Using hdf5 1.8.17, I ran your program on a lustre system using Cray’s mpi
wrappers for the intel compiler on 3072, 1536, 1200, 2016 processes with no
issues (it completed in under 20s). If you have not already done so, you might
want to make sure the hdf5 parallel test programs all passed.
FYI, I managed to get it to compile by adding the static flag for the compiler,
I had to hard code the option in cmake. Here is what I used to compile it,
cmake \
-D CMAKE_C_FLAGS:STRING="-g" \
-D CMAKE_Fortran_FLAGS:STRING="-g -static" \
-D CMAKE_BUILD_TYPE:STRING="Debug" \
-D XH5For_ENABLE_HDF5=ON \
-D XH5For_ENABLE_MPI=ON \
-D XH5For_ENABLE_TESTS=ON \
-D XH5For_ENABLE_EXAMPLES=ON \
-D BUILD_SHARED_LIBS=OFF \
-D HDF5_INCLUDE_DIRS:PATH=$HDF5_DIR/include \
-D HDF5_LIBRARY_DIRS:PATH=$HDF5_DIR/lib \
$XH5For
Scot
On Jul 26, 2016, at 11:09 AM, victor sv
<[email protected]<mailto:[email protected]>> wrote:
Hi Scott,
thanks for your response.
I've tried with GNU compilers, OpenMPI and HDF5 (1.8.15, 1.8.16, 1.18.17), but
in a local scope or small cluster, not in Marenostrum.
Ok, I'm going to try to compile all this tools to reproduce this environment
and I will tell you if there are some news.
Can you report the compilation errors you are talking about? I can help you in
this point or fix any issue!
Thank you again for your effort!
Víctor.
2016-07-26 16:41 GMT+02:00 Scot Breitenfeld
<[email protected]<mailto:[email protected]>>:
I suspect that it is an issue with the impi implementation. I have not been
able to compile your code on our systems due to various compilation errors
(this is using a different compiler as I don’t have access to impi). Have you
tried using mpich (or some other mpi implementation) instead to see if that
works? Also, have you tried using 1.10.0?
Scot
On Jul 23, 2016, at 1:12 PM, victor sv
<[email protected]<mailto:[email protected]>> wrote:
Hi again,
In order to help to understand what is happening, I've implemented and example
using the HDF5 library.
You can see it in the following link:
https://github.com/victorsndvg/XH5For/blob/master/src/examples/hdf5_performance_test/ch_unstructured_hexahedron_perf.f90
I've compiled and launched it reproducing the previous mail and I'm getting the
same behavior/errors with the new code.
I also compiled and linked against HDF5 1.8.17 by myself with the same results.
I'm not using any tunning hint ... this could be the problem?
Thanks!
Víctor
2016-07-19 11:08 GMT+02:00 victor sv
<[email protected]<mailto:[email protected]>>:
Hi all,
I'm developing XH5For<https://github.com/victorsndvg/XH5For>, an OO fortran
light-weight XDMF/HDF5 layer, and now I would like to test its scalability, but
I'm lost with an issue that i'm getting.
I'm going to try to explain it as best as I can.
I'm performing some weak scalability tests on Marenostrum
III<http://www.bsc.es/user-support/mn3.php> (GPFS file system) using Collective
Writing with the Contiguous HyperSlab strategy. I'm running tests with 1, 16,
32, 64, 128, 256, 512, 1024 and 2048 MPI tasks.
All seems to work as expected except for the 2048 MPI tasks test, where I think
I'm getting an MPI interlock (it's still running without doing anything till
the job time exceeds and the job is killed).
After that, i try to reproduce an error with a number of MPI tasks between
1024-2048, and I could get the following error message while launching a
smaller size job, with 1164 MPI tasks:
HDF5-DIAG: Error detected in HDF5 (1.8.16) MPI-process 1009:
#000: H5Dio.c line 271 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 352 in H5D__pre_write(): can't write data
major: Dataset
minor: Write failed
#002: H5Dio.c line 789 in H5D__write(): can't write data
major: Dataset
minor: Write failed
#003: H5Dmpio.c line 529 in H5D__contig_collective_write(): couldn't finish
shared collective MPI-IO
major: Low-level I/O
minor: Write failed
I have used the following libraries/versions during compilation stage:
* intel/16.0.1
* impi/5.1.2.150<http://5.1.2.150/>
* HDF5/1.8.16-mpi
Here you can see how I open the HDF5 file for Collective Writing:
https://github.com/victorsndvg/XH5For/blob/master/src/lib/hdf5_handler/hdf5_handler.f90#L531
And here, how I write HyperSlabs:
https://github.com/victorsndvg/XH5For/blob/master/src/lib/hdf5_handler/contiguous_hyperslab/hdf5_contiguous_hyperslab_handler.f90#L102
Note: ENABLE_MPI, ENABLE_HDF5. ENABLE_PARALLEL_HDF5 definition flags are enabled
Could anyone give me some ligth about this?
I would greatly appreciate your help!
Thank you in advance,
Víctor.
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_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]<mailto:[email protected]>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
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