Running "make check", the t_bigio test fails
When building HDF5 with OpenMPI 1.10.x, the t_bigio test will fail. The issue is due to a bug in the OpenMPI MPI datatype code that was fixed in current versions of OpenMPI 2.1.x, 3.0.x, 3.1.x, and 4.0.x. HDF5-1.10.x has been successfully tested with these versions (specifically, with OpenMPI versions 2.1.5, 3.0.3, 3.1.3, and 4.0). 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: Leaving directory /home/users/ntu/juntao00/hdf5-1.10.4/testpar' make: Entering directory/home/users/ntu/juntao00/hdf5-1.10.4/testpar'
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: *** [t_bigio.chkexe_] Error 1
Compiler complains about missing MPI calls
Please ensure that OpenMPI is built with MPI-1 backward compatibility. Otherwise the compiler will complain about missing MPI calls.
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: