HDF5-1.12.1 make check atomiticity test failure


#1

I’m trying to install a parallel enabled version of hdf5 using openmpi on ubuntu 20.04, but the testphd5 is failing
with:

Atomicity Test Failed Process 1: read_buf[2047] is 0, should be 5

at which point it continues with some other checks and finally mpi exits:

===================================
***PHDF5 tests detected 1536 errors***
===================================
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[21659,1],1]
  Exit code:    1
--------------------------------------------------------------------------
Command exited with non-zero status 1
3.23user 1.04system 0:02.51elapsed 170%CPU (0avgtext+0avgdata 250804maxresident)k
0inputs+23152outputs (2212major+155666minor)pagefaults 0swaps

The machine a large workstation with two Xeon 16 core nodes. Openmpi 3.1 version is 4.0.3-0ubuntu1. I’ve attached the check log: testphdf5.chklog (120.8 KB)