Use Fusion trace metrics to replace bash command-trace wrapper

[pditommaso]

Summary

• When Fusion is enabled, use metrics from .fusion/trace.json (proc, cgroup, gpu sections) to populate TraceRecord fields, replacing the bash command-trace.txt wrapper script
• Prefer cgroup memory metrics over proc-level metrics for more accurate container-aware measurements (vmem, rss, peak_vmem, peak_rss, %mem)
• Controlled via NXF_FUSION_TRACE env variable (defaults to true); set to false to revert to legacy behavior
• GPU metrics extraction is preserved regardless of the setting (backward compatible)

Changes

File	Change
Global.groovy	Add isFusionTraceEnabled() reading NXF_FUSION_TRACE env var
TraceRecord.groovy	parseFusionTraceFile returns full JSON; add toLong/toFloat helpers
TaskHandler.groovy	applyFusionMetrics maps Fusion JSON to TraceRecord; skip .command.trace when active
BashWrapperBuilder.groovy	Skip trace wrapper generation when Fusion trace is active
TaskBean.groovy	Add fusionEnabled field
TaskProcessor.groovy	Expose isFusionEnabled()

Trace field mapping

TraceRecord field	Fusion source	Notes
realtime	proc.realtime	Milliseconds
%cpu	proc.pct_cpu	Tenths of percent, divided by 10
cpu_model	proc.cpu_name	String
rchar, wchar	proc.rchar, proc.wchar	Bytes
syscr, syscw	proc.syscr, proc.syscw	Count
read_bytes, write_bytes	proc.read_bytes, proc.write_bytes	Bytes
vol_ctxt, inv_ctxt	proc.vol_ctxt, proc.inv_ctxt	Count
vmem	cgroup.memory_current	Bytes (cgroup preferred)
rss	cgroup.memory_rss	Bytes (cgroup preferred)
peak_vmem	cgroup.memory_peak	Bytes (cgroup preferred)
peak_rss	cgroup.memory_peak_rss	Bytes (cgroup preferred)
%mem	computed	memory_rss / memory_limit * 100

Test plan

• TraceRecordTest — parse full JSON, parse without gpu
• TaskHandlerTest — full metrics with cgroup, GPU-only when disabled, skip .command.trace when active
• BashWrapperBuilderTest — skip trace wrapper when active, keep when disabled
• CrgExecutorTest — no regression from fusionEnabled on TaskBean

🤖 Generated with Claude Code

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