想知道我是否可以问一下有关并行运行slurm作业的问题。
我 ），
我已经设计了以下bash脚本
#!/bin/bash
#SBATCH --job-name fmriGLM #job name을 다르게 하기 위해서
#SBATCH --nodes=1
#SBATCH -t 16:00:00 # Time for running job
#SBATCH -o /scratch/connectome/dyhan316/fmri_preprocessing/FINAL_loop_over_all/output_fmri_glm.o%j #%j : job id 가 [>
#SBATCH -e /scratch/connectome/dyhan316/fmri_preprocessing/FINAL_loop_over_all/error_fmri_glm.e%j
pwd; hostname; date
#SBATCH --ntasks=30
#SBATCH --mem-per-cpu=3000MB
#SBATCH --cpus-per-task=1
for num in {0..29}
do
srun --ntasks=1 python FINAL_ARGPARSE_RUN.py --n_division 30 --start_num ${num} &
done
wait
，我运行了以下内容： sbatch test_bash ，
但是，当我查看test_bash 时输出，很明显，正在执行BASH脚本中的 SRUNS ...有人可以告诉我我在哪里做错了什么以及如何修复它？
**更新：当我查看错误文件时，我将获得以下内容： srun：job 43969步骤创建暂时禁用，重试。我搜索了Internet，它说这可能是由于不指定内存而引起的，因此没有足够的内存来完成第二个作业。但是我认为当我做时，我已经将内存定义了 - mem_per_per_cpu = 300mb < /代码>？
**更新：我已经尝试更改此处所述的代码：为什么我的SLURM工作步骤不在并行启动？，但是..仍然没有起作用
**潜在的相关信息：我们的节点约为96厘米，与所说的教程相比，这似乎很奇怪一个节点有4张或
谢谢你！
I was wondering if I could ask something about running slurm jobs in parallel.(Please note that I am new to slurm and linux and have only started using it 2 days ago...)
As per the insturctions on the picture below (source : https://hpc.nmsu.edu/discovery/slurm/tasks/serial-execution/),
I have designed the following bash script
#!/bin/bash
#SBATCH --job-name fmriGLM #job name을 다르게 하기 위해서
#SBATCH --nodes=1
#SBATCH -t 16:00:00 # Time for running job
#SBATCH -o /scratch/connectome/dyhan316/fmri_preprocessing/FINAL_loop_over_all/output_fmri_glm.o%j #%j : job id 가 [>
#SBATCH -e /scratch/connectome/dyhan316/fmri_preprocessing/FINAL_loop_over_all/error_fmri_glm.e%j
pwd; hostname; date
#SBATCH --ntasks=30
#SBATCH --mem-per-cpu=3000MB
#SBATCH --cpus-per-task=1
for num in {0..29}
do
srun --ntasks=1 python FINAL_ARGPARSE_RUN.py --n_division 30 --start_num ${num} &
done
wait
The, I ran sbatch as follows: sbatch test_bash
However, when I view the outputs, it is apparent that only one of the sruns in the bash script are being executed... Could anyone tell me where I went wrong and how I can fix it?
**update : when I look at the error file I get the following : srun: Job 43969 step creation temporarily disabled, retrying. I searched the internet and it says that this could be caused by not specifying the memory and hence not having enough memory for the second job.. but I thought that I already specifeid the memory when I did --mem_per_cpu=300MB?
**update : I have tried changing the code as said as in here : Why are my slurm job steps not launching in parallel?, but.. still it didn't work
**potentially pertinent information: our node has about 96cores, which seems odd when compared to tutorials that say one node has like 4cores or something
Thank you!!
发布评论
评论（2）
尝试将
- 独家添加到srun命令行：这将指示
srun使用子分配并按照您的预期工作。请注意，
- 独家选项在此上下文中具有不同的含义，与sbatch一起使用。还要注意，不同版本的slurm具有独特的规范方法，但是使用
- 独家应该在大多数版本中使用。Try adding
--exclusiveto thesruncommand line:This will instruct
srunto use a sub-allocation and work as you intended.Note that the
--exclusiveoption has a different meaning in this context than if used withsbatch.Note also that different versions of Slurm have a distinct canonical way of doing this, but using
--exclusiveshould work across most versions.即使您解决了问题，但事实证明您已经指定了
-MEM_PER_CPU = 300MB在您的sbatch脚本中，我想添加就我而言，我的slurm设置不允许-Mem_per_cpuinsbatch，只有- mem。因此，srun命令仍将分配所有内存并阻止后续步骤。对我的关键是指定-MEM_PER_CPU（或- mem）srun命令。Even though you have solved your problem which turned out to be something else, and that you have already specified
--mem_per_cpu=300MBin yoursbatchscript, I would like to add that in my case, my Slurm setup doesn't allow--mem_per_cpuinsbatch, only--mem. So thesruncommand will still allocate all the memory and block the subsequent steps. The key for me, is to specify--mem_per_cpu(or--mem) in thesruncommand.