Mehdi,
I can't say for sure, but I remember encountering errors like that
pretty frequently when I ran meep-mpi with HDF5 on machines using
typical network file systems (NFS). I attributed the problem to too
much latency in the input/output process. When I switched to a
cluster environment with faster file systems like BlueArc NFS and
Panasas I no longer encountered the problem. What sort of file system
are you writing data to?
Best,
Alex
____________________________________________________________________
Alexander S. McLeod
B.A. Physics and Astrophysics - University of California at Berkeley
Simulation Engineer - Theory Group, Molecular Foundry (LBNL)
Site Lead - Network for Computational Nanotechnology at Berkeley / MIT
[email protected] 707-853-0716
____________________________________________________________________
On Aug 7, 2010, at 9:00 AM, [email protected]
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Today's Topics:
1. Problem with meep-mpi and HDF5 (mehdi kamali)
From: mehdi kamali <[email protected]>
Date: August 7, 2010 12:12:59 AM PDT
To: [email protected]
Subject: [Meep-discuss] Problem with meep-mpi and HDF5
Hello dear Steven and Meep users
I have a laptop with 4-core intel cpu Ubuntu 10.04 on it.
first as i saw on unbuntu packge manager website, i installed meep-
mpi 1.1.1 with hdf5-serial 1.8.4 but when i run meep for an example
it sounds the following error :
HDF5-DIAG: Error detected in HDF5 (1.8.4) MPI-process 0:
#000: ../../../src/H5F.c line 1512 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: ../../../src/H5F.c line 1307 in H5F_open(): unable to read
superblock
major: File accessability
minor: Read failed
#002: ../../../src/H5Fsuper.c line 322 in H5F_super_read(): unable
to load superblock
major: Object cache
minor: Unable to protect metadata
#003: ../../../src/H5AC.c line 1831 in H5AC_protect():
H5C_protect() failed.
major: Object cache
minor: Unable to protect metadata
#004: ../../../src/H5C.c line 6160 in H5C_protect(): can't load
entry
major: Object cache
minor: Unable to load metadata into cache
#005: ../../../src/H5C.c line 10990 in H5C_load_entry(): unable to
load entry
major: Object cache
minor: Unable to load metadata into cache
#006: ../../../src/H5Fsuper_cache.c line 467 in H5F_sblock_load():
truncated file
major: File accessability
minor: File has been truncated
HDF5-DIAG: Error detected in HDF5 (1.8.4) MPI-process 0:
#000: ../../../src/H5Ddeprec.c line 221 in H5Dopen1(): not a
location
major: Invalid arguments to routine
minor: Inappropriate type
#001: ../../../src/H5Gloc.c line 241 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.4) MPI-process 0:
#000: ../../../src/H5D.c line 420 in H5Dget_space(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.4) MPI-process 0:
#000: ../../../src/H5S.c line 743 in H5Sget_simple_extent_ndims():
not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
meep: error on line 549 of ../../../src/h5file.cpp: file data is
inconsistent rank for subsequent extend_data
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_4481: p4_error: : 1
so i thought maybe it is because of serial version of hdf5, so i
reinstalled the meep-mpi with hdf5-mpich but there is tha error yet!
by the way, i used " mpirun -np 4 meep-mpi filename.ctl"
it will be great if someone helps me .
Sincerely yours
Mehdi
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