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

[huong luu]

hic hic,
Thanks for your suggestion but it seems not working in my case :(. I add the
suggested flag option into my Makefile and nothing change. I tried it with
both serial and parallel version of HDF5.

I'll go through the page from hdfgroup to see if there's anyway to fix my
problem. Thanks a lot anyway.
:)

Huong

On Wed, Mar 31, 2010 at 4:18 PM, Samuel Friedman <friedman at astro.wisc.edu>wrote:

> 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
> >
>
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