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Building v3.13 rosetta.source.release-296 + MPI error

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Building v3.13 rosetta.source.release-296 + MPI error
#1

Hi all,

I'm trying to build Rosetta version 3.13 (rosetta.source.release-296) in a CentOS cluster with MPI. I have already installed version 3.7, 3.10 and 3.12 in the same machine. I'm using the very same options as used in older compiled versions (file site.settings indicating where are de mpicc and mpicxx compilers/libraries).

The command line is as below:

./scons.py mode=release bin extras=mpi 

After several minutes, I have the following error message:

/opt/programs/openmpi/3.0/bin/mpicxx -o build/src/release/linux/3.10/64/x86/gcc/6.4/mpi/protocols/stepwise/modeler/packer/StepWisePacker.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/6.4 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -I/opt/programs/openmpi/3.0/include src/protocols/stepwise/modeler/packer/StepWisePacker.cc

src/protocols/recces/sampler/MC_OneTorsion.cc: In member function 'virtual void protocols::recces::sampler::MC_OneTorsion::update()':

src/protocols/recces/sampler/MC_OneTorsion.cc:109:46: error: call of overloaded 'abs(core::Real)' is ambiguous

  if ( std::abs( update_angle - stored_angle_ ) < 1.0e-5 ) {

                                              ^

In file included from /opt/programs/gcc/6.4.0/include/c++/6.4.0/ext/string_conversions.h:41:0,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/bits/basic_string.h:5417,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/string:52,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/stdexcept:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/array:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/tuple:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/functional:55,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/memory:79,

                 from src/utility/pointer/std/owning_ptr.hh:20,

                 from src/utility/pointer/owning_ptr.hh:15,

                 from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,

                 from src/protocols/recces/sampler/MC_OneTorsion.hh:19,

                 from src/protocols/recces/sampler/MC_OneTorsion.cc:15:

/opt/programs/gcc/6.4.0/include/c++/6.4.0/cstdlib:172:3: note: candidate: long int std::abs(long int)

   abs(long __i) { return __builtin_labs(__i); }

   ^~~

In file included from /opt/programs/gcc/6.4.0/include/c++/6.4.0/cstdlib:75:0,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/ext/string_conversions.h:41,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/bits/basic_string.h:5417,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/string:52,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/stdexcept:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/array:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/tuple:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/functional:55,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/memory:79,

                 from src/utility/pointer/std/owning_ptr.hh:20,

                 from src/utility/pointer/owning_ptr.hh:15,

                 from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,

                 from src/protocols/recces/sampler/MC_OneTorsion.hh:19,

                 from src/protocols/recces/sampler/MC_OneTorsion.cc:15:

/usr/include/stdlib.h:770:12: note: candidate: int abs(int)

 extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;

            ^~~

In file included from /opt/programs/gcc/6.4.0/include/c++/6.4.0/ext/string_conversions.h:41:0,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/bits/basic_string.h:5417,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/string:52,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/stdexcept:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/array:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/tuple:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/functional:55,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/memory:79,

                 from src/utility/pointer/std/owning_ptr.hh:20,

                 from src/utility/pointer/owning_ptr.hh:15,

                 from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,

                 from src/protocols/recces/sampler/MC_OneTorsion.hh:19,

                 from src/protocols/recces/sampler/MC_OneTorsion.cc:15:

/opt/programs/gcc/6.4.0/include/c++/6.4.0/cstdlib:180:3: note: candidate: long long int std::abs(long long int)

   abs(long long __x) { return __builtin_llabs (__x); }

   ^~~

src/protocols/recces/sampler/MC_OneTorsion.cc:112:53: error: call of overloaded 'abs(core::Real)' is ambiguous

  } else if ( std::abs( update_angle - active_angle_ ) < 1.0e-5 ) {

                                                     ^

In file included from /opt/programs/gcc/6.4.0/include/c++/6.4.0/ext/string_conversions.h:41:0,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/bits/basic_string.h:5417,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/string:52,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/stdexcept:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/array:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/tuple:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/functional:55,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/memory:79,

                 from src/utility/pointer/std/owning_ptr.hh:20,

                 from src/utility/pointer/owning_ptr.hh:15,

                 from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,

                 from src/protocols/recces/sampler/MC_OneTorsion.hh:19,

                 from src/protocols/recces/sampler/MC_OneTorsion.cc:15:

/opt/programs/gcc/6.4.0/include/c++/6.4.0/cstdlib:172:3: note: candidate: long int std::abs(long int)

   abs(long __i) { return __builtin_labs(__i); }

   ^~~

In file included from /opt/programs/gcc/6.4.0/include/c++/6.4.0/cstdlib:75:0,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/ext/string_conversions.h:41,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/bits/basic_string.h:5417,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/string:52,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/stdexcept:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/array:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/tuple:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/functional:55,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/memory:79,

                 from src/utility/pointer/std/owning_ptr.hh:20,

                 from src/utility/pointer/owning_ptr.hh:15,

                 from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,

                 from src/protocols/recces/sampler/MC_OneTorsion.hh:19,

                 from src/protocols/recces/sampler/MC_OneTorsion.cc:15:

/usr/include/stdlib.h:770:12: note: candidate: int abs(int)

 extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;

            ^~~

In file included from /opt/programs/gcc/6.4.0/include/c++/6.4.0/ext/string_conversions.h:41:0,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/bits/basic_string.h:5417,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/string:52,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/stdexcept:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/array:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/tuple:39,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/functional:55,

                 from /opt/programs/gcc/6.4.0/include/c++/6.4.0/memory:79,

                 from src/utility/pointer/std/owning_ptr.hh:20,

                 from src/utility/pointer/owning_ptr.hh:15,

                 from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,

                 from src/protocols/recces/sampler/MC_OneTorsion.hh:19,

                 from src/protocols/recces/sampler/MC_OneTorsion.cc:15:

/opt/programs/gcc/6.4.0/include/c++/6.4.0/cstdlib:180:3: note: candidate: long long int std::abs(long long int)

   abs(long long __x) { return __builtin_llabs (__x); }

   ^~~

/opt/programs/openmpi/3.0/bin/mpicxx -o build/src/release/linux/3.10/64/x86/gcc/6.4/mpi/protocols/stepwise/modeler/packer/SideChainCopier.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/6.4 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -I/opt/programs/openmpi/3.0/include src/protocols/stepwise/modeler/packer/SideChainCopier.cc

/opt/programs/openmpi/3.0/bin/mpicxx -o build/src/release/linux/3.10/64/x86/gcc/6.4/mpi/protocols/stepwise/modeler/packer/util.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/6.4 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -I/opt/programs/openmpi/3.0/include src/protocols/stepwise/modeler/packer/util.cc

scons: *** [build/src/release/linux/3.10/64/x86/gcc/6.4/mpi/protocols/recces/sampler/MC_OneTorsion.os] Error 1

scons: building terminated because of errors.

 

As I said, I have never faced this error building older versions of Rosetta with exactly same options and compilers/libraries. Any ideas how to troubleshoot this?

Thanks in advance,

Danilo.

 

Category: 
Post Situation: 
Mon, 2022-03-21 11:58
dfcoelho