cmdstan fails to build #770

idontgetoutmuch · 2019-11-21T15:26:53Z

Summary:

clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -I stan/lib/stan_math/lib/tbb_2019_U8/include -O3 -I src -I stan/src -I lib/rapidjson_1.1.0/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.3 -I stan/lib/stan_math/lib/boost_1.69.0 -I stan/lib/stan_math/lib/sundials_4.1.0/include -DBOOST_DISABLE_ASSERTS -c -o bin/cmdstan/stansummary.o src/cmdstan/stansummary.cpp
In file included from src/cmdstan/stansummary.cpp:5:
In file included from stan/src/stan/mcmc/chains.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim/mat.hpp:142:
In file included from stan/lib/stan_math/stan/math/prim/mat/fun/lgamma.hpp:5:
stan/lib/stan_math/stan/math/prim/scal/fun/lgamma.hpp:65:12: error: no member named 'lgamma_r' in the global namespace
return ::lgamma_r(x, &sign);
~~^
stan/lib/stan_math/stan/math/prim/scal/fun/lgamma.hpp:84:12: error: no member named 'lgamma_r' in the global namespace
return ::lgamma_r(x, &sign);
~~^
2 errors generated.
make: *** [make/command:3: bin/cmdstan/stansummary.o] Error 1

Description:

Describe the issue as clearly as possible.

Reproducible Steps:

nix-shell -I nixpkgs=~/nixpkgs -p cmdstan

but I'll need to create a public branch for the modified nixpkgs.

Current Output:

See above

Expected Output:

I'd expect it to install.

Additional Information:

Current Version:

v2.21.0

The text was updated successfully, but these errors were encountered:

seantalts · 2019-11-21T15:40:33Z

Just to double check, is this on 2.21.0 or develop branch?

idontgetoutmuch · 2019-11-21T15:57:17Z

https://github.com/stan-dev/cmdstan/releases/download/v2.21.0/cmdstan-2.21.0.tar.gz

but there's no urgency - the problem I am investigating is why pystan and rstan give different results for the same .stan file with the same seed - they both seem to be using 2.19.1 and I have just built cmdstan 2.19.1 successfully and will continue my investigations with that. I am assuming that cmdstan gives the "ground truth" - we shall see

[nix-shell:~/Dropbox/Tidy/labeling-experiment]$ stanc --version
stanc version 2.19.1

wds15 · 2019-11-21T16:39:59Z

What OS is this?

You have issues with _REENTRANT which is odd as we tested this on all of our platforms we support.

You could start to define __MINGW32__ manually which tells the code to use code which is always available on all platforms.

idontgetoutmuch · 2019-11-21T16:55:57Z

Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64

idontgetoutmuch · 2019-11-21T17:46:59Z

This may be an extra data point

[nix-shell:~/Dropbox/Tidy/labeling-experiment-alt]$ gcc -I/Users/dom/cmdstan/stan/src -I/Users/dom/cmdstan/stan/lib/stan_math -I/Users/dom/cmdstan/stan/lib/stan_math/lib/eigen_3.3.3 -I/Users/dom/cmdstan/stan/lib/stan_math/lib/boost_1.69.0 -I/Users/dom/cmdstan/stan/lib/stan_math/lib/tbb_2019_U8/include -I/Users/dom/cmdstan/stan/lib/stan_math/lib/sundials_4.1.0/include FromPymc_model.cpp
In file included from /Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/mat/fun/lgamma.hpp:5,
                 from /Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/mat.hpp:142,
                 from /Users/dom/cmdstan/stan/lib/stan_math/stan/math/rev/mat.hpp:12,
                 from /Users/dom/cmdstan/stan/lib/stan_math/stan/math.hpp:4,
                 from /Users/dom/cmdstan/stan/src/stan/model/model_header.hpp:4,
                 from FromPymc_model.cpp:3:
/Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/scal/fun/lgamma.hpp:19:2: error: #error "stan-math requires _REENTRANT being defined during compilation" "to make lgamma_r available."
 #error \
  ^~~~~
In file included from /Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/mat/fun/lgamma.hpp:5,
                 from /Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/mat.hpp:142,
                 from /Users/dom/cmdstan/stan/lib/stan_math/stan/math/rev/mat.hpp:12,
                 from /Users/dom/cmdstan/stan/lib/stan_math/stan/math.hpp:4,
                 from /Users/dom/cmdstan/stan/src/stan/model/model_header.hpp:4,
                 from FromPymc_model.cpp:3:
/Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/scal/fun/lgamma.hpp: In function ‘double stan::math::lgamma(double)’:
/Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/scal/fun/lgamma.hpp:65:12: error: ‘::lgamma_r’ has not been declared
   return ::lgamma_r(x, &sign);
            ^~~~~~~~
/Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/scal/fun/lgamma.hpp:65:12: note: suggested alternative: ‘lgamma’
   return ::lgamma_r(x, &sign);
            ^~~~~~~~
            lgamma
/Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/scal/fun/lgamma.hpp: In function ‘double stan::math::lgamma(int)’:
/Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/scal/fun/lgamma.hpp:84:12: error: ‘::lgamma_r’ has not been declared
   return ::lgamma_r(x, &sign);
            ^~~~~~~~
/Users/dom/cmdstan/stan/lib/stan_math/stan/math/prim/scal/fun/lgamma.hpp:84:12: note: suggested alternative: ‘lgamma’
   return ::lgamma_r(x, &sign);
            ^~~~~~~~
            lgamma

mitzimorris · 2019-11-22T16:05:37Z

was this addressed by updating the submodules?

wds15 · 2019-11-23T10:54:39Z

if you put into your make/local

CXXFLAGS+=-D__MINGW32__

then it should work. Can you please try?

What is nixpkg? Darwin 17 is Mojave or Catalina?

rok-cesnovar · 2020-02-19T13:01:16Z

I am going to close this stale issue. Do reopen if it was not resolved.

idontgetoutmuch · 2022-03-01T13:36:27Z

It is not resolved.

barracuda156 · 2022-11-18T23:21:25Z

I am going to close this stale issue. Do reopen if it was not resolved.

@rok-cesnovar It is not resolved. Just got this on stanmath test-suite:

In file included from ./stan/math/prim/fun/beta.hpp:6,
                 from ./stan/math/prim/fun.hpp:31,
                 from ./stan/math/prim.hpp:14,
                 from test/unit/math/fwd/core/std_numeric_limits_test.cpp:2:
./stan/math/prim/fun/lgamma.hpp: In function 'double stan::math::lgamma(double)':
./stan/math/prim/fun/lgamma.hpp:66:12: error: '::lgamma_r' has not been declared; did you mean 'lgamma'?
   66 |   return ::lgamma_r(x, &sign);
      |            ^~~~~~~~
      |            lgamma
./stan/math/prim/fun/lgamma.hpp: In function 'double stan::math::lgamma(int)':
./stan/math/prim/fun/lgamma.hpp:85:12: error: '::lgamma_r' has not been declared; did you mean 'lgamma'?
   85 |   return ::lgamma_r(x, &sign);
      |            ^~~~~~~~
      |            lgamma
In file included from ./stan/math/prim/fun/beta.hpp:6,
                 from ./stan/math/fwd/fun/beta.hpp:6,
                 from ./stan/math/fwd/fun.hpp:19,
                 from ./stan/math/fwd.hpp:12,
                 from test/unit/math/fwd/fun/accumulator_test.cpp:1:
./stan/math/prim/fun/lgamma.hpp: In function 'double stan::math::lgamma(double)':
./stan/math/prim/fun/lgamma.hpp:66:12: error: '::lgamma_r' has not been declared; did you mean 'lgamma'?
   66 |   return ::lgamma_r(x, &sign);
      |            ^~~~~~~~
      |            lgamma
./stan/math/prim/fun/lgamma.hpp: In function 'double stan::math::lgamma(int)':
./stan/math/prim/fun/lgamma.hpp:85:12: error: '::lgamma_r' has not been declared; did you mean 'lgamma'?
   85 |   return ::lgamma_r(x, &sign);
      |            ^~~~~~~~
      |            lgamma
In file included from ./stan/math/prim/fun/beta.hpp:6,
                 from ./stan/math/fwd/fun/beta.hpp:6,
                 from ./stan/math/fwd/fun.hpp:19,
                 from ./stan/math/fwd.hpp:12,
                 from test/unit/math/fwd/eigen_plugins_test.cpp:1:
./stan/math/prim/fun/lgamma.hpp: In function 'double stan::math::lgamma(double)':
./stan/math/prim/fun/lgamma.hpp:66:12: error: '::lgamma_r' has not been declared; did you mean 'lgamma'?
   66 |   return ::lgamma_r(x, &sign);
      |            ^~~~~~~~
      |            lgamma
./stan/math/prim/fun/lgamma.hpp: In function 'double stan::math::lgamma(int)':
./stan/math/prim/fun/lgamma.hpp:85:12: error: '::lgamma_r' has not been declared; did you mean 'lgamma'?
   85 |   return ::lgamma_r(x, &sign);
      |            ^~~~~~~~
      |            lgamma
In file included from ./stan/math/prim/fun/beta.hpp:6,
                 from ./stan/math/fwd/fun/beta.hpp:6,
                 from ./stan/math/fwd/fun.hpp:19,
                 from ./stan/math/fwd.hpp:12,
                 from test/unit/math/fwd/fun/array_builder_test.cpp:1:
./stan/math/prim/fun/lgamma.hpp: In function 'double stan::math::lgamma(double)':
./stan/math/prim/fun/lgamma.hpp:66:12: error: '::lgamma_r' has not been declared; did you mean 'lgamma'?
   66 |   return ::lgamma_r(x, &sign);
      |            ^~~~~~~~
      |            lgamma
./stan/math/prim/fun/lgamma.hpp: In function 'double stan::math::lgamma(int)':
./stan/math/prim/fun/lgamma.hpp:85:12: error: '::lgamma_r' has not been declared; did you mean 'lgamma'?
   85 |   return ::lgamma_r(x, &sign);
      |            ^~~~~~~~
      |            lgamma

andrjohns · 2022-11-18T23:40:28Z

You have to update your makeflags, we covered this earlier: https://discourse.mc-stan.org/t/stan-in-r-on-powerpc-g5-10-6-ppc-help-needed/25176/29

barracuda156 · 2022-11-19T00:04:46Z

You have to update your makeflags, we covered this earlier: https://discourse.mc-stan.org/t/stan-in-r-on-powerpc-g5-10-6-ppc-help-needed/25176/29

I will try passing it to tests now, thank you!

barracuda156 · 2022-11-27T18:00:54Z

You have to update your makeflags, we covered this earlier: https://discourse.mc-stan.org/t/stan-in-r-on-powerpc-g5-10-6-ppc-help-needed/25176/29

@andrjohns By the way, lgamma_r in fact is available, but requires correct defines:

/*
 * Reentrant version of gamma & lgamma; passes signgam back by reference
 * as the second argument; user must allocate space for signgam.
 */
#ifdef _REENTRANT
extern double gamma_r ( double, int * );
extern double lgamma_r ( double, int * );
#endif /* _REENTRANT */
#endif /* (!_XOPEN_SOURCE || _DARWIN_C_SOURCE) */
#endif /* !_ANSI_SOURCE && (!_POSIX_C_SOURCE || _DARWIN_C_SOURCE) */

I.e. it needs _DARWIN_C_SOURCE and _REENTRANT defined prior to including system math.h. Alternatively, passing -D_DARWIN_C_SOURCE and -D_REENTRANT as cppflags should work, though perhaps may not be the best way (-D_DARWIN_C_SOURCE on macOS should be safe, but I am not sure if -D_REENTRANT may have some adverse effects if passed in general).

Followed these posts to identify fixes to compilation errors: https://discourse.mc-stan.org/t/problems-linking-to-tbb-with-latest-stanheaders/15562/33 stan-dev/cmdstan#770 https://discourse.mc-stan.org/t/stan-in-r-on-powerpc-g5-10-6-ppc-help-needed/25176/29

rok-cesnovar closed this as completed Feb 19, 2020

idontgetoutmuch mentioned this issue Mar 1, 2022

cmdstan fails to build #1083

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cmdstan fails to build #770

cmdstan fails to build #770

idontgetoutmuch commented Nov 21, 2019

seantalts commented Nov 21, 2019

idontgetoutmuch commented Nov 21, 2019 •

edited

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wds15 commented Nov 21, 2019

idontgetoutmuch commented Nov 21, 2019

idontgetoutmuch commented Nov 21, 2019

mitzimorris commented Nov 22, 2019

wds15 commented Nov 23, 2019

rok-cesnovar commented Feb 19, 2020

idontgetoutmuch commented Mar 1, 2022

barracuda156 commented Nov 18, 2022

andrjohns commented Nov 18, 2022

barracuda156 commented Nov 19, 2022

barracuda156 commented Nov 27, 2022

cmdstan fails to build #770

cmdstan fails to build #770

Comments

idontgetoutmuch commented Nov 21, 2019

Summary:

Description:

Reproducible Steps:

Current Output:

Expected Output:

Additional Information:

Current Version:

seantalts commented Nov 21, 2019

idontgetoutmuch commented Nov 21, 2019 • edited Loading

wds15 commented Nov 21, 2019

idontgetoutmuch commented Nov 21, 2019

idontgetoutmuch commented Nov 21, 2019

mitzimorris commented Nov 22, 2019

wds15 commented Nov 23, 2019

rok-cesnovar commented Feb 19, 2020

idontgetoutmuch commented Mar 1, 2022

barracuda156 commented Nov 18, 2022

andrjohns commented Nov 18, 2022

barracuda156 commented Nov 19, 2022

barracuda156 commented Nov 27, 2022

idontgetoutmuch commented Nov 21, 2019 •

edited

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