Nsys Profiling

nsys Profiling

You are helping a developer profile GPU workloads in a Rust + CUDA inference engine using NVIDIA Nsight Systems (nsys). The goal is always to answer "where is time going and what should I optimize next?"

Before you start

1. Confirm the workload. Ask which model, which path (prefill vs decode vs both), and what prompt/output shapes matter. If the user is vague, default to the two standard profiles:

   • Prefill-heavy: --prompt-len 2048 --output-len 1
   • Decode-heavy: --prompt-len 1 --output-len 128

2. Check --release. Debug builds slow GPU kernels by 10x+ and produce misleading traces. If you see cargo run without -r or --release, stop and fix this first.

3. Check nsys is available. Run nsys --version. If it fails, the user likely needs to add /usr/local/cuda/bin to PATH — a common gotcha in SSH or tmux sessions where ~/.bashrc doesn't source. Fix: export PATH="/usr/local/cuda/bin:$PATH", or use full path /usr/local/cuda/bin/nsys.

4. Check profiling environment. Run nsys status -e to verify the system can profile. It checks kernel paranoid level, perf_event support, and LBR availability. If paranoid level is too high (>1), CPU sampling won't work without root.

Capturing a trace

Standard capture command

nsys profile --force-overwrite=true --cuda-graph-trace=node \
  --export=sqlite -o target/profiling/<trace_name> \
  cargo run -r --bin bench_serving -- request \
    --prompt-len <PROMPT> --output-len <OUTPUT> --warmup 1 --iters 1

Build this command for the user based on their workload. Always include all four flags:

Precise capture with cudaProfilerApi

If the bench_serving binary supports --cuda-profiler-capture, use it to capture only the measured iterations — this excludes model loading and warmup from the trace, producing a much cleaner profile:

nsys profile --force-overwrite=true --cuda-graph-trace=node \
  -c cudaProfilerApi --export=sqlite -o target/profiling/<trace_name> \
  cargo run -r --bin bench_serving -- --cuda-profiler-capture request \
    --prompt-len <PROMPT> --output-len <OUTPUT> --warmup 1 --iters 1

Use --capture-range-end=repeat[:N] to capture multiple separate ranges (e.g., N iterations) into the same trace. Each range produces its own segment.

Delay/duration capture (when cudaProfilerApi isn't available)

For workloads without profiler API integration, use --delay to skip startup and --duration to limit capture:

nsys profile --delay=10 --duration=30 --cuda-graph-trace=node \
  --force-overwrite=true --export=sqlite -o target/profiling/<trace_name> \
  <command>

Disabling CUDA Graph for cleaner kernel analysis

CUDA Graph replay groups many kernels into a single opaque launch. Even with --cuda-graph-trace=node, profiler overhead inflates times differently than ungraphed launches. For precise per-kernel timing (e.g., comparing short vs long context), disable CUDA Graph:

cargo run -r --bin bench_serving -- --cuda-graph false request --prompt-len 2048 --output-len 32 ...

Tradeoff: ungraphed traces show true individual kernel times but include ~5μs CPU launch overhead per kernel that the production (graphed) path avoids. Use graphed traces for real TPOT, ungraphed for kernel-level comparison.

Interactive profiling (long-running servers)

For profiling a server that's already running, use the launch/start/stop workflow:

# Terminal 1: launch the server under nsys control, but don't start collecting yet
nsys launch --trace=cuda,nvtx --cuda-graph-trace=node \
  --session-new=my_session -- cargo run -r --bin pegainfer-server -- ...

# Terminal 2: start/stop collection on demand
nsys start --session=my_session
# ... send requests ...
nsys stop --session=my_session

Or use --start-later=true with nsys profile to get the same deferred-start behavior in a single command.

Lighter traces

If the trace is too large or slow to process, limit tracing scope:

# Only CUDA + NVTX, skip OS scheduling noise — smaller trace, faster to open
nsys profile --trace=cuda,nvtx --cuda-graph-trace=node ...

Other --trace options: cublas (trace cuBLAS API calls with parameters), cudnn, osrt (OS runtime like pthread), mpi, python-gil. Multiple values comma-separated.

Output naming tricks

The -o flag supports pattern substitution:

• %h — hostname (useful for multi-node)
• %p — PID of target process
• %n — auto-incrementing number (avoids overwrite without --force-overwrite)
• %q{ENV_VAR} — environment variable expansion
• %% — literal %

Example: -o traces/%h_rank%q{RANK}_%n → traces/gpu-node-01_rank0_1.nsys-rep

Reproducible configs with --command-file

Store nsys flags in a file to avoid long command lines:

# nsys_decode.cfg
--force-overwrite=true
--cuda-graph-trace=node
--export=sqlite
--trace=cuda,nvtx

Then: nsys profile --command-file=nsys_decode.cfg -o target/profiling/trace <command>

Command-line flags override file flags.

One-shot stats with --stats=true

Skip the separate nsys stats step entirely:

nsys profile --stats=true --force-overwrite=true --cuda-graph-trace=node \
  --export=sqlite -o target/profiling/trace <command>

This automatically generates all default summary reports (kern_sum, api_sum, mem_sum, etc.) to the console after collection finishes. Convenient for quick checks, but the output is long — better for scripted workflows.

Analyzing a trace

Run these analyses in sequence. Each answers a different question.

Step 1: Kernel time breakdown

nsys stats --report cuda_gpu_kern_sum target/profiling/<trace>.sqlite

This tells you which GPU kernels consume the most time. Normal patterns:

• MLP + GEMV typically >90% of decode time
• Attention grows with sequence length (O(seq_len)) while MLP/GEMV stay flat
• RMSNorm and activation kernels are lightweight (<3%)

Use :base to tame mangled names. By default, kernel names are fully mangled C++ templates — unreadable. Append :base to strip template parameters:

nsys stats --report cuda_gpu_kern_sum:base target/profiling/<trace>.sqlite

This turns std::enable_if<!T7, void>::type internal::gemvx::kernel<int, int, __nv_bfloat16, ...>(T13) into just kernel. Much easier to scan, but note that it merges kernels with different template instantiations. Use the full name when you need to distinguish shapes.

There's also :mangled if you need the raw linker symbol.

Step 2: CUDA API overhead

nsys stats --report cuda_api_sum target/profiling/<trace>.sqlite

This tells you where the CPU/host is spending time. Watch for:

• cuMemcpyHtoDAsync dominated by model loading (normal if one-time)
• cuStreamSynchronize — if this is large during inference (not loading), the host is unnecessarily waiting for the GPU
• cuMemAllocAsync / cuMemFreeAsync — high counts or time means hot-path allocation churn
• cudaLaunchKernel — large count × ~5μs each = significant CPU launch overhead

Step 3: Tail-aware stats

python3 tools/nsys_tail_stats.py target/profiling/<trace>.sqlite --limit 15

This is the team's custom tool that goes beyond nsys's built-in p50/avg reporting. It shows p50, p95, p99, max and a tail score for each kernel. The p50 can hide serious problems:

• max/p50 > 2×: Kernel has outlier invocations. Common causes: route imbalance in MoE, rank arrival skew in NCCL, allocator stalls.
• p99/p50 > 1.5×: Systematic tail — not a one-off spike. Look for stream contention or variable work per invocation.
• High tail score but low total time: The kernel is cheap on average but occasionally blocks everything. These are the sneakiest bottlenecks.

Step 4: Bandwidth efficiency (for GEMV-bound workloads)

When GEMV dominates (>90% of GPU time, typical for bs=1 decode), compute memory bandwidth utilization to answer "is there room to optimize, or are we already at the hardware limit?"

BW_achieved = weight_bytes / kernel_time
BW_efficiency = BW_achieved / GPU_peak_BW

For each major GEMV shape, calculate weight size (M × K × sizeof(bf16)) and divide by the nsys avg kernel time. Compare against GPU peak memory bandwidth (e.g., RTX 5070 Ti = 896 GB/s, H100 = 3.35 TB/s). Large GEMVs (>20MB weights) typically reach 85-90% efficiency; small GEMVs (<5MB) drop to 60-70% due to launch overhead and tail effects.

If overall efficiency is >80%, GEMV optimization has limited headroom — quantization or batching is the path forward. If <70%, there's room for custom kernels.

Step 5 (optional): Auto-analysis

nsys analyze target/profiling/<trace>.sqlite

Runs NVIDIA's built-in rules: cuda_memcpy_async, cuda_memcpy_sync, cuda_memset_sync, cuda_api_sync, gpu_gaps, gpu_time_util. It flags synchronous memcpy, unnecessary device syncs, and periods where the GPU is idle >500ms. Quick sanity check, but won't catch domain-specific problems.

Run a specific rule: nsys analyze --rule cuda_api_sync <trace>.sqlite

Advanced analysis techniques

Time-window filtering

Isolate just the inference phase by filtering out model loading:

# Skip first 5 seconds (model loading), analyze everything after
nsys stats --report cuda_gpu_kern_sum --filter-time "5s/" target/profiling/<trace>.sqlite

# Analyze only a specific 2-second window
nsys stats --report cuda_gpu_kern_sum --filter-time "5s/7s" target/profiling/<trace>.sqlite

Time units are composable: 1s2ms3us4ns = 1,002,003,004ns. This is much more precise than --delay/--duration — it's post-hoc filtering on an already-captured trace.

You can also filter by NVTX range if the code has NVTX annotations:

nsys stats --report cuda_gpu_kern_sum --filter-nvtx "decode_step@inference" target/profiling/<trace>.sqlite

Change time units

Default output is nanoseconds. Switch to milliseconds for readability:

nsys stats --report cuda_gpu_kern_sum --timeunit msec target/profiling/<trace>.sqlite

Machine-readable output

For scripted analysis or piping into other tools:

# JSON — directly parseable by Python/jq
nsys stats --report cuda_gpu_kern_sum --format json target/profiling/<trace>.sqlite

# CSV — for spreadsheets or pandas
nsys stats --report cuda_gpu_kern_sum --format csv --output . target/profiling/<trace>.sqlite

# Pipe to grep for quick filtering
nsys stats --report cuda_api_sum --format table --output @"grep -E '(-|Name|cudaFree)'" target/profiling/<trace>.sqlite

Launch-to-execution correlation

nsys stats --report cuda_kern_exec_sum target/profiling/<trace>.sqlite

This report shows three time columns per kernel:

• AAvg (API time) — how long the host-side launch API took
• QAvg (queue time) — how long the kernel sat in the stream queue before the GPU picked it up
• KAvg (kernel time) — actual GPU execution time

If QAvg is large compared to KAvg, kernels are queuing because the GPU is still busy with previous work, or the launch stream is congested.

Per-launch GPU trace

nsys stats --report cuda_gpu_trace target/profiling/<trace>.sqlite

Shows every individual kernel launch with its timestamp, grid dimensions (GrdX/Y/Z), block dimensions (BlkX/Y/Z), register count (Reg/Trd), and shared memory usage. Useful for:

• Verifying launch configurations match what you expect
• Finding specific outlier launches (sort by Duration)
• Checking if grid dimensions vary across iterations (sign of dynamic shapes)

Multi-report in one command

Generate multiple reports in a single pass:

nsys stats --report cuda_gpu_kern_sum --report cuda_api_sum --report cuda_gpu_mem_time_sum \
  target/profiling/<trace>.sqlite

GPU memory tracking

Capture GPU memory allocation/deallocation patterns over time:

nsys profile --cuda-memory-usage=true --force-overwrite=true --cuda-graph-trace=node \
  --export=sqlite -o target/profiling/trace <command>

Adds overhead but shows memory watermarks. Useful when debugging OOM or fragmentation.

CUDA backtrace for slow API calls

Find which host code is issuing slow CUDA API calls:

nsys profile --cudabacktrace=kernel:500 --force-overwrite=true --cuda-graph-trace=node \
  --export=sqlite -o target/profiling/trace <command>

Collects CPU backtraces for CUDA kernel launches that take >500ns (the threshold). The backtrace tells you exactly which Rust/C++ function triggered the launch. Options: all, kernel, memory, sync, other, or comma-combined. Significant overhead — use selectively.

GPU hardware metrics

nsys profile --gpu-metrics-devices=all --gpu-metrics-frequency=10000 \
  --force-overwrite=true --export=sqlite -o target/profiling/trace <command>

Samples SM utilization, memory throughput, and other hardware counters at 10kHz. Check available metric sets: nsys profile --gpu-metrics-set=help.

Caveat: on consumer GPUs (GeForce), this requires setting GPU performance counter access. If you see ERR_NVGPUCTRPERM, run nsys status -e and check NVIDIA's permission guide.

Experimental plugins

# Power and temperature monitoring during profiling
nsys profile --enable=nvml_metrics --force-overwrite=true --export=sqlite -o target/profiling/trace <command>

# Network adapter metrics
nsys profile --enable=network_interface --force-overwrite=true --export=sqlite -o target/profiling/trace <command>

List all plugins: nsys profile --enable=help

Export to other formats

# Parquet — for pandas/Spark analysis on large traces
nsys export --type=parquetdir -o target/profiling/trace_parquet target/profiling/trace.nsys-rep

# Arrow — for Apache Arrow consumers
nsys export --type=arrowdir -o target/profiling/trace_arrow target/profiling/trace.nsys-rep

# Export only specific tables (faster for large traces)
nsys export --type=sqlite --tables=CUPTI_ACTIVITY_KIND_KERNEL,StringIds \
  -o target/profiling/kernels_only target/profiling/trace.nsys-rep

# Time-filtered export — extract just the interesting window
nsys export --type=sqlite --times=5s/10s \
  -o target/profiling/inference_only target/profiling/trace.nsys-rep

Recipes (multi-file analysis)

nsys recipe runs higher-level analyses across one or more trace files. Requires pandas — install with:

python3 /opt/nvidia/nsight-systems/*/target-linux-x64/python/packages/nsys_recipe/install.py

Useful recipes for this project:

Example:

# Diff two traces to see what changed
nsys recipe diff -i trace_before.sqlite trace_after.sqlite

# NCCL analysis for distributed profiling
nsys recipe nccl_sum -i rank0.sqlite rank1.sqlite rank2.sqlite rank3.sqlite

Available report types (quick reference)

Full list: nsys stats --help-reports

Interpreting results

What to report to the user

After analysis, present:

1. Top 3-5 kernels by total time — with percentage of total GPU time
2. Any tail anomalies — kernels where max/p50 > 2×
3. Host overhead — is cuStreamSynchronize or cudaLaunchKernel significant?
4. Diagnosis — which kernel family is the optimization target?
5. Next action — what to microbench or optimize

Mapping kernel names to model operations

nsys kernel names are mangled C++ symbols. Map them to logical operations:

• gemvx::kernel → cuBLAS GEMV (matrix-vector multiply for all linear projections)
• FusedAddRMSNormKernel → residual connection + RMS normalization
• BatchDecodeWithPagedKVCacheKernel → FlashInfer paged attention decode
• BatchPrefillWithPagedKVCacheKernel → FlashInfer paged attention prefill
• AppendPagedKVCacheKernel → KV cache page append
• RadixTopKKernel_Unified → FlashInfer sampling (token selection)
• silu_mul_fused_kernel → SiLU activation × gate (MLP)
• prefill_qk_norm_rope_kernel → QK normalization + rotary position embedding
• embedding_batched_kernel → token embedding lookup

Use :base to get these short names directly: nsys stats --report cuda_gpu_kern_sum:base.

Diagnosing sequence-length degradation

If TPOT grows with context length, run two traces with different prompt lengths:

# Short context
nsys profile ... -o target/profiling/ctx_short \
  cargo run -r --bin bench_serving -- request --prompt-len 1 --output-len 128 --warmup 1 --iters 1

# Long context
nsys profile ... -o target/profiling/ctx_long \
  cargo run -r --bin bench_serving -- request --prompt-len 2048 --output-len 128 --warmup 1 --iters 1

Compare cuda_gpu_kern_sum between the two. Only attention decode should scale with context — if other kernels also grow, investigate.

If nsys recipe diff is available (pandas installed), use it for an automated side-by-side:

nsys recipe diff -i target/profiling/ctx_short.sqlite target/profiling/ctx_long.sqlite

Critical pitfalls (team knowledge)

These are real lessons from production profiling on this codebase:

1. --cuda-graph-trace=node inflates absolute times by 30-60%. Always measure actual TPOT with bench_serving without nsys, and use nsys only for kernel time proportions and composition. Never quote a TPOT number from an nsys trace as ground truth.

2. Default --cuda-graph-trace is graph, not node. On driver ≥11.7, nsys defaults to graph granularity — the entire CUDA Graph replay appears as a single opaque block. You MUST explicitly pass --cuda-graph-trace=node to see individual kernels. This is the #1 "my trace is useless" moment.

3. p50 is not enough. A kernel can look cheap at p50 while dominating p99. In MoE workloads, NCCL all-reduce and routed expert kernels are especially prone to this — the p50 reflects pure compute but the p99 includes rank arrival skew. Always run nsys_tail_stats.py when tail behavior matters.

4. CPU launch overhead is multiplicative. Each cudaLaunchKernel costs ~5μs on the host. A per-token loop launching 20,000 tiny kernels adds ~100ms of pure CPU overhead per decode step. If cudaLaunchKernel count is surprisingly high, look for kernel fusion or CUDA Graph opportunities. Use cuda_kern_exec_sum to see queue time vs execution time.

5. cuStreamSynchronize during inference is a red flag. During model loading it's normal. During decode it means the host is blocking — look for unnecessary D2H copies or sync points. Use --filter-time to isolate inference-only API stats.

6. NCCL wait-inclusive time ≠ pure transfer time. In distributed traces, if NCCL collectives look expensive, separate rank arrival skew from actual data movement. Two ranks may do the same collective but one "takes 1.2ms" only because the other arrived 1.18ms late. Use nsys recipe nccl_gpu_overlap_trace to analyze this.

7. CUDA toolkit version affects kernel performance. Same code, same GPU: CUDA 13.1 generates ~3% faster code than 12.8 for custom CUDA kernels on sm_120. Always note the toolkit version in profiling reports. Check with nvcc --version.

8. Allocation churn on the hot path. High cuMemAllocAsync / cuMemFreeAsync counts during inference (not loading) indicate per-step allocations that should be pre-allocated or pooled. Check the CUDA API tail candidates table — allocation stalls show up as high max/p50 ratios.

9. PATH in non-interactive shells. When profiling via SSH or detached tmux, nsys may not be in PATH because ~/.bashrc is only sourced for interactive shells. Either export PATH explicitly or use the full path /usr/local/cuda/bin/nsys.

10. GPU metrics require privilege on consumer GPUs. --gpu-metrics-devices=all fails on GeForce cards with ERR_NVGPUCTRPERM. On datacenter GPUs (A100/H100/B200), it works out of the box. Run nsys status -e to check.