如何将 SLURM-jobID 作为输入参数传递给 python？

Question

我刚开始使用 SLURM 训练一批卷积神经网络。为了轻松跟踪所有训练有素的 CNN，我想将 SLURM jobID 作为输入参数传递给 python。将其他变量作为参数传递很好。但是，我无法访问要通过的 SLURM jobid。

我已经尝试使用 ${SLURM_JOBID}、${SLURM_JOB_ID}、%j 和 %J。我还尝试将这些 slurm env 变量写入变量，然后再传递到 python。

这是我的最新代码：

#!/bin/bash

# --- info to user
echo "script started ... "

# --- setup environment
module purge            # clean up
module load python/3.6
module load nvidia/10.0
module load cudnn/10.0-v7 

# --- display information
HOST=`hostname`
echo "This script runs the CNN. Slurm scheduled it on node $HOST"
echo "I am interested of all environment variables Slurm adds:"
env | grep -i slurm

# --- start running ... 
echo " --- run --- "

# --- define some varibles
dc="dice"
sm="softmax"

# --- run a job using a slurm batch script
for layer in {3..15..2}
  do
    sbatch -N 1 -n 1 --mem=20G --mail-type=END --gres=gpu:V100:3 --wrap="singularity --noslurm tensorflow_19.03-py3.simg python run_CNN_dynlayer.py ${SLURM_JOBID} ${layer} ${dc}"
    sleep 1 # pause 1s to be kind to the scheduler...
    echo "jobid: "+${SLURM_JOBID}
    echo " --- next --- "
  done

cmd 看起来像这样：

femonk@rarp1 [CNN] ./run_CNN_test.slurm
script started ... 
This script runs the CNN. Slurm scheduled it on node rarp1
I am interested of all environment variables Slurm adds:
SLURM_ACCOUNT=AI
PYTHONPATH=/cluster/slurm/lib64/python3.6/site-packages:/cluster/slurm/lib64/python3.6/site-packages:/cluster/slurm/lib64/python3.6/site-packages:
 --- run --- 
Submitted batch job 3182711
jobid: 
 --- next --- 
femonk@rarp1 [CNN]

有人知道我的代码有什么问题吗？提前致谢。

Answer 1

SLURM_JOBID 环境变量仅可用于作业进程，不适用于提交作业的进程。作业 ID 是从 sbatch 命令返回的，所以如果你想在变量中使用它，你需要分配它。

  do
    SLURM_JOBID=$(sbatch --parsable -N 1 -n 1 --mem=20G --mail-type=END --gres=gpu:V100:3 --wrap="singularity --noslurm tensorflow_19.03-py3.simg python run_CNN_dynlayer.py ${SLURM_JOBID} ${layer} ${dc}")
    sleep 1 # pause 1s to be kind to the scheduler...
    echo "jobid: "+${SLURM_JOBID}
    echo " --- next --- "
  done

注意命令替换 $() 与 sbatch 的 --parsable 参数一起使用。

另请注意，当前输出的行 Submitted batch job 3182711 将消失，因为它用于填充 SLURM_JOBID 变量。

如何将 SLURM-jobID 作为输入参数传递给 python？

How to pass the SLURM-jobID as an input argument to python?

slurm

deep-learning

python-3.6