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[Libmesh-users] Ran into the error "invalid time_solver DIE" when trying fem_system_ex3.C
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From: Yuxiang W. <yw...@vi...> - 2018-10-28 00:14:16
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Dear libmesh community,
Sorry for the spam again.
I have compiled my libmesh stable release 1.3.0 with PETSc and it was able
to run most examples perfectly (for example, the Systems of Equations
Example 6 which is the implicit version of this example). The environment
is 64-bit Windows 10, in Windows Subsystem for Linux, Ubuntu 18.04.
However, when I tried to run fem_system_ex3.C, it built fine but gave the
following error:
yw5aj@Shawn-K430:/mnt/x/libmesh/with_vtk/examples/fem_system/ex3-test$
make;./example-opt -ksp_type cg -pc_type jacobi
Can't open perl script "/mnt/x/libmesh/with_vtk/contrib/bin/
make_dependencies.pl": No such file or directory
Compiling C++ (in optimized mode) elasticity_system.C...
mpicxx -DNDEBUG -O2 -felide-constructors -funroll-loops -fstrict-aliasing
-Wdisabled-optimization -fopenmp -I/mnt/x/libmesh/with_vtk/include
-I/usr/include/eigen3 -I/usr/include/vtk-7.1
-I/home/yw5aj/deal.ii-candi/trilinos-release-12-10-1/include
-I/home/yw5aj/deal.ii-candi/parmetis-4.0.3/include
-I/home/yw5aj/deal.ii-candi/slepc-3.7.3/include
-I/home/yw5aj/deal.ii-candi/petsc-3.7.6/include
-I/home/yw5aj/deal.ii-candi/petsc-3.7.6//include -I/usr/include -c
elasticity_system.C -o elasticity_system.x86_64-unknown-linux-gnu.opt.o
Compiling C++ (in optimized mode) fem_system_ex3.C...
mpicxx -DNDEBUG -O2 -felide-constructors -funroll-loops -fstrict-aliasing
-Wdisabled-optimization -fopenmp -I/mnt/x/libmesh/with_vtk/include
-I/usr/include/eigen3 -I/usr/include/vtk-7.1
-I/home/yw5aj/deal.ii-candi/trilinos-release-12-10-1/include
-I/home/yw5aj/deal.ii-candi/parmetis-4.0.3/include
-I/home/yw5aj/deal.ii-candi/slepc-3.7.3/include
-I/home/yw5aj/deal.ii-candi/petsc-3.7.6/include
-I/home/yw5aj/deal.ii-candi/petsc-3.7.6//include -I/usr/include -c
fem_system_ex3.C -o fem_system_ex3.x86_64-unknown-linux-gnu.opt.o
Linking example-opt...
libtool: link: mpicxx -O2 -felide-constructors -funroll-loops
-fstrict-aliasing -Wdisabled-optimization -fopenmp
elasticity_system.x86_64-unknown-linux-gnu.opt.o
fem_system_ex3.x86_64-unknown-linux-gnu.opt.o -o example-opt -Wl,-rpath
-Wl,/mnt/x/libmesh/with_vtk/lib -Wl,-rpath
-Wl,/home/yw5aj/deal.ii-candi/trilinos-release-12-10-1/lib
/usr/lib/x86_64-linux-gnu/libdl.so
/home/yw5aj/deal.ii-candi/parmetis-4.0.3/lib/libparmetis.so
/usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so
-Wl,-rpath -Wl,/home/yw5aj/deal.ii-candi/slepc-3.7.3/lib -Wl,-rpath
-Wl,/home/yw5aj/deal.ii-candi/petsc-3.7.6/lib -Wl,-rpath
-Wl,/home/yw5aj/deal.ii-candi/parmetis-4.0.3/lib -Wl,-rpath -Wl,/usr/lib
-Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-rpath
-Wl,/usr/lib/gcc/x86_64-linux-gnu/7 -Wl,-rpath -Wl,/lib/x86_64-linux-gnu
-Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu -L/mnt/x/libmesh/with_vtk/lib
/mnt/x/libmesh/with_vtk/lib/libmesh_opt.so
-L/home/yw5aj/deal.ii-candi/trilinos-release-12-10-1/lib
-L/home/yw5aj/deal.ii-candi/slepc-3.7.3/lib
-L/home/yw5aj/deal.ii-candi/petsc-3.7.6/lib
-L/home/yw5aj/deal.ii-candi/parmetis-4.0.3/lib -L/usr/lib
/mnt/x/libmesh/with_vtk/lib/libnetcdf.so
/usr/lib/x86_64-linux-gnu/libcurl-gnutls.so -lvtkIOCore-7.1
-lvtkCommonCore-7.1 -lvtkCommonDataModel-7.1 -lvtkFiltersCore-7.1
-lvtkIOXML-7.1 -lvtkImagingCore-7.1 -lvtkIOImage-7.1 -lvtkImagingMath-7.1
-lvtkIOParallelXML-7.1 -lvtkParallelMPI-7.1 -lvtkParallelCore-7.1 -lz
-lmuelu-adapters -lmuelu-interface -lmuelu -lteko -lstratimikos
-lstratimikosbelos -lstratimikosaztecoo -lstratimikosamesos -lstratimikosml
-lstratimikosifpack -lifpack2-adapters -lifpack2 -lanasazitpetra
-lModeLaplace -lanasaziepetra -lanasazi -lamesos2 -lbelostpetra
-lbelosepetra -lbelos -lml -lifpack -lzoltan2 -lpamgen_extras -lpamgen
-lamesos -lgaleri-xpetra -lgaleri-epetra -laztecoo -lisorropia -lxpetra-sup
-lxpetra -lthyratpetra -lthyraepetraext -lthyraepetra -lthyracore
-lepetraext -ltpetraext -ltpetrainout -ltpetra -lkokkostsqr -ltpetrakernels
-ltpetraclassiclinalg -ltpetraclassicnodeapi -ltpetraclassic -ltriutils
-lzoltan -lepetra -lsacado -lrtop -lteuchoskokkoscomm -lteuchoskokkoscompat
-lteuchosremainder -lteuchosnumerics -lteuchoscomm -lteuchosparameterlist
-lteuchoscore -lkokkosalgorithms -lkokkoscontainers -lkokkoscore -lslepc
-lpetsc -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord
-lparmetis -lmetis -lscalapack -lHYPRE -llapack -lblas -lhwloc
-lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lgfortran -lquadmath
-lmpi_cxx -lstdc++ -lm -lmpi -lgcc_s -lpthread -ldl
-L/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/7
-L/usr/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -pthread -fopenmp
-Wl,-rpath -Wl,/mnt/x/libmesh/with_vtk/lib -Wl,-rpath
-Wl,/mnt/x/libmesh/with_vtk/lib
Mesh Information:
elem_dimensions()={3}
spatial_dimension()=3
n_nodes()=1485
n_local_nodes()=1485
n_elem()=1024
n_local_elem()=1024
n_active_elem()=1024
n_subdomains()=1
n_partitions()=1
n_processors()=1
n_threads()=1
processor_id()=0
ERROR: invalid time_solver DIE!
Stack frames: 5
0: libMesh::print_trace(std::ostream&)
1: libMesh::MacroFunctions::report_error(char const*, int, char const*,
char const*)
2: ./example-opt(+0x22b16) [0x7fcbd5022b16]
3: __libc_start_main
4: ./example-opt(+0x22dca) [0x7fcbd5022dca]
[0] fem_system_ex3.C, line 211, compiled Oct 27 2018 at 17:07:29
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Could anyone please share any thoughts that you might have, maybe just
ideas on where to start the troubleshooting? I'd really appreciate it.
Best,
Shawn
--
Yuxiang "Shawn" Wang, PhD
yw...@vi...
+1 (434) 284-0836
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