hic hic,<div>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.</div><div><br></div>
<div>I'll go through the page from hdfgroup to see if there's anyway to fix my problem. Thanks a lot anyway.</div><div>:)</div><div><br></div><div>Huong<br><br><div class="gmail_quote">On Wed, Mar 31, 2010 at 4:18 PM, Samuel Friedman <span dir="ltr"><<a href="mailto:friedman@astro.wisc.edu">friedman@astro.wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">I had errors like this before. My problem was that I was not correctly<br>
interfacing with HDF5 because of intergace issues.<br>
<br>
See this webpage for an overview:<br>
<br>
<a href="http://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html" target="_blank">http://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html</a><br>
<br>
My solution was essentially to set this line in my Makefile.h file:<br>
<br>
CFLAGS_HDF5 = -I $(HDF5_PATH)/include -D H5_USE_16_API<br>
<br>
Now my version of HDF5 is serial. But I definitely saw errors like you<br>
had and they went away with the flag change.<br>
<br>
Sam<br>
<div><div></div><div class="h5"><br>
On Wed, 31 Mar 2010, huong luu wrote:<br>
<br>
> Hi,<br>
> I am a newbie to Flash and I am trying to get FLASH code running (any<br>
> simulation problem is good).<br>
> I have install MPICH2, HDF5-1.8.4 (with default api version = v1.6 and<br>
> enable parallel). I did successfully make the executable file flash3 appear.<br>
> However, when I run it, then it has error detected. The weird thing is I<br>
> tried with Sedov, Sod, Pancake problem and all of them have similar error<br>
> messages.<br>
> For more details, here is what I did:<br>
><br>
> ./setup Sedov -auto<br>
> cd object<br>
> gmake<br>
> cp ../source/Simulation/SimulationMain/Sedov/flash.par ./<br>
> ./flash3<br>
><br>
> ===><br>
> <some initial computation result here><br>
> MaterialProperties initialized<br>
> Cosmology initialized<br>
> Source terms initialized<br>
> iteration, no. not moved = 0 0<br>
> refined: total leaf blocks = 1<br>
> refined: total blocks = 1<br>
> ......<br>
> Gravity initialized<br>
> Initial dt verified<br>
> HDF5-DIAG: Error detected in HDF5 library version: 1.6.4 MPI-process 0.<br>
> Back trace follows.<br>
> #000: H5D.c line 1145 in H5Dopen(): not found<br>
> major(15): Dataset interface<br>
> minor(48): Object not found<br>
> #001: H5G.c line 2334 in H5G_find(): object not found<br>
> major(10): Symbol table layer<br>
> minor(48): Object not found<br>
> #002: H5G.c line 1531 in H5G_namei(): component not found<br>
> major(10): Symbol table layer<br>
> minor(48): Object not found<br>
> #003: H5Gstab.c line 169 in H5G_stab_find(): not found<br>
> major(10): Symbol table layer<br>
> minor(48): Object not found<br>
> #004: H5Gnode.c line 984 in H5G_node_found(): not found<br>
> major(10): Symbol table layer<br>
> minor(48): Object not found<br>
> Driver_abortC called<br>
> Error: H5Dopen io_h5write_lrefine<br>
><br>
> Calling MPI_Abort for immediate shutdown<br>
> [0] MPI Abort by user Aborting program !<br>
> [0] Aborting program!<br>
> p0_20283: p4_error: : 1<br>
><br>
> =============================================<br>
><br>
> I tried it again with Sod and Pancake:<br>
><br>
> ./setup Sod -auto<br>
> cd object<br>
> gmake<br>
> cp ../source/Simulation/SimulationMain/Sod/flash.par ./<br>
> ./flash3<br>
> ----------> Here's what I got:<br>
><br>
> MaterialProperties initialized<br>
> Cosmology initialized<br>
> Source terms initialized<br>
> iteration, no. not moved = 0 0<br>
> refined: total leaf blocks = 1<br>
> refined: total blocks = 1<br>
> .................<br>
><br>
> Gravity initialized<br>
> Initial dt verified<br>
> HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) MPI-process 0:<br>
> #000: H5Ddeprec.c line 232 in H5Dopen1(): not found<br>
> major: Dataset<br>
> minor: Object not found<br>
> #001: H5Gloc.c line 468 in H5G_loc_find(): can't find object<br>
> major: Symbol table<br>
> minor: Object not found<br>
> #002: H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal<br>
> failed<br>
> major: Symbol table<br>
> minor: Object not found<br>
> #003: H5Gtraverse.c line 703 in H5G_traverse_real(): traversal operator<br>
> failed<br>
> major: Symbol table<br>
> minor: Callback failed<br>
> #004: H5Gloc.c line 423 in H5G_loc_find_cb(): object doesn't exist<br>
> major: Symbol table<br>
> minor: Object not found<br>
> Driver_abortC called<br>
> Error: H5Dopen io_h5write_lrefine<br>
><br>
> Calling MPI_Abort for immediate shutdown<br>
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0<br>
><br>
><br>
> Everything starts to get wrong after Gravity initialized and Initial dt<br>
> verified.<br>
><br>
> I don't know what's wrong with my compilation/configuration. Could anyone<br>
> give me some advices?<br>
><br>
> I attach here my Makefile.h.<br>
><br>
> Thanks in advance<br>
> Huong Luu<br>
><br>
</div></div></blockquote></div><br></div>