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OpenMPI Build Issues

What version of HDF5 supports OpenMPI ?

HDF5-1.10.5 is the earliest version of HDF5 that was tested with and which supports OpenMPI. HDF5-1.10.5 was tested with OpenMPI versions 2.1.5, 3.0.3, 3.1.3, and 4.0.

Running "make check", the t_bigio test fails

When building HDF5 with OpenMPI 1.10.x, the t_bigio test will fail.  Users should update to a more recent version of OpenMPI to resolve the the issue.

The issue is due to a bug in the OpenMPI MPI datatype code. This bug was fixed in current versions of OpenMPI 2.1.x, 3.0.x, 3.1.x, and 4.0.x.

Following are the errors that occur if the tests fail with this issue:

MPI tests finished with no errors

0.87user 1.38system 0:01.21elapsed 186%CPU (0avgtext+0avgdata 123696maxresident)k

0inputs+128outputs (7major+84441minor)pagefaults 0swaps
Finished testing t_mpi
make[4]: Leaving directory /home/users/ntu/juntao00/hdf5-1.10.4/testpar' make[4]: Entering directory/home/users/ntu/juntao00/hdf5-1.10.4/testpar'
Testing t_bigio
t_bigio Test Log
Testing Dataset1 write by ROW
Testing Dataset2 write by COL
Testing Dataset3 write select ALL proc 0, NONE others
Testing Dataset4 write point selection
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
[ntu02:26084] 2 more processes have sent help message help-mpi-api.txt / mpi-abort
[ntu02:26084] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
13.80user 3.49system 0:05.98elapsed 289%CPU (0avgtext+0avgdata 804020maxresident)k
0inputs+112outputs (7major+376166minor)pagefaults 0swaps
make[4]: *** [t_bigio.chkexe_] Error 1

Compiler complains about missing MPI calls

Please be aware that releases prior to HDF5-1.10.5 used MPI functions that were deprecated since MPI 2.0. With OpenMPI 4.0, those deprecated functions were deleted. This caused the compiler to complain about missing MPI calls. An example of APIs that have been deprecated are:  MPI_Type_extent, MPI_Address and MPI_Type_struct

To work around this issue build OpenMPI with MPI-1 backward compatibility. Otherwise the compiler will complain about the missing MPI calls.

(HDF5-1.10.5 is scheduled to be released in the first quarter of 2019.)

The parallel flush test fails

Prior to HDF5-1.10.5 the parallel flush test failed. This failure can be ignored. Redirect the "make check" output to a file and use the "i" option to ignore errors:

make -i check >& check.output

Then view the output file (check.output) for any errors that occurred. If this is the only error, then you can ignore it:

(HDF5-1.10.5 is scheduled to be released in the first quarter of 2019.)