Crash with system-provided OpenMPI and HDF5_jll v1.14

[mfsch]

When I set up a simple project with the latest MPI and HDF5 packages and configure it to use the system-provided OpenMPI installation, the call to MPI.Init() crashes with “orte_init failed” errors. I am observing issue on both Ubuntu 18.04 (OpenMPI 3.1.2) and 20.04 (OpenMPI 4.0.3). Downgrading to HDF5_jll v1.12 fixes the issue.

Steps to reproduce:

• create a new folder and launch Julia with julia --project=.
• install dependencies with ]add MPI HDF5
• run using MPI; MPI.MPIPreferences.use_system_binary()
• attempt to run mpirun -n 4 julia --project -e "using MPI, HDF5; MPI.Init()" (or mpiexecjl), observe crash
• downgrade with ]add [email protected], rerun without crash

On Ubuntu 18.04, the error includes the line mca_base_component_repository_open: unable to open mca_pmix_pmix3x: /home/user/.julia/artifacts/f9744710560ba3ddc00cd9df62ac7dfcd18c8649/lib/openmpi/mca_pmix_pmix3x.so: undefined symbol: opal_envar_t_class, in case this is helpful.

[simonbyrne]

ah, I've seen something similar! The problem appears to be that we're opening two different MPI libraries (the system one from MPI.jl, and the JLL one (from HDF5_jll).

Easy workarounds:

• use a system HDF5 (see HDF5.jl docs)
• cap HDF5_jll at 1.12 (set the compat HDF5_jll = "~1.12".

In the longer term we need a better fix. @giordano @eschnett any suggestions on how we can deal with this?

[giordano]

I thought HDF5_jll.jl would use the MPI library chosen by MPIPreferences.jl

[simonbyrne]

Yeah, i don't quite get why it's pulling in OpenMPI_jll?

[simonbyrne]

Ah, I see.

It augments based on the value of the MPI abi:
https://github.com/JuliaBinaryWrappers/HDF5_jll.jl/blob/b96de8ada558f8d70e27b5561d4f5df815b01ebf/.pkg/platform_augmentation.jl#L13

But the augmentation for abi = "openmpi" always loads OpenMPI_jll:
https://github.com/JuliaBinaryWrappers/HDF5_jll.jl/blob/main/src/wrappers/x86_64-linux-gnu-libgfortran5-cxx03-mpi%2Bopenmpi.jl#L9

[eschnett]

My approch, of course, would be to use the Julia-provided MPItrampoline as MPI implementation, and to use the system MPI via MPItrampoline...

[JoshuaLampert]

Would it be possible to print a warning if a system-provided MPI installation, but no system-provided HDF5 is detected?

[mmesiti]

I have been affected by this very problem. A package I am working on (let's call it PMFRG) depends on HDF5 and if I do

using MPI
using PMFRG # using HDF5
MPI.Init()

I get a crash without much explanation.
Interestingly, instead

using MPI
MPI.Init()
using PMFRG # using HDF5

works.
I had to dig some hours to find out that HDF5+MPIPreferences.use_system_binary() is the problem, missed the existence of this issue, crafted a repro case, started to open anoter issue and finally found this one.
So, yes, I am sorry I do not have the knowledge to make a PR for this but I wanted to say I have been affected.

[giordano]

I believe using mpitrampoline as suggested above should help, see documentation added in JuliaParallel/MPI.jl#838