Hello!
I’m trying to install libmesh on my computer (OS X version 10.10.3) and I’m
having a series of MPI errors during the compilation:
src/base/libmesh.C:492:24: error: assigning to 'MPI_Comm' (aka
'ompi_communicator_t *')
from incompatible type 'int'
PETSC_COMM_WORLD = libMesh::GLOBAL_COMM_WORLD;
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~
src/base/libmesh.C:498:7: error: no matching function for call to 'MPI_Abort'
CHKERRABORT(libMesh::GLOBAL_COMM_WORLD,ierr);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/breubreubreu/Execs/petsc-3.6.0/include/petscerror.h:237:150: note:
expanded from
macro 'CHKERRABORT'
...");MPI_Abort(comm,n);}} while (0)
^~~~~~~~~
/opt/local/include/openmpi-mp/mpi.h:1169:20: note: candidate function not
viable: no known
conversion from 'int' to 'MPI_Comm' (aka 'ompi_communicator_t *') for 1st
argument
OMPI_DECLSPEC int MPI_Abort(MPI_Comm comm, int errorcode);
^
src/base/libmesh.C:520:11: error: no matching function for call to 'MPI_Abort'
CHKERRABORT(libMesh::GLOBAL_COMM_WORLD,ierr);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/breubreubreu/Execs/petsc-3.6.0/include/petscerror.h:237:150: note:
expanded from
macro 'CHKERRABORT'
...");MPI_Abort(comm,n);}} while (0)
^~~~~~~~~
/opt/local/include/openmpi-mp/mpi.h:1169:20: note: candidate function not
viable: no known
conversion from 'int' to 'MPI_Comm' (aka 'ompi_communicator_t *') for 1st
argument
OMPI_DECLSPEC int MPI_Abort(MPI_Comm comm, int errorcode);
I searched a bit on the internet for the first error message, and I’ve found an
archived thread from this mailing list
(http://sourceforge.net/p/libmesh/mailman/libmesh-users/thread/CACH89CO2fUVAE2FB8DNYFOpbzUQPzn0u3VcH9jEMOQPQ_2wJfw%40mail.gmail.com/#msg32339445).
In that case, it seems that the problem was a badly defined PETSC_ARCH
variable. I verified my environment variables, and both PETSc and SLEPc
variables are correctly defined (I hope …)
breubreubreu$ echo $PETSC_ARCH $PETSC_DIR $SLEPC_DIR
arch-darwin-c-debug /Users/breubreubreu/Execs/petsc-3.6.0
/Users/breubreubreu/Execs/slepc-3.6.0
Does anyone have an idea of what could be wrong? I’m trying to configure
libmesh using the command
./configure --with-vtk-lib=/opt/local/bin
--with-vtk-include=/opt/local/include/vtk-5.10
--with-eigen-include=/opt/local/include/eigen3 --enable-mpi
--prefix=/Users/breubreubreu/Execs/libmesh-0.9.4
I’m using OpenMPI 1.7.5 (installed through MacPorts) and PETSc / SLEPc 3.6.0
(installed “by hand” with MPI compilers). The configure summary is given below.
Thanks in advance,
Thiago Milanetto Schlittler
----------------------------------- SUMMARY -----------------------------------
Package version.................... : libmesh-0.9.4
C++ compiler type.................. : clang
C++ compiler....................... : mpicxx
C compiler......................... : mpicc
Fortran compiler................... : mpif90
Build Methods...................... : dbg devel opt
CPPFLAGS...(dbg)................... : -DDEBUG
CXXFLAGS...(dbg)................... : -std=gnu++11 -O0 -felide-constructors -g
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat
-Wparentheses -Qunused-arguments -std=gnu++11
CFLAGS.....(dbg)................... : -g -Wimplicit -Qunused-arguments
CPPFLAGS...(devel)................. :
CXXFLAGS...(devel)................. : -std=gnu++11 -O2 -felide-constructors -g
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat
-Wparentheses -Wuninitialized -Qunused-arguments -std=gnu++11
CFLAGS.....(devel)................. : -O2 -Qunused-arguments -g -Wimplicit
CPPFLAGS...(opt)................... : -DNDEBUG
CXXFLAGS...(opt)................... : -std=gnu++11 -O2 -felide-constructors
-Qunused-arguments -std=gnu++11
CFLAGS.....(opt)................... : -O2 -Qunused-arguments
Install dir........................ : /Users/breubreubreu/Execs/libmesh-0.9.4
Build user......................... : breubreubreu
Build host......................... : dhcp-103-99.wifi-auth.ecp.fr
Build architecture................. : x86_64-apple-darwin14.3.0
Git revision....................... : external
Library Features:
library warnings................. : yes
adaptive mesh refinement......... : yes
blocked matrix/vector storage.... : no
complex variables................ : no
example suite.................... : yes
ghosted vectors.................. : yes
high-order shape functions....... : yes
unique-id support................ : no
id size (boundaries)............. : 2 bytes
id size (dofs)................... : 4 bytes
id size (processors)............. : 2 bytes
id size (subdomains)............. : 2 bytes
infinite elements................ : no
Dirichlet constraints............ : yes
node constraints................. : no
parallel mesh.................... : no
performance logging.............. : no
periodic boundary conditions..... : yes
reference counting............... : yes
shape function 2nd derivatives... : yes
stack trace files................ : no
track node valence............... : yes
variational smoother............. : yes
xdr binary I/O................... : yes
providing libMesh::CommWorld..... : yes ***LEGACY FEATURE***
Optional Packages:
boost............................ : yes
cppunit.......................... : no
eigen............................ : yes
exodus........................... : yes
version....................... : v5.22
fparser.......................... : yes
build from version............ : release
glpk............................. : no
gmv.............................. : yes
gzstream......................... : yes
hdf5............................. : yes
laspack.......................... : no
libhilbert....................... : yes
metis............................ : yes
mpi.............................. : yes
nanoflann........................ : yes
nemesis.......................... : yes
version....................... : v5.22
netcdf........................... : yes
version....................... : 4
openmp........................... : no
parmetis......................... : yes
petsc............................ : yes
version....................... : 3.6.0
slepc............................ : no
pthreads......................... : yes
qhull............................ : yes
sfcurves......................... : no
slepc............................ : no
tbb.............................. : no
c++ threads...................... : no
c++ rtti ........................ : yes
tecio............................ : no
tecplot...(vendor binaries)...... : no
tetgen........................... : yes
triangle......................... : no
trilinos......................... : no
vtk.............................. : no
libmesh_optional_INCLUDES........ : -I/opt/local/include/eigen3
-D_THREAD_SAFE -pthread -I/Users/breubreubreu/Execs/petsc-3.6.0/include
-I/Users/breubreubreu/Execs/petsc-3.6.0/arch-darwin-c-debug/include
-I/opt/local/include -I/opt/local/include/openmpi-mp
libmesh_optional_LIBS............ : -lz
-Wl,-rpath,/Users/breubreubreu/Execs/petsc-3.6.0/arch-darwin-c-debug/lib
-L/Users/breubreubreu/Execs/petsc-3.6.0/arch-darwin-c-debug/lib -lpetsc
-llapack -lblas -Wl,-rpath,/opt/local/lib -L/opt/local/lib -lhwloc -lssl
-lcrypto -L/opt/local/lib/openmpi-mp
-L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.1.0/lib/darwin
-lmpi_usempi -lmpi_mpifh
-Wl,-rpath,/opt/local/lib/gcc49/gcc/x86_64-apple-darwin14/4.9.2
-L/opt/local/lib/gcc49/gcc/x86_64-apple-darwin14/4.9.2
-Wl,-rpath,/opt/local/lib/gcc49 -L/opt/local/lib/gcc49 -lgfortran
-lgcc_ext.10.5 -lquadmath -lm -lmpi_cxx -lc++
-Wl,-rpath,/opt/local/lib/openmpi-mp -lmpi -lSystem
-Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.1.0/lib/darwin
-lclang_rt.osx -ldl
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