Make check HDF5 parallel in t_mpi.c

HDF5 Library
1

Hello everyone, I am trying to build parallel HDF5 on my laptop and I followed the instruction:

$CC=/usr/bin/mpicc ./configure --enable-parallel --prefix=/home/shiqihe/local/hdf5-1.10.5
$make
$make check

And then I got stuck in t_mpi.c. Here is my error:

make check-TESTS
make[2]: Entering directory '/home/shiqihe/local/hdf5-1.10.5/testpar’
make[3]: Entering directory '/home/shiqihe/local/hdf5-1.10.5/testpar’
make[4]: Entering directory '/home/shiqihe/local/hdf5-1.10.5/testpar’
make[4]: Nothing to be done for ‘_exec_check-s’.
make[4]: Leaving directory '/home/shiqihe/local/hdf5-1.10.5/testpar’
make[3]: Leaving directory '/home/shiqihe/local/hdf5-1.10.5/testpar’
make[3]: Entering directory '/home/shiqihe/local/hdf5-1.10.5/testpar’
===Parallel tests in testpar begin Thu Oct 24 21:27:49 EDT 2019===
****** Hint ******
Parallel test files reside in the current directory by default.
Set HDF5_PARAPREFIX to use another directory. e.g.,
** HDF5_PARAPREFIX=/PFS/user/me**
** export HDF5_PARAPREFIX**
** make check**
****** end of Hint ******
make[4]: Entering directory '/home/shiqihe/local/hdf5-1.10.5/testpar’
============================
Testing t_mpi **
============================
** t_mpi Test Log
============================
===================================
MPI functionality tests
===================================
--------------------------------
Proc 0: *** MPIO 1 write Many read test…
--------------------------------
Proc 0: hostname=shiqihe-Aspire-E5-571G
--------------------------------
Proc 0: *** MPIO File size range test…
--------------------------------
MPI_Offset is signed 8 bytes integeral type
MPIO GB file write test /home/shiqihe/Documents/test/MPItest.h5
MPIO GB file read test /home/shiqihe/Documents/test/MPItest.h5
Proc 0: *** Parallel ERROR *****
** VRFY () failed at line 341 in t_mpi.c
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.

My OS is

Ubuntu 18.04.3 LTS

My mpicc version is

gcc (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0

My openMPI version is

mpirun (Open MPI) 2.1.1

Does suggestion? Thank you!

2

I experienced the same test error when trying to build HDF5 with parallel-enabled on CentOS-7 x64, using OpenMPI 3.1.3. I had to install it to /opt/openmpi-3 since we already have an earlier version of installed that would mess with my company’s existing scripts.

Log below:

Testing: t_mpi

Test log for t_mpi

[achilles:72762] OPAL ERROR: Not initialized in file pmix2x_client.c at line 109
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[achilles:72762] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!

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: [[381,1],0]
Exit code: 1

0.11user 0.15system 0:00.16elapsed 158%CPU (0avgtext+0avgdata 6172maxresident)k
0inputs+8outputs (0major+33374minor)pagefaults 0swaps
make[4]: *** [t_mpi.chkexe_] Error 1
make[4]: Leaving directory /home/henderson/Build/HDF5_/hdf5-1.12.0/testpar' make[3]: *** [build-check-p] Error 1 make[3]: Leaving directory/home/henderson/Build/HDF5_/hdf5-1.12.0/testpar’
make[2]: *** [test] Error 2
make[2]: Leaving directory /home/henderson/Build/HDF5_/hdf5-1.12.0/testpar' make[1]: *** [check-am] Error 2 make[1]: Leaving directory/home/henderson/Build/HDF5_/hdf5-1.12.0/testpar’
make: *** [check-recursive] Error 1