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open-mpi
Try to install mpi4py+openmpi using conda on Ubuntu 20.04 but failed
Thank you for taking the time to submit an issue!
Background information
Distributor ID: Ubuntu Description: Ubuntu 20.04.3 LTS Release: 20.04 Codename: focal
What version of Open MPI are you using? (e.g., v3.0.5, v4.0.2, git branch name and hash, etc.)
Install using
conda create -n ENV_NAME -c conda-forge 'python=3.10.*' openmpi mpi4py
Describe how Open MPI was installed (e.g., from a source/distribution tarball, from a git clone, from an operating system distribution package, etc.)
as stated above
If you are building/installing from a git clone, please copy-n-paste the output from git submodule status.
Please describe the system on which you are running
- Operating system/version:
- Computer hardware:
- Network type:
For hardware details:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Address sizes: 48 bits physical, 48 bits virtual
CPU(s): 240
On-line CPU(s) list: 0-239
Thread(s) per core: 2
Core(s) per socket: 60
Socket(s): 2
NUMA node(s): 8
Vendor ID: AuthenticAMD
CPU family: 23
Model: 49
Model name: AMD EPYC 7742 64-Core Processor
Stepping: 0
CPU MHz: 2245.780
BogoMIPS: 4491.56
Virtualization: AMD-V
Hypervisor vendor: KVM
Virtualization type: full
L1d cache: 7.5 MiB
L1i cache: 7.5 MiB
L2 cache: 60 MiB
L3 cache: 128 MiB
NUMA node0 CPU(s): 0-29
NUMA node1 CPU(s): 30-59
NUMA node2 CPU(s): 60-89
NUMA node3 CPU(s): 90-119
NUMA node4 CPU(s): 120-149
NUMA node5 CPU(s): 150-179
NUMA node6 CPU(s): 180-209
NUMA node7 CPU(s): 210-239
Vulnerability Itlb multihit: Not affected
Vulnerability L1tf: Not affected
Vulnerability Mds: Not affected
Vulnerability Meltdown: Not affected
Vulnerability Mmio stale data: Not affected
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled v
ia prctl and seccomp
Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user
pointer sanitization
Vulnerability Spectre v2: Mitigation; Retpolines, IBPB conditional, IBRS_
FW, STIBP conditional, RSB filling
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Not affected
483G
Details of the problem
activate conda environment and run mpiexec and mpirun both returns
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
opal_shmem_base_select failed
--> Returned value -1 instead of OPAL_SUCCESS
Tried to set LD_PRELOAD to corresponding libmpi.so in conda /root/anaconda3/envs/mpi-test/lib/libmpi.so or export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so, not working for both cases
Are you running a MPI program or a python mpi4py script?
If the former, did you build your program within the conda environment?
From the conda environment, what does type mpiexec and ompi_info --all report?
@ggouaillardet Thanks for your help. Tried to install with pip in CLI and success. I am running a .py script. Not so sure if conda caused this problem so I decide not to use conda now. You may keep this issue and see if can re-produce this issue on Ubuntu 20.04.3 LTS , installed with conda create -n ENV_NAME -c conda-forge 'python=3.10.*' openmpi mpi4py, activate the env created, set flags allow run as root ,then run mpiexec or mpirun should give out the issue. If run like mpirun -np or mpiexec -n should return n , np not found.
FWIW, I tried and it works for me (I used miniconda from wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh)
How did you install conda?
@ggouaillardet I installed using Anaconda https://www.anaconda.com/products/distribution. I will try miniconda see if it works