uge2slurm 0.1.3

Grid Engine to Slurm command converter

uge2slurm

Grid Engine to Slurm command converter

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Installation

uge2slurm provides conversion from qsub command in UGE/SGE to Slurm's sbatch command.

pip install uge2slurm

After installation, the following commands are available.

• uge2slurm [{qsub}]
• qsub <qsub args>

The following commands are installed as a part of uge2slurm but current version does not support command conversions.

• qacct
• qalter
• qconf
• qdel
• qhold
• qhost
• qlogin
• qmake
• qmod
• qmon
• qping
• qquota
• qralter
• qrdel
• qresub
• qrls
• qrsh
• qrstat
• qrsub
• qselect
• qsh
• qstat

Command usage

These options are commonly available for all subcommands.

-?/--help

Show help message and exit.

--version

Show version info and exit.

--ignore-coloring

Disable colored output.

--verbose [{"critical"|"fatal","error","warn"|"warning","info","debug",int}]

Set verbosity in Python logging level. Default is "warning". If only --verbose flag is given, level is set to info.

uge2slurm

List Grid Engine and Slurm commands' existence and exit.

qsub

Convert qsub command to sbatch command and execute.
The following options can be specified besides qsub arguments.

-n/--dry-run

Print converted Slurm command and exit.

-y/--non-interactive

By default, uge2slurm shows a converted command line and get confirmation before the execution when a TTY is allocated. This option disables the preview and the command will be executed immediately.

--memory resource [...]

Specify which resource value should be mapped into --mem-per-cpu option. If multiple values are specified, the first valid value will be used.

--cpus parallel_env [...]

Specify which parallel_environment should be mapped into --cpus-per-task option. If multiple values are specified, the first valid value will be used.
Note that range values are not supported and its minimum value will be used as the number of cpus.

--partition resource=partition [...]

Specify which resource name should be mapped into partition (queue) via --partition option. Resource-partition pairs must be specified by '=' separated strings.

The partition mapping is solved by the following order:

1. use relations specified by --partition option when the partition name is exactly matched.
2. split partition name by punctuations except '-' and '_' then try exact match on the prefix and resource names.
3. try forward matching on partition names and resource names.

Examples:

% sinfo --format "%P"
PARTITION
gpu.q
gpu_intr.q

% uge2slurm qsub -n -l gpu_in test.sh
sbatch
	 --partition gpu_intr.q

% uge2slurm qsub -n -l gp test.sh
ERROR: Resource specification "gp" matches multiple partitions.
WARNING: 	gp -> gpu.q, gpu_intr.q
WARNING: Try to add implicit mapping option like `--partition gp=gpu.q`.
CRITICAL: Error: failed to map resource into partition.

% uge2slurm qsub -n -l gpu test.sh
sbatch
	 --partition gpu.q

% uge2slurm qsub -n --partition gpu=gpu_intr -l gpu test.sh
sbatch
    --partition gpu_intr