[MOAB-dev] error while loading shared libraries: libnetcdf.so.7:

Xu Wu xuwu2 at illinois.edu
Mon Jul 13 23:23:05 CDT 2015 

Dear MOAB developers,


I was trying to play with MOAB on my own laptop (Ubuntu 14.04).
I was able to compile those examples, but when I try to run them the 
following error occured:



However, as you can see above, I do have netcdf libraries installed and 
they are on the search path for MOAB.
I attached the configuration log, the "makefile" in " /examples", as 
well as the "moab.make" in "/moab-4.8.1/lib/".

Thank you,


-Xu
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# The values below are for an un-installed copy of MOAB used directly
# from its build build directory.  These values will be overridden below
# for installed copies of MOAB.
MOAB_LIBDIR = /home/xu/research/softwares/sharp_dependencies/source/moab-4.8.1/src/.libs
MOAB_INCLUDES = -I/home/xu/research/softwares/sharp_dependencies/source/moab-4.8.1/src \
                -I/home/xu/research/softwares/sharp_dependencies/source/moab-4.8.1/src \
                -I/home/xu/research/softwares/sharp_dependencies/source/moab-4.8.1/src/oldinc \
                -I/home/xu/research/softwares/sharp_dependencies/source/moab-4.8.1/src/parallel \
                -I/home/xu/research/softwares/sharp_dependencies/source/moab-4.8.1/src/parallel

MOAB_INCLUDES += 

MOAB_CPPFLAGS =  -D_REENTRANT -D_POSIX_PTHREAD_SEMANTICS -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set  -I/home/xu/research/softwares/sharp_dependencies/netcdf-4.3.2/include -I/home/xu/research/softwares/sharp_dependencies/parallel-netcdf-1.6.1/include    -I/home/xu/research/softwares/sharp_dependencies/hdf5-1.8.15/include -isystem /home/xu/research/softwares/sharp_dependencies/hdf5-1.8.15/include  -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64   -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DPNETCDF_FILE -DNETCDF_FILE
MOAB_CXXFLAGS =  -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align  -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG 
MOAB_CFLAGS =  -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align  -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG 
MOAB_FFLAGS =   -O2 -lstdc++ -fcray-pointer
MOAB_FCFLAGS =   -O2 -lstdc++ -fcray-pointer
MOAB_LDFLAGS =   -L/home/xu/research/softwares/sharp_dependencies/netcdf-4.3.2/lib -lnetcdf -L/home/xu/research/softwares/sharp_dependencies/parallel-netcdf-1.6.1/lib      -L/home/xu/research/softwares/sharp_dependencies/hdf5-1.8.15/lib 


MOAB_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR} -lMOAB -lpnetcdf -lnetcdf -lpnetcdf  -lhdf5    -lpthread -lz -ldl -lm     -lpthread -lz -ldl -lm
DAGMC_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR}  -lMOAB -lpnetcdf -lnetcdf -lpnetcdf  -lhdf5    -lpthread -lz -ldl -lm     -lpthread -lz -ldl -lm

MOAB_CXX = mpicxx
MOAB_CC  = mpicc
MOAB_FC  = mpif90
MOAB_F77  = mpif77

# Override MOAB_LIBDIR and MOAB_INCLUDES from above with the correct
# values for the installed MOAB.

MOAB_LIBDIR=/home/xu/research/softwares/sharp_dependencies/moab-4.8.1/lib
MOAB_INCLUDES=-I/home/xu/research/softwares/sharp_dependencies/moab-4.8.1/include
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# MOAB_DIR points to top-level install dir, below which MOAB's lib/ and include/ are located
MOAB_DIR := /home/xu/research/softwares/sharp_dependencies/moab-4.8.1
include ${MOAB_DIR}/lib/moab.make
include ${MOAB_DIR}/lib/iMesh-Defs.inc

.SUFFIXES: .o .cpp .F90

# MESH_DIR is the directory containing mesh files that come with MOAB source
MESH_DIR="/home/xu/research/softwares/sharp_dependencies/source/moab-4.8.1/MeshFiles/unittest"

EXAMPLES = HelloMOAB GetEntities SetsNTags LoadPartial structuredmesh StructuredMeshSimple DirectAccessWithHoles DirectAccessNoHoles point_in_elem_search VisTags UniformRefinement
PAREXAMPLES = HelloParMOAB ReduceExchangeTags LloydRelaxation CrystalRouterExample ReadWriteTest GenLargeMesh
EXOIIEXAMPLES = TestExodusII
F90EXAMPLES = DirectAccessNoHolesF90 PushParMeshIntoMoabF90
ERROREXAMPLES = ErrorHandlingSimulation TestErrorHandling TestErrorHandlingPar

default: ${EXAMPLES} ${PAREXAMPLES} ${EXOIIEXAMPLES} ${F90EXAMPLES} ${ERROREXAMPLES}

HelloMOAB: HelloMOAB.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

GetEntities: GetEntities.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

SetsNTags: SetsNTags.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

LloydRelaxation: LloydRelaxation.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

LoadPartial: LoadPartial.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK} ${MOAB_LIBS_LINK}

structuredmesh: structuredmesh.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

StructuredMeshSimple: StructuredMeshSimple.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

DirectAccessWithHoles: DirectAccessWithHoles.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

DirectAccessNoHoles: DirectAccessNoHoles.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

DirectAccessNoHolesF90: DirectAccessNoHolesF90.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_FC} -o $@ $< ${IMESH_LIBS}

ReduceExchangeTags: ReduceExchangeTags.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

HelloParMOAB: HelloParMOAB.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

CrystalRouterExample: CrystalRouterExample.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

TestExodusII: TestExodusII.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

point_in_elem_search: point_in_elem_search.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

PushParMeshIntoMoabF90: PushParMeshIntoMoabF90.o
	${MOAB_FC} -o $@ $< ${IMESH_LIBS}

VisTags: VisTags.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

ReadWriteTest: ReadWriteTest.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

GenLargeMesh: GenLargeMesh.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

ErrorHandlingSimulation: ErrorHandlingSimulation.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

TestErrorHandling: TestErrorHandling.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

TestErrorHandlingPar: TestErrorHandlingPar.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK} 

UniformRefinement: UniformRefinement.o ${MOAB_LIBDIR}/libMOAB.la
	${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}

clean:
	rm -rf *.o *.mod *.h5m ${EXAMPLES} ${PAREXAMPLES} ${EXOIIEXAMPLES} ${F90EXAMPLES} ${ERROREXAMPLES}

.cpp.o:
	${MOAB_CXX} ${CXXFLAGS} ${MOAB_CXXFLAGS} ${MOAB_CPPFLAGS} ${MOAB_INCLUDES} -DMESH_DIR=\"${MESH_DIR}\" -c $<

.F90.o:
	${IMESH_FC} ${FCFLAGS} ${IMESH_FCFLAGS} ${MOAB_CPPFLAGS} ${IMESH_INCLUDES} ${IMESH_FCDEFS} -DMESH_DIR=\"${MESH_DIR}\" -c $<
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