[FLASH-USERS] Flash I/O Benchmark fails

[Islam, Tanzima]

Hi Klaus,
On Sep 11, 2013, at 10:31 AM, Klaus Weide <klaus at flash.uchicago.edu> wrote:

> On Mon, 9 Sep 2013, Islam, Tanzima wrote:
> 
>> Hi,
>> I am a new user of the Flash Benchmark I/O code. I have been trying to generate HDF5 checkpoints from the benchmark application. I can compile successfully with parallel HDF5 library but it fails when I try to run the code.
>> 
>> This is my output from the compilation step:
>> /usr/local/tools/mvapich2-gnu-1.9/bin/mpif90 -c -DN_DIM=3 -DMAXBLOCKS=100 -DIONMAX=13  get_mfluid_property.F90
>> /usr/local/tools/mvapich2-gnu-1.9/bin/mpif90 -c -DN_DIM=3 -DMAXBLOCKS=100 -DIONMAX=13  flash_release.f
>> /usr/local/tools/mvapich2-gnu-1.9/bin/mpif90 -c -DN_DIM=3 -DMAXBLOCKS=100 -DIONMAX=13  flash_benchmark_io.F90
>> /usr/local/tools/mvapich2-gnu-1.9/bin/mpif90 -c -DN_DIM=3 -DMAXBLOCKS=100 -DIONMAX=13  checkpoint_hdf5_parallel.F90
>> /usr/local/tools/mvapich2-gnu-1.9/bin/mpif90 -c -DN_DIM=3 -DMAXBLOCKS=100 -DIONMAX=13  plotfile_hdf5_parallel.F90
>> /usr/local/tools/mvapich2-gnu-1.9/bin/mpicc -c -I /usr/local/tools/hdf5-gnu-parallel-1.8.10/include -DTFLOPS -DN_DIM=3 -DH5_USE_16_API h5_file_interface.c
>> /usr/local/tools/mvapich2-gnu-1.9/bin/mpicc -c -I /usr/local/tools/hdf5-gnu-parallel-1.8.10/include -DTFLOPS -DN_DIM=3 -DH5_USE_16_API h5_parallel_write.c
>> /usr/local/tools/mvapich2-gnu-1.9/bin/mpicc -c -I /usr/local/tools/hdf5-gnu-parallel-1.8.10/include -DTFLOPS -DN_DIM=3 -DH5_USE_16_API h5_parallel_write_single.c
> 
> 
> Hello,
> 
> I am not familiar with the "Flash Benchmark I/O code".  However, I notice 
> that your compiler flags don't include any for propagating all 
> Fortran reals to double precision. Those are alwaus neededs when compiling 
> FLASH. Something like, in the case of GNU compilers, 
> 
>   -fdefault-real-8 -fdefault-double-8
> 
> HTH,
> Klaus

Thank you for the flags. However, it still does not work and I think the problem is with a missing compilation flag that enable proper woring of MPI datatypes. Is there anyone who has compiled this code on a simple linux machine? I will apprecaite your compilation flags if it is different from mine (listed following):


*********************************************** Makefile.linux ************************************************
# compiler and linker commands
FCOMP   = /usr/local/tools/mvapich2-gnu-1.9/bin/mpif90
CCOMP   = /usr/local/tools/mvapich2-gnu-1.9/bin/mpicc
CPPCOMP = /usr/local/tools/mvapich2-gnu-1.9/bin/mpic++
LINK    = /usr/local/tools/mvapich2-gnu-1.9/bin/mpif90 


# library locations
HDF5path = /usr/local/tools/hdf5-gnu-parallel-1.8.10
ZLIBpath = /usr

# compiler flags
FFLAGS = -c \
         -DN_DIM=3 -DMAXBLOCKS=100 -DIONMAX=13 

F90FLAGS = -fdefault-real-8 -fdefault-double-8

CFLAGS = -c -O3 -I$(HDF5path)/include -I/usr/local/tools/mvapich2-gnu-1.9/include -DN_DIM=3 -DH5_USE_16_API -DTFLOPS -DCHUNK


# linker flags
LFLAGS = -L$(HDF5path)/lib -L$(ZLIBpath) -L/usr/local/tools/mvapich2-gnu-1.9/lib -o 

# libraries to include
LIB = -lhdf5 -lz 

.SUFFIXES: .f .F .f90 .F90 .c .C .o

.F90.o :
	$(FCOMP) $(F90FLAGS) $(FFLAGS) $<

.f.o :
	$(FCOMP) $(F90FLAGS) $(FFLAGS) $<

.c.o :
	$(CCOMP) $(CFLAGS) $<

flash_benchmark_io: $(OBJS) \
                    $(OBJS_HDF5_PARALLEL_IO) 
	$(LINK) $(LFLAGS) $@ $(OBJS) $(OBJS_HDF5_PARALLEL_IO) $(LIB)
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