[FLASH-USERS] problem with FLASH2.5/source/mesh/amr/init_mesh.F90 on zeus.llnl.gov
Clint Young
cyoung at grad.physics.sunysb.edu
Tue May 8 15:15:46 CDT 2007
On Tue, 8 May 2007, Christopher W. Mauche wrote:
> Dear fellow FLASHers,
>
> I just downloaded a new clean version of flash v2.5 to zeus.llnl.gov, and
> attempted to test/verify it by running the sedov test problem. I was able to
> unpack and compile the code, but find an error when I run it. Specifically:
>
> > ./setup sedov -auto
> > gmake
> > cd object
> > cp ../setups/sedov/flash.par flash.par
> > srun -N1 -n2 -p pdebug flash2
> "get_parm_from_context: igeomx,igeomy,igeomz: 4599616371426034975
> 4621819117588971520 4591870180066957722"
> ERROR: invalid mesh geometry, check igeom{x,y,z}
> "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1"
> [1] [MPI Abort by user] Aborting Program!
> srun: mvapich: May 08 11:18:01: ABORT from MPI rank 1 [on zeus13]
> srun: error: zeus13: task1: Exited with exit code 1
> srun: error: zeus13: task0: Killed
>
> where the lines in quotes are from a print statement I added to
> FLASH2.5/source/mesh/amr/init_mesh.F90 [just below the line
> "call get_parm_from_context(GLOBAL_PARM_CONTEXT, "igeomz", igeomz)"],
> which is the source of the error. It appears that igeom{x,y,z} is read in
> properly by one of the processors, but not by the second one.
>
> If I restrict the run to one processor, I get a different error:
>
> > srun -N1 -n1 -p pdebug flash2
> "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1"
> flash: initializing for sedov problem.
> p_ambient = 1.00000000000000008E-5
> rho_ambient= 1.
> gamma = 1.3999999999999999
> exp_energy = 1.
> r_init = 1.3671875E-2
> p_exp = 681.16756574500903
> xctr = 0.5
> yctr = 0.5
> zctr = 0.5
> ndim = 2
> nsubzones = 7
> 0 - MPI_SSEND : Invalid rank 1
> [0] [] Aborting Program!
> srun: mvapich: May 08 11:23:39: ABORT from MPI rank 0 [on zeus13]
> srun: error: zeus13: task0: Exited with exit code 70
>
> Does anyone have an idea what might be causing these problems, and what I can do
> about them? Please note that Flash v2.5 _used_ to work for me on zeus, but now
> it fails with these errors.
>
> Thanks,
> Chris Mauche
>
> PS: For the record, my FLASH2.5/source/sites/zeus.llnl.gov/Makefile.h is:
>
> # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux
> # Created for zeus.llnl.gov by nathan and cal.
> #
> # Fedora Core 3
> # Intel Linux Fortran 9.0
> # hdf5-1.6.5 (icc90)
> # mpich-1.2.7 (icc90)
>
> #----------------------------------------------------------------------------
> # Set the HDF/HDF5 library paths -- these need to be updated for your system
> #----------------------------------------------------------------------------
>
> MPI_PATH =
> HDF4_PATH =
> HDF5_PATH =
> /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel
>
> ZLIB_PATH =
>
> PAPI_PATH =
> PAPI_FLAGS =
>
> NCMPI_PATH =
> MPE_PATH =
>
> #----------------------------------------------------------------------------
> # Compiler and linker commands
> #
> # We use the f90 compiler as the linker, so some C libraries may explicitly
> # need to be added into the link line.
> #----------------------------------------------------------------------------
>
> FCOMP = mpipathf90
> CCOMP = mpipathcc
> CPPCOMP = mpipathCC
> LINK = mpipathf90
>
> # pre-processor flag
>
> PP = -D
>
> #-----------------------------------------------------------------------------
> # Compilation flags
> #
> # Three sets of compilation/linking flags are defined: one for optimized code
> # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test").
> # Passing these flags to the setup script will cause the value associated with
> # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to
> # be incorporated into the final Makefile. For example, passing "-opt" to the
> # setup script will cause the flags following "FFLAGS_OPT" to be assigned to
> # "FFLAGS" in the final Makefile. If none of these flags passed, the default
> # behavior will match that of the "-opt" flag.
> # In general, "-opt" is meant to optimize compilation and linking. "-debug"
> # should enable runtime bounds checking, debugger symbols, and other compiler-
> # specific debugging options. "-test" is useful for testing different
> # combinations of compiler flags particular to your individual system.
> #----------------------------------------------------------------------------
>
> FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g
> FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check
> output_conversion -warn all -real_size 64
> FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64
>
>
> CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g
> CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE
> CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE
>
> CFLAGS_HDF5 = -I $(HDF5_PATH)/include
> CFLAGS_NCMPI = -I $(NCMPI_PATH)/include
> CFLAGS_MPI = -I$(MPI_PATH)/include
>
> #----------------------------------------------------------------------------
> # Linker flags
> #
> # There is a seperate version of the linker flags for each of the _OPT,
> # _DEBUG, and _TEST cases.
> #----------------------------------------------------------------------------
>
> LFLAGS_OPT = -r8 -i8 -Ur -g -o
> LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o
> LFLAGS_TEST = -r8 -i4 -Vaxlib -o
>
> #----------------------------------------------------------------------------
> # Library specific linking
> #
> # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to
> # create a macro in this Makefile.h for LIB_xxx, which will be added to the
> # link line when FLASH is built. This allows us to switch between different
> # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST
> # library macro to add any performance-minded libraries (like fast math),
> # depending on how FLASH was setup.
> #----------------------------------------------------------------------------
>
> LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg
> LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz
> LIB_PNG = -lpng
>
> LIB_MPI =
> LIB_NCMPI =
> LIB_MPE =
>
>
> #----------------------------------------------------------------------------
> # Additional machine-dependent object files
> #
> # Add any machine specific files here -- they will be compiled and linked
> # when FLASH is built.
> #----------------------------------------------------------------------------
>
> MACHOBJ =
>
> #----------------------------------------------------------------------------
> # Additional commands
> #----------------------------------------------------------------------------
>
> MV = mv -f
> AR = ar -r
> RM = rm -f
> CD = cd
> RL = ranlib
> ECHO = echo
>
> zeus287{mauche}445: cat Makefile.h
> # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux
> # Created for zeus.llnl.gov by nathan and cal.
> #
> # Fedora Core 3
> # Intel Linux Fortran 9.0
> # hdf5-1.6.5 (icc90)
> # mpich-1.2.7 (icc90)
>
> #----------------------------------------------------------------------------
> # Set the HDF/HDF5 library paths -- these need to be updated for your system
> #----------------------------------------------------------------------------
>
> MPI_PATH =
> HDF4_PATH =
> HDF5_PATH =
> /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel
>
> ZLIB_PATH =
>
> PAPI_PATH =
> PAPI_FLAGS =
>
> NCMPI_PATH =
> MPE_PATH =
>
> #----------------------------------------------------------------------------
> # Compiler and linker commands
> #
> # We use the f90 compiler as the linker, so some C libraries may explicitly
> # need to be added into the link line.
> #----------------------------------------------------------------------------
>
> FCOMP = mpipathf90
> CCOMP = mpipathcc
> CPPCOMP = mpipathCC
> LINK = mpipathf90
>
> # pre-processor flag
>
> PP = -D
>
> #-----------------------------------------------------------------------------
> # Compilation flags
> #
> # Three sets of compilation/linking flags are defined: one for optimized code
> # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test").
> # Passing these flags to the setup script will cause the value associated with
> # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to
> # be incorporated into the final Makefile. For example, passing "-opt" to the
> # setup script will cause the flags following "FFLAGS_OPT" to be assigned to
> # "FFLAGS" in the final Makefile. If none of these flags passed, the default
> # behavior will match that of the "-opt" flag.
> # In general, "-opt" is meant to optimize compilation and linking. "-debug"
> # should enable runtime bounds checking, debugger symbols, and other compiler-
> # specific debugging options. "-test" is useful for testing different
> # combinations of compiler flags particular to your individual system.
> #----------------------------------------------------------------------------
>
> FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g
> FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check
> output_conversion -warn all -real_size 64
> FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64
>
>
> CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g
> CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE
> CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE
>
> CFLAGS_HDF5 = -I $(HDF5_PATH)/include
> CFLAGS_NCMPI = -I $(NCMPI_PATH)/include
> CFLAGS_MPI = -I$(MPI_PATH)/include
>
> #----------------------------------------------------------------------------
> # Linker flags
> #
> # There is a seperate version of the linker flags for each of the _OPT,
> # _DEBUG, and _TEST cases.
> #----------------------------------------------------------------------------
>
> LFLAGS_OPT = -r8 -i8 -Ur -g -o
> LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o
> LFLAGS_TEST = -r8 -i4 -Vaxlib -o
>
> #----------------------------------------------------------------------------
> # Library specific linking
> #
> # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to
> # create a macro in this Makefile.h for LIB_xxx, which will be added to the
> # link line when FLASH is built. This allows us to switch between different
> # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST
> # library macro to add any performance-minded libraries (like fast math),
> # depending on how FLASH was setup.
> #----------------------------------------------------------------------------
>
> LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg
> LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz
> LIB_PNG = -lpng
>
> LIB_MPI =
> LIB_NCMPI =
> LIB_MPE =
>
>
> #----------------------------------------------------------------------------
> # Additional machine-dependent object files
> #
> # Add any machine specific files here -- they will be compiled and linked
> # when FLASH is built.
> #----------------------------------------------------------------------------
>
> MACHOBJ =
>
> #----------------------------------------------------------------------------
> # Additional commands
> #----------------------------------------------------------------------------
>
> MV = mv -f
> AR = ar -r
> RM = rm -f
> CD = cd
> RL = ranlib
> ECHO = echo
>
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