[FLASH-USERS] Flash I/O Benchmark fails

[Islam, Tanzima]

Fixed the problem. Thought might be useful for other people: after comparing with a previous makefile that worked, I found that this problem started appearing after I started using a newer version of HDF5 library. Changed it to an old version and it started working again. 

Thanks,
--Tanzima

On Sep 13, 2013, at 2:51 PM, "Islam, Tanzima" <islam3 at llnl.gov> wrote:

> 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)
> ***********************************************************************************************