Error getting document path: TypeError: win is null
solution: allow the browwer to open pop ups (Preferences /allow...)
Error performing special action discretizeProblem: AGDMException: External error (AGDMException: Schema not applicable to this problem (The operator all does not have compatible spatial discretization.))
solution: the operator has different names in the model and in the discretization policy (change it in the latter)
It does not generate the equations for a new field
solution: in the problem/regions, one has to add the new field either in the high order or low order discretization groups.
ld: warning: libhdf5.so.103, needed by /gpfs/projects/uib46/apps/SAMRAI_4.1.0//lib/libSAMRAI_algs.so, not found (try using -rpath or -rpath-link)
solution: SAMRAI has been compiled with a version of hdf5 that can not find (i.e., it is not in the PATH) (module show hdf5/1.10.5_serial to know what is the path of the library in HDF5_HOME=/apps/HDF5/1.10.5/INTEL/SERIAL)
usr/bin/ld: /home/palen/Lorene/Lib/liblorenef77.a(integrale2d.o): undefined reference to symbol '_gfortran_transfer_real_write@@GFORTRAN_8' /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libgfortran.so.5: error adding symbols: DSO missing from command line
solution: add -lgfortran in LIBS
LIBS= $(EXTERNAL_LIB) -L$(LORENE_HOME)/Lib -L$(MPI_HOME)/lib -L$(HDF5_HOME)/lib -L$(SAMRAI_HOME)/lib -lSAMRAI_algs -lSAMRAI_appu -lSAMRAI_geom -lSAMRAI_hier -lSAMRAI_math -lSAMRAI_mesh -lSAMRAI_pdat -lSAMRAI_solv -lSAMRAI_tbox -lSAMRAI_xfer -lmpi -lmpi_cxx -llorene_export -llorene -llorenef77 -ldl -lpthread -lutil -lhdf5 -lgsl -lgslcblas -llapack -lblas -lX11 -lfftw3 -lstdc++ -lgfortran -lm
command line warning #10006: ignoring unknown option '-fno-signaling-nans' In file included from /gpfs/projects/uib46/apps/SAMRAI_4.1.0_fuka/include/SAMRAI/hier/GlobalId.h(16), from /gpfs/projects/uib46/apps/SAMRAI_4.1.0_fuka/include/SAMRAI/hier/BoxId.h(18), from /gpfs/projects/uib46/apps/SAMRAI_4.1.0_fuka/include/SAMRAI/hier/Box.h(16), from TimeInterpolateOperator.h(17), from TimeInterpolator.h(14), from TimeInterpolator.C(10): /gpfs/projects/uib46/apps/SAMRAI_4.1.0_fuka/include/SAMRAI/tbox/SAMRAI_MPI.h(20): catastrophic error: cannot open source file "mpi.h" #include "mpi.h" ^
solution: it is not finding the path to the MPI include
/lib -L/opt/hdf5_parallel/lib -L/opt/amrex_3D/lib -pthread -lamrex -lmpi -lmpi_cxx -lquadmath -lhdf5 -lgfortran /usr/bin/ld: /home/palen/Programs/Lorene/Lib/liblorene.a(solh_helmholtz_minus.o): undefined reference to symbol 'gsl_sf_bessel_il_scaled' /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libgsl.so.27: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status
solution: gsl library missing in the Makefile
g++ AdvanceLevel.o AmrCoreProblem.o AMReX_FillPatchUtil_mod.o Commons.o ExternalInitialData.o Functions.o HDF5DataWriter.o IntegrateDataWriter.o LagrangianPolynomicInterpolater.o main.o PointDataWriter.o SliceDataWriter.o SphereDataWriter.o -o main -L/opt/Reprimand_1.4/lib/x86_64-linux-gnu -lRePrimAnd -L/usr/lib/x86_64-linux-gnu/openmpi/lib -L/opt/hdf5_parallel/lib -L/opt/amrex_3D/lib -pthread -lamrex -lmpi -lmpi_cxx -lquadmath -lhdf5 -lgsl -lgfortran /home/palen/Programs/fuka/lib/libkadath.a -lgsl -lfftw3 -llapack -lblas /usr/bin/ld: AmrCoreProblem.o: undefined reference to symbol 'omp_in_parallel@@OMP_1.0' /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libgomp.so.1: error adding symbols: DSO missing from command line
solution: -fopenmp missing in the Makefile
main: $(OBJECTS) $(CXX) -fopenmp $(LINKCUDA) $^ -o $@ $(LFLAGS)
./main_fuka: symbol lookup error: ./main_fuka: undefined symbol: _ZN5amrex13BLProfileSync15StartSyncRegionEPKc
solution: the path in the Makefile of AMReX does not match the one in LD_LIBRARY_PATH
ld: /gpfs/projects/uib46/apps/Lorene2/Lib/liblorenef77.a(tfmzs.o): undefined reference to symbol 'for_write_seq_fmt' /apps/ONEAPI/2022.3.0.8767/compiler/2022.2.0/linux/compiler/lib/intel64/libifcoremt.so.5: error adding symbols: DSO missing from command line
solution: -lifcoremt missing in the Makefile, put it at the very end
CFLAGS= -std=c++17 -I. $(EXTERNAL_INCLUDE) -I$(MPI_HOME)/include64 -I$(HDF5_HOME)/include -I$(SAMRAI_HOME)/include $(FUKA_INCLUDE) $(LORENE_INCLUDE) LIBS= $(EXTERNAL_LIB) $(LORENE_LIBS) -L$(MPI_HOME)/lib -L$(HDF5_HOME)/lib -L$(SAMRAI_HOME)/lib -lSAMRAI_algs -lSAMRAI_appu -lSAMRAI_geom -lSAMRAI_hier -lSAMRAI_math -lSAMRAI_mesh -lSAMRAI_pdat -lSAMRAI_solv -lSAMRAI_tbox -lSAMRAI_xfer -ldl -lpthread -lutil -lhdf5 -lgsl -lX11 -lfftw3 -lstdc++ -lm $(FUKA_LIBS) -mkl -lifcoremt