如何让SBATCH通过电子邮件发送标准输出？

Question

我想让 slurm 系统myprogram在计算完成后通过电子邮件发送输出。所以我写了SBATCH如下

#!/bin/bash -l
#SBATCH -J MyModel
#SBATCH -n 1 # Number of cores
#SBATCH -t 1-00:00 # Runtime in D-HH:MM
#SBATCH -o JOB%j.out # File to which STDOUT will be written
#SBATCH -e JOB%j.err # File to which STDERR will be written
#SBATCH --mail-type=END
#SBATCH --mail-user=my@email.com
echo $SLURM_JOB_ID 
echo $SLURM_JOB_NAME 
/usr/bin/mpirun -np 1 ./myprogram
/usr/bin/mail -s $SLURM_JOB_NAME my@email.com < JOB${SLURM_JOB_ID}.out

邮件系统报告

file .out not found

我如何构建邮件命令来让主题行$SLURM_JOB_NAME和文件中的邮件内容STDOUT，例如JOB${SLURM_JOBID}.out在我的例子中？

Answer 1

这是我的解决方案：

#!/bin/bash
#SBATCH -J MyModel
#SBATCH -n 1 # Number of cores
#SBATCH -t 1-00:00 # Runtime in D-HH:MM
#SBATCH -o JOB%j.out # File to which STDOUT will be written
#SBATCH -e JOB%j.out # File to which STDERR will be written
#SBATCH --mail-type=BEGIN
#SBATCH --mail-user=my@email.com

echo "$(date "+%Y-%m-%d %H:%M:%S"): $SLURM_JOB_NAME start id=$SLURM_JOB_ID"

/usr/bin/mpirun -np 1 ./myprogram

cat JOB${SLURM_JOB_ID}.out | mail -s "$SLURM_JOB_NAME Ended id=$SLURM_JOB_ID"" my@email.com

此外，我们可以添加更多信息并保留退出代码：

#!/bin/bash
#SBATCH -J MyModel
#SBATCH -n 1 # Number of cores
#SBATCH -t 1-00:00 # Runtime in D-HH:MM
#SBATCH -o JOB%j.out # File to which STDOUT will be written
#SBATCH -e JOB%j.out # File to which STDERR will be written
#SBATCH --mail-type=BEGIN
#SBATCH --mail-user=my@email.com

secs_to_human(){
    echo "$(( ${1} / 3600 )):$(( (${1} / 60) % 60 )):$(( ${1} % 60 ))"
}
start=$(date +%s)
echo "$(date -d @${start} "+%Y-%m-%d %H:%M:%S"): ${SLURM_JOB_NAME} start id=${SLURM_JOB_ID}\n"

### exec task here
( << replace with your task here >> ) \
&& (cat JOB$SLURM_JOB_ID.out |mail -s "$SLURM_JOB_NAME Ended after $(secs_to_human $(($(date +%s) - ${start}))) id=$SLURM_JOB_ID" my@email.com && echo mail sended) \
|| (cat JOB$SLURM_JOB_ID.out |mail -s "$SLURM_JOB_NAME Failed after $(secs_to_human $(($(date +%s) - ${start}))) id=$SLURM_JOB_ID" my@email.com && echo mail sended && exit $?)

您还可以编辑它以发送单独的 stdout/stderr 日志或将它们附加为文件。

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