Here is the summary of the output, and the complete log file is attached.
----------------------------------- SUMMARY
-----------------------------------
Package version.................... : libmesh-1.0.0-pre
C++ compiler type.................. : gcc4.9
C++ compiler....................... : mpicxx
C compiler......................... : mpicc
Fortran compiler................... : mpif90
Build Methods...................... : opt dbg
CPPFLAGS...(opt)................... : -DNDEBUG
CXXFLAGS...(opt)................... : -O2 -felide-constructors
-funroll-loops -fstrict-aliasing -Wdisabled-optimization -fopenmp
CFLAGS.....(opt)................... : -O2 -funroll-loops -fstrict-aliasing
-fopenmp
CPPFLAGS...(dbg)................... : -DDEBUG
CXXFLAGS...(dbg)................... : -O0 -felide-constructors -g -pedantic
-W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat
-Wparentheses -Woverloaded-virtual -fopenmp
CFLAGS.....(dbg)................... : -g -Wimplicit -fopenmp
Install dir........................ :
/Users/xzhao/software/libmesh/libmesh-1.0.0-pre-dbg
Build user......................... : xzhao
Build host......................... : inl424641
Build architecture................. : x86_64-apple-darwin14.4.0
Git revision....................... :
aa42f75df77912c6d637da379cf3c77de3a06800
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................ : yes
id size (boundaries)............. : 2 bytes
id size (dofs)................... : 4 bytes
id size (unique)................. : 8 bytes
id size (processors)............. : 2 bytes
id size (subdomains)............. : 2 bytes
infinite elements................ : yes
Dirichlet constraints............ : yes
node constraints................. : yes
parallel mesh.................... : yes
performance logging.............. : yes
periodic boundary conditions..... : yes
reference counting............... : yes
shape function 2nd derivatives... : yes
stack trace files................ : yes
track node valence............... : yes
variational smoother............. : yes
xdr binary I/O................... : yes
Optional Packages:
boost............................ : yes
capnproto........................ : no
cppunit.......................... : no
eigen............................ : yes
exodus........................... : yes
version....................... : v5.22
fparser.......................... : yes
build from version............ : release
glpk............................. : no
gmv.............................. : yes
gzstream......................... : yes
hdf5............................. : yes
laspack.......................... : yes
libhilbert....................... : yes
metis............................ : yes
mpi.............................. : yes
nanoflann........................ : yes
nemesis.......................... : yes
version....................... : v5.22
netcdf........................... : yes
version....................... : 4
nlopt............................ : no
openmp........................... : yes
parmetis......................... : yes
petsc............................ : yes
version....................... : 3.5.4
pthreads......................... : yes
qhull............................ : yes
sfcurves......................... : yes
slepc............................ : yes
version....................... : 3.5.4
tbb.............................. : no
c++ threads...................... : yes
flavor........................ : std::thread
c++ rtti ........................ : yes
tecio............................ : no
tecplot...(vendor binaries)...... : no
tetgen........................... : yes
triangle......................... : yes
trilinos......................... : no
vtk.............................. : yes
version....................... : 6.2.0
libmesh_optional_INCLUDES........ : -I/usr/local/include/vtk-6.2
-D_THREAD_SAFE -pthread
-I/Users/xzhao/software/slepc/slepc-3.5.4-dbg/include
-I/Users/xzhao/software/slepc/slepc-3.5.4-dbg/arch-darwin-c-debug/include
-I/Users/xzhao/software/petsc/petsc-3.5.4-dbg/include
-I/Users/xzhao/software/petsc/petsc-3.5.4-dbg/arch-darwin-c-debug/include
-I/usr/local/include
libmesh_optional_LIBS............ : -Wl,-rpath,/usr/local/lib
-L/usr/local/lib -lvtkIOCore-6.2 -lvtkCommonCore-6.2
-lvtkCommonDataModel-6.2 -lvtkFiltersCore-6.2 -lvtkIOXML-6.2
-lvtkImagingCore-6.2 -lvtkIOImage-6.2 -lvtkImagingMath-6.2
-lvtkIOParallelXML-6.2 -lz
-L/Users/xzhao/software/slepc/slepc-3.5.4-dbg/arch-darwin-c-debug/lib
-lslepc -lBLOPEX
-L/Users/xzhao/software/petsc/petsc-3.5.4-dbg/arch-darwin-c-debug/lib
-L/usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9/gcc/x86_64-apple-darwin14.4.0/4.9.3
-L/usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9 -lpetsc -lelemental -lpmrrr
-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack
-lHYPRE -lml -lflapack -lfblas -lparmetis -lmetis -ltriangle -lchaco -lssl
-lcrypto -lmpichf90 -lpthread -lgfortran -lquadmath -lm -lmpichcxx -lstdc++
-lpmpich -lmpich -lopa -lmpl -lSystem -lgcc_ext.10.5 -ldl
-------------------------------------------------------------------------------
On Fri, Jul 31, 2015 at 1:34 AM, Dmitry Karpeyev <karp...@mcs.anl.gov>
wrote:
> Can you send the output of libMesh's configure and make?
> Are you sure that Exodus/NetCDF etc. are compiled?
> With the same compiler and all?
>
> On Thu, Jul 30, 2015 at 11:08 PM Xujun Zhao <xzha...@gmail.com> wrote:
>
>> I rebuilt the PETSc/SLEPc and libMesh, but still fails to output .e file.
>> I am not clear the reasons, but it works well if I use GMVIO and VTKIO.
>> The
>> ParaView can read the output files for these two cases. :-(
>>
>> On Thu, Jul 30, 2015 at 1:45 PM, Xujun Zhao <xzha...@gmail.com> wrote:
>>
>> > Yes, I enabled parmesh when configuring libmesh.
>> > Probably as you said, there is something wrong with my compiler/build. I
>> > will try to rebuild everything and see if it works.
>> > Thanks, John.
>> >
>> > Xujun
>> >
>> > On Thu, Jul 30, 2015 at 1:30 PM, John Peterson <jwpeter...@gmail.com>
>> > wrote:
>> >
>> >>
>> >>
>> >> On Thu, Jul 30, 2015 at 10:51 AM, Xujun Zhao <xzha...@gmail.com>
>> wrote:
>> >>
>> >>> Hi all,
>> >>>
>> >>> Writing out equations systems failed during run, which used to work
>> >>> before.
>> >>> Just go to examples/system_equations/ex1/, make and run, it gives the
>> >>> following error msgs:
>> >>>
>> >>> --->test: write out the Exodus file ...
>> >>>
>> >>> Warning: This MeshOutput subclass only supports meshes which have
>> been
>> >>> serialized!
>> >>>
>> >>> [0]PETSC ERROR:
>> >>>
>> >>> However, if I comment on the following line, everything is good.
>> >>> ExodusII_IO(mesh).write_equation_systems ("out.e", equation_systems);
>> >>>
>> >>
>> >> You configured libmesh with --enable-parmesh, right? I ran the same
>> >> example, swapping out Mesh for ParallelMesh and it works just fine.
>> >>
>> >> Furthermore, this example is run by the continuous integration system
>> >> every time someone opens a PR in libmesh, so I'm pretty confident it
>> works.
>> >>
>> >> I suspect something is wrong with your compiler/build instead...
>> >>
>> >> --
>> >> John
>> >>
>> >
>> >
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Libmesh-users mailing list
>> Libmesh-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>
>
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