SlurmStepd: error: execve (): mkdir: нет такого файла или каталога ⇐ Linux

[Anonymous]

Я попытался использовать файл Sbatch по этой ссылке (запуск Windninja на кластере HPC) для запуска программного обеспечения Windninja (Windninja), установленного на HPC. Тем не менее, он всегда дает « slurmstepd: error: execve (): mkdir: нет такого файла или каталога ». Я не уверен, совершил ли я ошибку в переменных пути или настройке среды. run.sh используется для настройки среды и выполнения Windninja, base_cli.cfg - файл конфигурации для параметров Windninja. Но сообщение об ошибке каталогов было создано, когда я запускаю файл SBATCH в режиме пакетного режима. Структура пути, файл sbatch, файл run.sh и файл base_cli.cfg все прикреплены.
Файл: < /p>

Код: Выделить всё

#!/bin/bash
#SBATCH --job-name=WindNinja_Minimal
#SBATCH --output=windninja_%j.log
#SBATCH --error=windninja_%j.err
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=5
#SBATCH --cpus-per-task=5
#SBATCH --mem-per-cpu=2000

### === USER-DEFINED PATHS === ###
WINDNINJA_SIF="/rds/bear-apps/container-images/singularity/x86_64/w/windninja/windninja_latest.sif"    # Path to .sif container
SHARED_STORAGE="/rds/projects/h/hemidah10/Kaiyuan/WindNinja/momWindNinja/temp/Shap"                  # Input/Output directory (shared across nodes)
LOCAL_DIR="/rds/projects/h/hemidah10/Kaiyuan/WindNinja/momWindNinja/temp/data/Shap"                                  # Temporary working directory (local to node)
SCRIPT_DIR="/rds/projects/h/hemidah10/Kaiyuan/WindNinja/momWindNinja/temp/Shap/test"                                       # Where run.sh and config file will go

### === CREATE LOCAL DIRS ON ALL NODES === ###
srun --exclusive mkdir -p ${LOCAL_DIR}
srun --exclusive mkdir -p ${SCRIPT_DIR}
srun --exclusive rsync -av --progress ${WINDNINJA_SIF} ${LOCAL_DIR}/
srun --exclusive bash -c "rsync -av --progress ${SHARED_STORAGE}/run.sh ${SCRIPT_DIR}/"
srun --exclusive bash -c "rsync -av --progress ${SHARED_STORAGE}/base_cli.cfg ${SCRIPT_DIR}/"
echo ".sif file and scripts copied to all compute nodes."

### === DEFINE WHICH FOLDERS TO RUN === ###
task_queue=()
FOLDERS=(0 1 2 3)  # 
#!/bin/bash

### === USER-DEFINED VARIABLES === ###
FOLDER=$1
OUTPUT_FOLDER="./output"                          # &1
EXIT_CODE=$?

export ${SLURM_ENV}

if [ $EXIT_CODE -eq 0 ]; then
echo "WindNinja CLI run completed for folder ${FOLDER}."
else
echo "WindNinja CLI run failed for folder ${FOLDER} with exit code $EXIT_CODE."
exit 1
fi

### === SYNC AND CLEANUP === ###
start_time=$(date +%s)
rm -r "${LOCAL_DIR}/${FOLDER}/dems_folder/dem0/NINJA"* 2>/dev/null
cp -r "${LOCAL_DIR}/${FOLDER}/dems_folder/dem0/mass"  "${SHARED_STORAGE}/${FOLDER}/dems_folder/dem0/"
cp -r "${LOCAL_DIR}/${FOLDER}/dems_folder/dem0/momentum" "${SHARED_STORAGE}/${FOLDER}/dems_folder/dem0/"
cp -r "${LOCAL_DIR}/${FOLDER}/simulation.log" "${SHARED_STORAGE}/${FOLDER}/simulation.log"

end_time=$(date +%s)
echo "Execution time = $((end_time - start_time)) seconds"
rm -rf "${LOCAL_DIR}/${FOLDER}"
< /code>
Файл base_cli_cfg: < /p>
# for the momentum solver, need to uncomment out momentum_flag.  And do the following:
# otherwise, set any non $ symbol value to whatever you want, the $ symbol values will be replaced by the custom python script

num_threads                = 9
momentum_flag              = true
elevation_file             = $dem_file
initialization_method      = domainAverageInitialization
input_speed                = 5.0
input_speed_units          = mph
input_direction            = 0
input_wind_height          = 10.0
units_input_wind_height    = m
output_wind_height         = 10.0
units_output_wind_height   = m
mesh_resolution            = 120.0
units_mesh_resolution      = m
write_ascii_output         = true
output_path                = $output_directory
< /code>
Сообщение об ошибке: < /p>
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
srun: error: bear-pg0104u25b: tasks 15-19: Exited with exit code 2
srun: error: bear-pg0104u16b: tasks 5-9: Exited with exit code 2
srun: error: bear-pg0104u17a: tasks 10-14: Exited with exit code 2
srun: error: bear-pg0104u16a: tasks 0-4: Exited with exit code 2
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
slurmstepd: error: execve(): mkdir: No such file or directory
srun: error: bear-pg0104u16b: tasks 5-9: Exited with exit code 2
srun: error: bear-pg0104u17a: tasks 10-14: Exited with exit code 2
srun: error: bear-pg0104u25b: tasks 15-19: Exited with exit code 2
srun: error: bear-pg0104u16a: tasks 0-4: Exited with exit code 2
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync:  No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
slurmstepd: error: execve(): rsync: No such file or directory
srun: error: bear-pg0104u17a: tasks 10-14: Exited with exit code 2
srun: error: bear-pg0104u16b: tasks 5-9: Exited with exit code 2
srun: error: bear-pg0104u25b: tasks 15-19: Exited with exit code 2
srun: error: bear-pg0104u16a: tasks 0-4: Exited with exit code 2
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
srun: error: bear-pg0104u16b: tasks 5-9: Exited with exit code 2
srun: error: bear-pg0104u17a: tasks 10-14: Exited with exit code 2
srun: error: bear-pg0104u25b: tasks 15-19: Exited with exit code 2
srun: error: bear-pg0104u16a: tasks 0-4: Exited with exit code 2
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
slurmstepd: error: execve(): bash: No such file or directory
srun: error: bear-pg0104u17a: tasks 10-14: Exited with exit code 2
srun: error: bear-pg0104u16b: tasks 5-9: Exited with exit code 2
srun: error: bear-pg0104u25b: tasks 15-19: Exited with exit code 2
srun: error: bear-pg0104u16a: tasks 0-4: Exited with exit code 2

Я очень новичок в Linux и HPC, так что кто -нибудь может помочь мне определить проблему?

Подробнее здесь: https://stackoverflow.com/questions/796 ... -directory