Dear all,
I am implementing a parallel IO solution based on ADIOS into a
structured flow solver, in order to replace an CGNS host slave approach
with is not competitive for HPC.
In this context, it seems using PHDF5 requires each process writes the
same quantity of data, or more precisely, each process have to call the
write functions N times per process. If I do not make mistake, it is due
to some synchronous MPI function.
Here the back trace of a process while my host, which does not write
anything, is waiting into the close function:
#0 0x00007f4ce7e45d05 in raise (sig=6) at
../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1 0x00007f4ce7e49ab6 in abort () at abort.c:92
#2 0x00007f4ce7e7ed7b in __libc_message (do_abort=2, fmt=0x7f4ce7f67400
"*** glibc detected *** %s: %s: 0x%s ***\n") at
../sysdeps/unix/sysv/linux/libc_fatal.c:189
#3 0x00007f4ce7e88bb6 in malloc_printerr (action=3, str=0x7f4ce7f67980
"malloc(): memory corruption (fast)", ptr=<value optimized out>) at
malloc.c:6283
#4 0x00007f4ce7e8be78 in _int_malloc (av=0x7f4ce81a11c0, bytes=<value
optimized out>) at malloc.c:4308
#5 0x00007f4ce7e8e31e in __libc_malloc (bytes=48) at malloc.c:3660
#6 0x0000000001a792ac in H5FL_blk_malloc ()
#7 0x0000000001a7945d in H5FL_blk_calloc ()
#8 0x0000000001abaf7b in H5O_create ()
#9 0x0000000001a88166 in H5G_obj_create_real ()
#10 0x0000000001a8859f in H5G_obj_create ()
#11 0x0000000001a7cab5 in H5G_create ()
#12 0x0000000001bf9ec0 in H5O_group_create ()
#13 0x0000000001ac0446 in H5O_obj_create ()
#14 0x0000000001ab2076 in H5L_link_cb ()
#15 0x0000000001a8e140 in H5G_traverse_real ()
#16 0x0000000001a8e50b in H5G_traverse ()
#17 0x0000000001aaef08 in H5L_create_real ()
#18 0x0000000001ab2c9a in H5L_link_object ()
#19 0x0000000001a7b396 in H5G_create_named ()
#20 0x0000000001a7f1cb in H5Gcreate1 ()
#21 0x0000000001a05d85 in hw_gopen ()
#22 0x0000000001a04a5c in hw_var ()
#23 0x0000000001a036ae in adios_phdf5_write ()
#24 0x00000000019a5207 in common_adios_write ()
#25 0x00000000019a4786 in adios_write ()
So, does someone has any idea? Does HDF5 in parallel forces all the
processes to write the same quantity of data or did I make a mistake?...
Thanks for your help.
--
/
Mathieu Gontier
skype: mathieu_gontier /
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