Building CmdStan on Debian Bullseye
I encountered the following trace when building CmdStan on a Debian server:
make: Entering directory '/tmp/cmdstan-2.30.1/stan/lib/stan_math/lib/tbb' g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I../tbb_2020.3/src/tbbmalloc -I../tbb_2020.3/src/tbbmalloc ../tbb_2020.3/src/tbbmalloc/backend.cpp In file included from ../tbb_2020.3/include/tbb/tbb_config.h:36, from ../tbb_2020.3/include/tbb/tbb_stddef.h:91, from ../tbb_2020.3/src/tbbmalloc/Customize.h:21, from ../tbb_2020.3/src/tbbmalloc/TypeDefinitions.h:54, from ../tbb_2020.3/src/tbbmalloc/tbbmalloc_internal.h:21, from ../tbb_2020.3/src/tbbmalloc/backend.cpp:19: /usr/include/c++/10/cstddef:49:10: fatal error: bits/c++config.h: No such file or directory 49 | #include <bits/c++config.h> | ^~~~~~~~~~~~~~~~~~ compilation terminated. make: *** [/tmp/cmdstan-2.30.1/stan/lib/stan_math/lib/tbb_2020.3/build/Makefile.tbbmalloc:65: backend.o] Error 1 make: Leaving directory '/tmp/cmdstan-2.30.1/stan/lib/stan_math/lib/tbb' make: *** [stan/lib/stan_math/make/libraries:173: stan/lib/stan_math/lib/tbb/tbbmalloc.def] Error 2 make: *** Waiting for unfinished jobs....
I won’t bother you with how I figured out the solution, and instead just give it to you:
- Download the 2.30.1 release of CmdStan
- Download the
debiantarballs from Debian’s package site
tbb_2020.3-1.debian.tar.xz, keeping note of where the extracted
tbb_2020.3.orig.tar.xz(obtained above) and
cdinto the extracted
- Apply the following patches with this command (same order I did):
patch -p1 < /PATH/TO/PATCH.patch:
- Rename the existing
- Symlink your patched
oneTBB-2020.3directory to replace the above:
ln -s /PATH/TO/oneTBB-2020.3 /PATH/TO/cmdstan-2.30.1/stan/lib/stan_math/lib/tbb_2020.3
makethe project. I had to do this from here, rather than allow CmdStan’s build system handle it
- If you’ve successfully built TBB, go back to the root
make build, which should work fine this time around.
My selection of patches is pretty arbitrary and I do not claim that is it precisely correct; I’m just a superstitious pigeon trying to make food appear here, sharing the dance that made that happen.
I posted this solution to Stan’s discourse forum, but it was immediately flagged as spam by the community there. Nice folks!