I just updated my mac OS to Ventura, and I’m having issues running cmdstan. I updated XTools and reinstalled cmdstan from GitHub. But I’m not able to build the library. Here is the error message.
MacBook-Pro-257:cmdstan charlesm$ make build
curl -L https://github.com/stan-dev/stanc3/releases/download/nightly/mac-stanc -o bin/stanc --retry 5 --retry-delay 10
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 10.8M 100 10.8M 0 0 4923k 0 0:00:02 0:00:02 --:--:-- 9410k
chmod +x bin/stanc
--- Compiling the main object file. This might take up to a minute. ---
clang++ -c -o src/cmdstan/main.o src/cmdstan/main.cpp
src/cmdstan/main.cpp:1:10: fatal error: 'cmdstan/command.hpp' file not found
#include <cmdstan/command.hpp>
^~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [src/cmdstan/main.o] Error 1
And I get the same error message when I try to transpile the original Bernoulli example.
The missing file does exist under source/cmsdtan/command.hpp, so I’m not sure what’s causing the error.
I’m using Xcode version 14.3 and xcode-select version 2397. Here are the versions of the compilers:
make --version
GNU Make 3.81
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
This program built for i386-apple-darwin11.3.0
MacBook-Pro-257:cmdstan charlesm$ clang++ --version
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
Target: x86_64-apple-darwin22.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
MacBook-Pro-257:cmdstan charlesm$ g++ --version
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
Target: x86_64-apple-darwin22.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
Any guidance as to what might be going wrong is greatly appreciated.
Upgrade for the Mac OS, clean install for cmdstan.
I downloaded the released version. Running make build works (although it generates a lot of warning messages). On the other hand, make examples/bernoulli/bernoulli returns an error.
MacBook-Pro-257:cmdstan-2.31.0 charlesm$ make examples/bernoulli/bernoulli
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2020.3/include -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.9 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DBOOST_DISABLE_ASSERTS -c -MT stan/src/stan/model/model_header.hpp.gch -MT stan/src/stan/model/model_header.d -MM -E -MG -MP -MF stan/src/stan/model/model_header.d stan/src/stan/model/model_header.hpp
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2020.3/include -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.9 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DBOOST_DISABLE_ASSERTS -c -MT src/cmdstan/main.o -MM -E -MG -MP -MF src/cmdstan/main.d src/cmdstan/main.cpp
--- Translating Stan model to C++ code ---
bin/stanc --o=examples/bernoulli/bernoulli.hpp examples/bernoulli/bernoulli.stan
--- Compiling, linking C++ code ---
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2020.3/include -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.9 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DBOOST_DISABLE_ASSERTS -c -include-pch stan/src/stan/model/model_header.hpp.gch -x c++ -o examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.hpp
examples/bernoulli/bernoulli.hpp:15:7: warning: abstract class is marked 'final' [-Wabstract-final-class]
class bernoulli_model final : public model_base_crtp<bernoulli_model> {
^
/Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/src/stan/model/model_base.hpp:75:16: note: unimplemented pure virtual method 'get_param_names' in 'bernoulli_model'
virtual void get_param_names(std::vector<std::string>& names) const = 0;
^
/Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/src/stan/model/model_base.hpp:94:16: note: unimplemented pure virtual method 'get_dims' in 'bernoulli_model'
virtual void get_dims(std::vector<std::vector<size_t> >& dimss) const = 0;
^
examples/bernoulli/bernoulli.hpp:302:23: error: allocating an object of abstract class type 'stan_model' (aka 'bernoulli_model_namespace::bernoulli_model')
stan_model* m = new stan_model(data_context, seed, msg_stream);
^
In file included from examples/bernoulli/bernoulli.hpp:1:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/stan/math/rev.hpp:10:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/stan/math/rev/fun.hpp:198:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/stan/math/prim/functor.hpp:14:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
In file included from /Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
/Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: 'unary_function<const std::error_category *, unsigned long>' is deprecated [-Wdeprecated-declarations]
struct hash_base : std::unary_function<T, std::size_t> {};
^
/Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:692:18: note: in instantiation of template class 'boost::hash_detail::hash_base<const std::error_category *>' requested here
: public boost::hash_detail::hash_base<T*>
^
/Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:420:24: note: in instantiation of template class 'boost::hash<const std::error_category *>' requested here
boost::hash<T> hasher;
^
/Users/charlesm/Desktop/Teaching/cmdstan-2.31.0/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:551:9: note: in instantiation of function template specialization 'boost::hash_combine<const std::error_category *>' requested here
hash_combine(seed, &v.category());
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<const std::error_category *, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
2 warnings and 1 error generated.
make: *** [examples/bernoulli/bernoulli] Error 1
If it helps, I can post the output of make build (very long).
Ah, it looks like I was using a nightly version. I downloaded cmdstan-2.31.0-linux-arm64.tar.gz (since it was the tar at the top) got the nightly version. Downloading cmdstan-2.31.0.tar.gz gives me the released version. I’m able to build Stan and transpile Bernoulli. (still with warning messages).
think this might be a case of cloning just cmdstan and not cloning recursively.
@rok_cesnovar what would I need to do to clone recursively, and moreover why does installing via git clone not work? (@yizhang this could be an issue for installing Torsten).
It only clones the cmdstan files & headers, not the Stan and Math files - because those are git submodules that need to be initialised first. This can be done automatically by adding the --recursive flag, which will initialise and clone all submodules:
Note also that the arch-specific release (e.g., -arm64, -s90x, etc.) are targeted for linux distributions.
Mac users can download the ‘normal’ release (i.e., no arch suffix), since the mac stanc is compiled for x86_64, but run through rosetta on Apple Silicon.
I ran into the above problem as well, I am running on M2 and figured I’d better just compile from source.
Works fine once the recursive git clone is done.
However, I am getting a ton of deprecation warnings from boost, setup is:
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
Target: arm64-apple-darwin22.3.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
% make --version
GNU Make 3.81
I assume we are stuck with this due to boost not being sorted out.
However testing the install generates a bunch of text with a warning again from boost:
cmdstan % make examples/bernoulli/bernoulli
--- Translating Stan model to C++ code ---
bin/stanc --o=examples/bernoulli/bernoulli.hpp examples/bernoulli/bernoulli.stan
--- Compiling, linking C++ code ---
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2020.3/include -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DBOOST_DISABLE_ASSERTS -c -include-pch stan/src/stan/model/model_header.hpp.gch -x c++ -o examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.hpp
In file included from examples/bernoulli/bernoulli.hpp:1:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/src/stan/model/model_header.hpp:4:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:10:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/stan/math/rev/fun.hpp:198:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/stan/math/prim/functor.hpp:15:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
In file included from /Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
/Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: 'unary_function<const std::error_category *, unsigned long>' is deprecated [-Wdeprecated-declarations]
struct hash_base : std::unary_function<T, std::size_t> {};
^
/Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:692:18: note: in instantiation of template class 'boost::hash_detail::hash_base<const std::error_category *>' requested here
: public boost::hash_detail::hash_base<T*>
^
/Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:420:24: note: in instantiation of template class 'boost::hash<const std::error_category *>' requested here
boost::hash<T> hasher;
^
/Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:551:9: note: in instantiation of function template specialization 'boost::hash_combine<const std::error_category *>' requested here
hash_combine(seed, &v.category());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<const std::error_category *, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
1 warning generated.
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes -I stan/lib/stan_math/lib/tbb_2020.3/include -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DBOOST_DISABLE_ASSERTS -Wl,-L,"/Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/tbb" examples/bernoulli/bernoulli.o src/cmdstan/main.o -Wl,-L,"/Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Users/fbaldw522/Downloads/cmdstan/stan/lib/stan_math/lib/tbb" stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a stan/lib/stan_math/lib/tbb/libtbb.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc_proxy.dylib -o examples/bernoulli/bernoulli
rm -f examples/bernoulli/bernoulli.o
I assume that nothing can be done about this since we don’t run boost but thought I’d check.
Mac users can download the ‘normal’ release (i.e., no arch suffix), since the mac stanc is compiled for x86_64, but run through rosetta on Apple Silicon.
Are there any plans for an Apple silicon version? (I understand the actual models are native, which I know is more important. )
We haven’t yet seen the need for an Apple silicon-specific build of stanc. I believe it would be possible, since OCaml now supports native builds on that platform and we have a CI machine which is Apple silicon based, but at the moment it doesn’t seem like there’s a particular advantage.
Our current build pipeline for stanc builds a mac binary which can be used all the way back on MacOS 10.11 El Capitan