尝试在 slurm 群集上将 MPI 与 emcee 一起使用时出错

Question

嗨，谢谢你的帮助！

我正在尝试让 emcee 在 Slurm 集群上使用 mpi 运行，但是当我启动我的代码时，它在几分钟后返回一个错误，下面描述了一个大错误，这似乎围绕着"无效的通信器"错误。

你知道我可能做错了什么吗？

我正在使用 anaconda，所以我尝试重新安装环境，更改使用的软件包，并删除所有可能不必要的内容，但错误总是相同的。

这是我通过 sbatch 提交的脚本：

#!/bin/bash
#SBATCH --partition=largemem
#SBATCH --ntasks=40
#SBATCH --ntasks-per-node=40
#SBATCH --mem-per-cpu=4000
#SBATCH --mail-user=(my email)
#SBATCH --mail-type=ALL
#SBATCH --output=results/LastOpti.out
#SBATCH --error=results/LastOpti.err
#SBATCH --job-name=gal
source ~/anaconda3/etc/profile.d/conda.sh
conda activate EmceeMPI
cd ~/GalarioFitting
srun -n $SLURM_NTASKS python3 OptimizationGalarioMPI.py --nwalkers 560 --iterations 3000 --suffix _lasttest
conda deactivate

在我的python代码中，我使用schwimmbad的MPIPool。

错误是这个大块：

Traceback (most recent call last):
  File "OptimizationGalarioMPI.py", line 303, in <module>
    pos, prob, state = sampler.run_mcmc(pos, iterations, progress=True)
  File "/home/mbenisty/anaconda3/envs/EmceeMPI/lib/python3.7/site-packages/emcee-3.0rc2-py3.7.egg/emcee/ensemble.py", line 346, in run_mcmc
  File "/home/mbenisty/anaconda3/envs/EmceeMPI/lib/python3.7/site-packages/emcee-3.0rc2-py3.7.egg/emcee/ensemble.py", line 305, in sample
  File "/home/mbenisty/anaconda3/envs/EmceeMPI/lib/python3.7/site-packages/emcee-3.0rc2-py3.7.egg/emcee/moves/red_blue.py", line 92, in propose
  File "/home/mbenisty/anaconda3/envs/EmceeMPI/lib/python3.7/site-packages/emcee-3.0rc2-py3.7.egg/emcee/ensemble.py", line 389, in compute_log_prob
  File "/home/mbenisty/anaconda3/envs/EmceeMPI/lib/python3.7/site-packages/schwimmbad/mpi.py", line 168, in map
    status=status)
  File "mpi4py/MPI/Comm.pyx", line 1173, in mpi4py.MPI.Comm.recv
  File "mpi4py/MPI/msgpickle.pxi", line 302, in mpi4py.MPI.PyMPI_recv
  File "mpi4py/MPI/msgpickle.pxi", line 261, in mpi4py.MPI.PyMPI_recv_match
mpi4py.MPI.Exception: Invalid communicator, error stack:
PMPI_Mprobe(120):  MPI_Mprobe(source=-2, tag=-1, comm=MPI_COMM_WORLD, message=0x7ffed877b790, status=0x7ffed877b7a0)
PMPI_Mprobe(85).: Invalid communicator
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "OptimizationGalarioMPI.py", line 303, in <module>
    pos, prob, state = sampler.run_mcmc(pos, iterations, progress=True)
  File "/home/mbenisty/anaconda3/envs/EmceeMPI/lib/python3.7/site-packages/schwimmbad/pool.py", line 46, in __exit__
    self.close()
  File "/home/mbenisty/anaconda3/envs/EmceeMPI/lib/python3.7/site-packages/schwimmbad/mpi.py", line 188, in close
    self.comm.send(None, worker, 0)
  File "mpi4py/MPI/Comm.pyx", line 1156, in mpi4py.MPI.Comm.send
  File "mpi4py/MPI/msgpickle.pxi", line 174, in mpi4py.MPI.PyMPI_send

Answer 1

可能是 Conda 附带的 MPI 实现不包括 Slurm 支持。如果是这样，您应该尝试使用 mpirun 而不是 srun 启动程序。但该错误通常表示 MPI 的多个实现同时处于活动状态。请确保在提交作业时未加载任何环境模块，并且未安装与 MPI 相关的操作系统包。