Closed Will338 closed 6 years ago
@Will338 I got the same error with the distributed binary. However, as the manual says:
you may need to recompile the code
I did this and things work well. (Compiling only takes a, er, compiler, and the command make
in the sources directory (binaries are put into the data
directory).
HTH :bowtie:
We have the same issue here:
pb_mpi: error while loading shared libraries: libmpi_cxx.so.0:
But we are also unable to re-compile a functional binary:
...
In file included from AACodonMutSelProfileProcess.h:20:0,
from AACodonMutSelSBDPProfileProcess.h:21,
from AACodonMutSelSBDPSubstitutionProcess.h:20,
from AACodonMutSelSBDPPhyloProcess.h:20,
from Model.h:23,
from PB.cpp:17:
CodonSubMatrix.h:70:33: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double AAMutSelProfileSubMatrix::TOOSMALL’ of non-integral type [-fpermissive]
static const double TOOSMALL = 1e-30;
^~~~~
CodonSubMatrix.h:71:33: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double AAMutSelProfileSubMatrix::TOOLARGE’ of non-integral type [-fpermissive]
static const double TOOLARGE = 500;
^~~
CodonSubMatrix.h:72:42: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double AAMutSelProfileSubMatrix::TOOLARGENEGATIVE’ of non-integral type [-fpermissive]
static const double TOOLARGENEGATIVE = -500;
^~~
CodonSubMatrix.h:99:33: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double AACodonMutSelProfileSubMatrix::TOOSMALL’ of non-integral type [-fpermissive]
static const double TOOSMALL = 1e-30;
^~~~~
CodonSubMatrix.h:100:33: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double AACodonMutSelProfileSubMatrix::TOOLARGE’ of non-integral type [-fpermissive]
static const double TOOLARGE = 500;
^~~
CodonSubMatrix.h:101:42: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double AACodonMutSelProfileSubMatrix::TOOLARGENEGATIVE’ of non-integral type [-fpermissive]
static const double TOOLARGENEGATIVE = -50;
^~
CodonSubMatrix.h:122:33: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double CodonMutSelProfileSubMatrix::TOOSMALL’ of non-integral type [-fpermissive]
static const double TOOSMALL = 1e-30;
^~~~~
CodonSubMatrix.h:123:33: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double CodonMutSelProfileSubMatrix::TOOLARGE’ of non-integral type [-fpermissive]
static const double TOOLARGE = 500;
^~~
CodonSubMatrix.h:124:42: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double CodonMutSelProfileSubMatrix::TOOLARGENEGATIVE’ of non-integral type [-fpermissive]
static const double TOOLARGENEGATIVE = -50;
^~
make: *** [Makefile:55: PB.o] Error 1
make: *** Waiting for unfinished jobs....
Our versions:
reneum@mphn ~/builder/pbmpi/sources $ mpic++ -showme:version
mpic++: Open MPI 2.0.2 (Language: C++)
reneum@mphn ~/builder/pbmpi/sources $ mpic++ -showme
x86_64-pc-linux-gnu-g++ -pthread -Wl,-rpath -Wl,/usr/lib64 -Wl,--enable-new-dtags -L/usr/lib64 -lmpi_cxx -lmpi
gcc-6.4
Any advise?
should recompile now, with the new version
Also, I have removed the binary files: you need to recompile on most machines anyway.
I'm getting the following errors when trying to run pb_mpi using this command:
mpirun -np 6 pb_mpi ~/Path/to/data Chain1
Please can anyone give me some guidance in how to get it working?