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Profiling
Is the skill and art of finding which part of your code needs the most time, and therefore to find the place where you can (should, need to) optimize (first). The optimization can be different things, like using library functions instead of self-written ones, re-arranging memory access, removing function calls, writing C/Fortran functions for your Python code.
The profiling can be done manually by adding time and print statements to your code or (better) by using tools like Valgrind, TAU, HPCToolkit, Score-P or Python’s Scalene or cProfile.
Tools to profile applications and perform efficiency, scaling and energy analysis are described in this document by the Virtual Institute High Performance Computing: https://www.vi-hps.org/cms/upload/material/general/ToolsGuide.pdf
Monitoring jobs on the node
It is possible to submit a second (this time) interactive job to the node where the main job is running, check with squeue where your job is running, then submit
srun -w <nodename> --pty htop
Note that there must be free slots on the machine, so you cannot use -n 80 or --exclusive for your main job (use -n 78).
Alternative method if you have X11, e.g. on Linux computers:
When you login to base, use ssh -X -Y UniID@base.hpc.taltech.ee,
then submit your main job with srun --x11 -n <numtasks> --cpus-per-task=<numthreads> --pty bash and start an xterm -e htop &` in the session.
In sbatch the option --x11=batch can be used, note that the ssh session to base needs to stay open!
Valgrind
Manual: http://valgrind.org/docs/manual/manual.html
Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.
The Valgrind distribution currently includes seven production-quality tools: a memory error detector, two thread error detectors, a cache and branch-prediction profiler, a call-graph generating cache and branch-prediction profiler, and two different heap profilers. It also includes an experimental SimPoint basic block vector generator.
Callgrind
Cachegrind
Profiling Python
Python is very slow, the best improvement is achieved by rewriting (parts of) the program in Fortran or C. See also “Python Performance Matters” by Emery Berger (Strange Loop 2022) https://www.youtube.com/watch?v=vVUnCXKuNOg
Python Scalene
Scalene is a CPU, GPU and memory profiler for Python that is very performant (introduces very little overhead).
Installation: load your favourite Python module, e.g.
module load green-spack
module load python/3.8.7-gcc-10.3.0-plhb
py-pip/21.1.2-gcc-10.3.0-python-3.8.7-bj7d
then install using pip:
python -m pip install --user scalene
Homepage and quickstart: https://github.com/plasma-umass/scalene
Python cProfile
perf
https://perf.wiki.kernel.org/index.php/Main_Page
perf is powerful: it can instrument CPU performance counters, tracepoints, kprobes, and uprobes (dynamic tracing). It is capable of lightweight profiling. It is also included in the Linux kernel, under tools/perf, and is frequently updated and enhanced.
perf began as a tool for using the performance counters subsystem in Linux, and has had various enhancements to add tracing capabilities.
TAU, Jumpshot, Paraprof
TAU can be used for profiling and for MPI tracing (not at the same time, though). See e.g. https://wiki.mpich.org/mpich/index.php/TAU_by_example
Load the spack TAU module:
module load green-spack
module load tau/2.30.2-gcc-10.3.0-2wge
Profiling
TAU supports different methods of instrumentation:
- Dynamic: statistical sampling of a binary through preloading of libraries
- Source: parser-aided automatic instrumentation at compile time
- Selective: a subcategory of source, it is automatic, but guided source code instrumentation
The simplest and only for existing binary software is dynamic profiling through tau_exec, just run
srun tau_exec your_program
several profile.* files will be created. This method can unfortunately only profile MPI functions and not user-defined ones.
Note, that profile files are only generated if the program exits normally, not if an error occurs or SLURM kills it!
You can generate reports with pprof and visualize with paraprof.
MPI tracing
The tracing can take a lot of space, it is not uncommon that tracefiles are several GB in size for each MPI-task!
export TAU_TRACE=1
srun -n 2 tau_exec ./pingpong-lg-mpi4
tau_treemerge.pl
TAU does not have a tracing visualizer, but provides tools to convert its traces to other formats, e.g. slog2 for jumpshot, otf(2) or paraver:
tau2slog2 tau.trc tau.edf -o tau.slog2
tau_convert -paraver tau.trc tau.edf trace.prv
The traces can be visualized using jumpshot (in the tau module), just run
jumpshot tau.slog2
jumpshot may open a huge window (larger than screen size), in this case use the “maximize” option of your window manager (fvwm: in the left window corner menu), jumpshot opens 3 windows: “jumpshot-4”, “Legend” and “Timeline” (if you cannof find them, use window manager menu, e.g. fvwm: right mouse button on desktop background).
EZTrace + ViTE
EZTrace 1.1 and ViTE 1.2 are installed on amp and viz.
EZTrace is a tool to analyze event traces, it has several modules:
stdio Module for stdio functions (read, write, select, poll, etc.)
starpu module for StarPU framework
pthread Module for PThread synchronization functions (mutex, semaphore, spinlock, etc.)
papi Module for PAPI Performance counters
openmpi Module for MPI functions
memory Module for memory functions (malloc, free, etc.)
ViTE is the visualization tool to visualize the generated traces, it can visualize also .otf2 traces obtained from other MPI tracing tools (e.g. converted from TAU)
HPCToolkit
Load modules
module load hpctoolkit
run application with binary instrumentation
srun -n 2 -p green-ib hpcrun <your_application>
hpcstruct `which <your_application>`
hpcprof hpctoolkit-<your_application>-measurements-<PID>
run GUI tool for interpretation
hpcviewer hpctoolkit-<your_application>-database-<PID>
starts hpcviewer and opens the database.
Paraver trace visualizer
Load the module
module load green
module load Paraver
start paraver
wxparaver
then load the .prv trace file
Extrae
Score-P
Scalable Performance Measurement Infrastructure for Parallel Codes
module load green-spack
module load scorep
The module with hash “mlw5” contains the PDT instrumenter. The module with hash “o4v3” contains the PDT instrumenter and libunwind.
https://scorepci.pages.jsc.fz-juelich.de/scorep-pipelines/docs/scorep-4.1/html/quickstart.html
compilation: prefix the compiler command with “scorep”, e.g. scorep gcc ... or scorep mpicc ..., this can also be used in Makefiles:
MPICC = $(PREP) mpicc
(and analogously for linkers and other compilers). One can then use the same makefile to either build an instrumented version with the
make PREP="scorep"
a simple make will generate an uninstrumented binary.
The environment variables SCOREP_ENABLE_TRACING and SCOREP_ENABLE_PROFILING control whether event trace data or profiles are stored in this directory. By setting either variable to true, the corresponding data will be written to the directory. The default values are true for SCOREP_ENABLE_PROFILING and false for SCOREP_ENABLE_TRACING.
Scalasca
Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks – in particular those concerning communication and synchronization – and offers guidance in exploring their causes.
module load green-spack
module load scalasca
Open|SpeedShop
module load green-spack
module load openspeedshop
module load openspeedshop-utils
DiscoPoP
to be installed
analyses source-code to find areas that can be parallelized
works only with LLVM 11.1 (included in the module)
module load green
module load discopop
PGI / Nvidia HPC SDK
On the GPU servers, the Nvidia HPC SDK is installed, which contains the PGI compilers and profilers.
IgProf
The Ignominous Profiler. IgProf is a simple nice tool for measuring and analysing application memory and performance characteristics. IgProf requires no changes to the application or the build process.
Quick start: https://igprof.org/running.html