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

[huong luu]

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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