[FLASH-USERS] Error detected in HDF5 while running ./flash3 for Sedov, Sod, Pancake, ...

[Samuel Friedman]

I had errors like this before.  My problem was that I was not correctly 
interfacing with HDF5 because of intergace issues.  

See this webpage for an overview:

http://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html

My solution was essentially to set this line in my Makefile.h file:

CFLAGS_HDF5  = -I $(HDF5_PATH)/include -D H5_USE_16_API

Now my version of HDF5 is serial.  But I definitely saw errors like you 
had and they went away with the flag change.

Sam

On Wed, 31 Mar 2010, huong luu wrote:

> Hi,
> I am a newbie to Flash and I am trying to get FLASH code running (any
> simulation problem is good).
> I have install MPICH2, HDF5-1.8.4 (with default api version = v1.6 and
> enable parallel). I did successfully make the executable file flash3 appear.
> However, when I run it, then it has error detected. The weird thing is I
> tried with Sedov, Sod, Pancake problem and all of them have similar error
> messages.
> For more details, here is what I did:
> 
> ./setup Sedov -auto
> cd object
> gmake
> cp ../source/Simulation/SimulationMain/Sedov/flash.par ./
> ./flash3
> 
> ===>
> <some initial computation result here>
> MaterialProperties initialized
>  Cosmology initialized
>  Source terms initialized
>   iteration, no. not moved =            0           0
>  refined: total leaf blocks =            1
>  refined: total blocks =            1
> ......
> Gravity initialized
>  Initial dt verified
> HDF5-DIAG: Error detected in HDF5 library version: 1.6.4 MPI-process 0.
>  Back trace follows.
>   #000: H5D.c line 1145 in H5Dopen(): not found
>     major(15): Dataset interface
>     minor(48): Object not found
>   #001: H5G.c line 2334 in H5G_find(): object not found
>     major(10): Symbol table layer
>     minor(48): Object not found
>   #002: H5G.c line 1531 in H5G_namei(): component not found
>     major(10): Symbol table layer
>     minor(48): Object not found
>   #003: H5Gstab.c line 169 in H5G_stab_find(): not found
>     major(10): Symbol table layer
>     minor(48): Object not found
>   #004: H5Gnode.c line 984 in H5G_node_found(): not found
>     major(10): Symbol table layer
>     minor(48): Object not found
> Driver_abortC called
> Error: H5Dopen io_h5write_lrefine
> 
> Calling MPI_Abort for immediate shutdown
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_20283:  p4_error: : 1
> 
> =============================================
> 
> I tried it again with Sod and Pancake:
> 
> ./setup Sod -auto
> cd object
> gmake
> cp ../source/Simulation/SimulationMain/Sod/flash.par ./
> ./flash3
> ----------> Here's what I got:
> 
> MaterialProperties initialized
>  Cosmology initialized
>  Source terms initialized
>   iteration, no. not moved =            0           0
>  refined: total leaf blocks =            1
>  refined: total blocks =            1
> .................
> 
> Gravity initialized
>  Initial dt verified
> HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) MPI-process 0:
>   #000: H5Ddeprec.c line 232 in H5Dopen1(): not found
>     major: Dataset
>     minor: Object not found
>   #001: H5Gloc.c line 468 in H5G_loc_find(): can't find object
>     major: Symbol table
>     minor: Object not found
>   #002: H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal
> failed
>     major: Symbol table
>     minor: Object not found
>   #003: H5Gtraverse.c line 703 in H5G_traverse_real(): traversal operator
> failed
>     major: Symbol table
>     minor: Callback failed
>   #004: H5Gloc.c line 423 in H5G_loc_find_cb(): object doesn't exist
>     major: Symbol table
>     minor: Object not found
> Driver_abortC called
> Error: H5Dopen io_h5write_lrefine
> 
> Calling MPI_Abort for immediate shutdown
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> 
> 
> Everything starts to get wrong after Gravity initialized and Initial dt
> verified.
> 
> I don't know what's wrong with my compilation/configuration. Could anyone
> give me some advices?
> 
> I attach here my Makefile.h.
> 
> Thanks in advance
> Huong Luu
>