Implement SGE (Sun Grid Engine) Job Submission Support #85

Overview

The SGE (Sun Grid Engine) scheduler support is currently incomplete with NotImplementedError placeholders.

Current Status

• Location: clustrix/executor.py:195
• Method: _submit_sge_job()
• Status: Raises NotImplementedError("SGE support not yet implemented")

Requirements

1. Job Submission (_submit_sge_job)

• Implement SGE job submission using qsub command
• Handle SGE-specific job configuration parameters
• Parse job ID from qsub output
• Store job information in active_jobs

2. Status Checking (_check_job_status)

• Add SGE case to status checking logic
• Use qstat command to check job status
• Map SGE status codes to internal status strings
• Handle completed/failed job detection

3. Script Generation (_create_sge_script)

• Location: clustrix/utils.py:407
• Generate SGE batch scripts with proper directives
• Support SGE-specific parameters (queues, resources, etc.)
• Include environment setup and job execution logic

Implementation Details

SGE Directives to Support

#$ -N job_name
#$ -o output_file
#$ -e error_file  
#$ -pe parallel_env slots
#$ -l h_vmem=memory
#$ -l h_rt=walltime
#$ -q queue_name

Status Mapping

• qw (queued waiting) → "pending"
• r (running) → "running"
• s (suspended) → "running"
• Job not found → check for result files → "completed" or "failed"

Acceptance Criteria

• _submit_sge_job() successfully submits jobs to SGE
• _check_job_status() correctly reports SGE job status
• _create_sge_script() generates valid SGE batch scripts
• All existing SGE tests pass
• Add comprehensive SGE integration tests

Related Files

• clustrix/executor.py - Job submission and status checking
• clustrix/utils.py - Script generation
• tests/test_executor.py - Tests expecting SGE functionality
• tests/test_utils.py - Script generation tests

Labels: enhancement, scheduler-support, sge
Priority: Medium

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