2023, 6:02pm

Awesome, it works. Thank you @WardBrian

WardBrian · April 19, 2023, 8:31pm

Thank you for reporting! We should have this patched in the actual 2.32 release

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Cmdstan installation fails on linux - issue with tbb?

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