Building MPI version with gcc 6.3 and OpenMPI 2.0.2 on CentOS7 fails.

[jhein32]

I am trying to build rb-mpi on our CentOS 7 cluster for a user. I succeeded in building a serial excutable, doing:

export CC=gcc
export CXX=g++

cd revbayes-master/projects/cmake

./build.sh

Once the build has succeeded, I issued a:

./build.sh -mpi true

in the same directory (without any cleaning). That fails. I think the critial issue is quite early in the build

[  5%] Building CXX object revlanguage/CMakeFiles/rb-parser.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/revlanguage/analysis/RlValidationAnalysis.cpp.o
[  5%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/WangLandauMcmc.cpp.o
[  5%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/convergence/BurninEstimatorContinuous.cpp.o
[  5%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/convergence/ConvergenceDiagnosticContinuous.cpp.o
[  5%] Building CXX object revlanguage/CMakeFiles/rb-parser.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/revlanguage/analysis/mcmc/RlMcmc.cpp.o
[  5%] Building CXX object revlanguage/CMakeFiles/rb-parser.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/revlanguage/analysis/mcmc/RlMcmcmc.cpp.o
[  5%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/convergence/EssMax.cpp.o
[  5%] Building CXX object revlanguage/CMakeFiles/rb-parser.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/revlanguage/analysis/mcmc/RlMonteCarloAnalysis.cpp.o
[  5%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/convergence/EssTest.cpp.o
[  5%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/convergence/GelmanRubinTest.cpp.o
[  5%] Building CXX object revlanguage/CMakeFiles/rb-parser.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/revlanguage/analysis/mcmc/RlPathSampler.cpp.o
[  5%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/convergence/GewekeTest.cpp.o
[  5%] Building CXX object revlanguage/CMakeFiles/rb-parser.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/revlanguage/analysis/mcmc/RlSteppingStoneSampler.cpp.o
/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/revlanguage/analysis/mcmc/RlMonteCarloAnalysis.cpp: In member function ‘virtual RevLanguage::RevPtr<RevLanguage::RevVariable> RevLanguage::MonteCarloAnalysis::executeMethod(const string&, const std::vector<RevLanguage::Argument>&, bool&)’:
/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/revlanguage/analysis/mcmc/RlMonteCarloAnalysis.cpp:102:53: error: ‘tuning_interval’ was not declared in this scope
             value->run( gen, rules, MPI_COMM_WORLD, tuning_interval );
                                                     ^~~~~~~~~~~~~~~
[  6%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/convergence/HeidelbergerWelchTest.cpp.o
make[2]: *** [revlanguage/CMakeFiles/rb-parser.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/revlanguage/analysis/mcmc/RlMonteCarloAnalysis.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[  6%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/convergence/SemMin.cpp.o
[  6%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/convergence/StationarityTest.cpp.o
[  6%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/output/AncestralStateTrace.cpp.o
[  6%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/output/ModelTrace.cpp.o
[  6%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/output/Trace.cpp.o
make[1]: *** [revlanguage/CMakeFiles/rb-parser.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[  6%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/output/TraceAnalysisContinuous.cpp.o
[  6%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/analysis/mcmc/output/TraceNumeric.cpp.o

After this the build continues to fail later with:

[ 54%] Building CXX object core/CMakeFiles/rb-core.dir/sw/src/revbayes/Revbayes_22Nov2017/revbayes-master/src/core/utils/TreeUtilities.cpp.o
[ 54%] Linking CXX static library librb-core.a
[ 54%] Built target rb-core
make: *** [all] Error 2

I am working with a zip file, (master) which I downloaded earlier today.

Please let me know if you need any further information.

[jsigao]

Hi,

I think this issue should have been fixed on the development branch. Would you mind give that a try?

Jiansi

[jhein32]

Hi Jiansi,

Thanks for the fast reaction. I took a zip file of the development branch and that builds an rb-mpi in addition to the rb executable.

Best wishes
Joachim