hpc-tests

NB This is a fork for the NREL prototype environment and is not fully complete

Performance testing-as-code for HPC systems.

This package defines automated performance tests for HPC systems using both synthetic and MPI-based application benchmarks. It is designed to easily compare results from different systems, system configurations and/or environments (e.g. compilers & MPI libraries). At present results are included for 2x systems, with comparisons of performance using InfiniBand and RoCE (RDMA over Converged Ethernet) interconnects.

The current test matrix is shown below - NB: Note only IMB and CP2K have been updated for the NREL prototype environment at present.

Application	Benchmark	MPI Library	Notes
OSU Micro Benchmarks (OMB)	latency, bandwidth, alltoall, allgather, allreduce, mbw_mr	IntelMPI, OpenMPI
Intel MPI Benchmarks (IMB)	PingPong, uniband, biband	IntelMPI, OpenMPI
High Performance Linpack (HPL)	-	IntelMPI	Uses Intel-optimised version with MKL
Castep	TiN, Al3x3, DNA	IntelMPI	Requires licence
CP2K	H20-256	IntelMPI, OpenMPI
OpenFOAM	Motorbike	IntelMPI, OpenMPI
GROMACS	HECBioSim benchmarks: 61k, 1.4M and 3M atom cases	IntelMPI, OpenMPI
WRF	CONUS 2.5km, CONUS 12.5kms	IntelMPI, OpenMPI

For more information on the actual tests defined and how to run them see the README file in the relevant benchmark directory.

The ReFrame framework is used to define tests in a portable fashion in the reframe_<application>.py file in each application directory.

Results are compared and plotted using juypter notebooks, with a <application>.ipynb file in each application directory.

This package does not automate build/install of the benchmarked applications themselves for your system. This allows it to be used to assess performance of current system application installs, custom builds, or for performance comparisons between different builds. However, for each benchmark installation instructions are provided using OpenHPC-provided packages (where relevant) and/or Spack (which does not require root).

Repository Contents

Key repository contents are as follows:

apps/
    <application>/
        reframe_<application>.py    - the ReFrame tests for <application>
        <application>.ipynb         - jupyter notebook plotting results for <application>
modules/                            - python modules for functionality common to multiple tests
reframe/                            - the ReFrame installation
reframe_config.py                   - the description of each system for ReFrame
output/                             - ReFrame test output - see Reframe Concepts below
perflogs/                           - ReFrame performance logs - see Reframe Concepts below

Installation

Ensure you have an HPC system with:

• slurm (while ReFrame itself can use other schedulers some extensions provided here are are currently slurm-specific)
• a module system
• git

Python 3.6+ and various python modules will be required (due to ReFrame) - instructions here use conda to provide this. Some way of compiling applications is required - instructions here use spack which has its own prerequisites.

1. Clone this repo:

    cd /projects/benchmarks
    git clone git@github.com:stackhpc/nrel-benchmarks.git
   

2. Load reframe via spack:

    spack load reframe
   

3. Create and activate an hpc-tests conda environment:

    spack load miniconda3
    conda init bash
    conda env create -f environment.yml
    # now logout and back in:
    conda activate hpc-tests
   

4. Set up a public Jupyter notebook server:

    cd setup
    ./jupyter-server.sh <<< PASSWORD
   

   Replacing PASSWORD with a password for Jupyter. This only needs to be done once and sets up a self-signed SSL certificate - note your browser will complain when connecting to the notebook.

5. If using spack to compile applications, install and set it up - see sections below. NB: The Slurm appliance's spack.yml playbook will install Intel MPI Benchmarks and CP2K.

6. For a new system, add it to the reframe configuration file reframe_config.py - see separate section below. NB: This should already be done for Vermilion's lg partition.

ReFrame Concepts & Configuration

To configure these tests for a new system some understanding of ReFrame is necessary, so key aspects are defined here.

Tests in ReFrame are defined by Python scripts - here, the apps/<application>/reframe_<application>.py files. These define a generic test, independent of system details like scheduler, MPI libraries, launcher etc. These aspects are defined for the system(s) under test in the reframe configuration file reframe_config.py. A system definition contains one or more partitions which are not necessarily actual scheduler partitions, but simply logical separations within the system. Partitions then support one or more environments which describe the modules to be loaded, enviroment variables, options etc. Environments are defined separately from partitions so they may be specific to a system + partition, common to multiple systems or partitions, or a default environment may be overridden for specific systems and/or partitions. The third level is the tests themselves, which may also define modules to load etc. as well as which environments, partitions and systems they are valid for. ReFrame then runs tests on combinations of valid partitions + environments.

Despite this flexibility, in practice the features ReFrame exposes at each level affect how the system configuration should be defined. As an example, the setup for AlaSKA given in reframe_config.py covers:

• Both HDR 100 InfiniBand and 25G Ethernet (RoCE) networks
• Various MPI libraries and fabric libraries etc
• Various compilers.

Note that:

• The environment variables used to select a network varies, depending on the MPI+fabric libraries. Therefore the compiler, MPI library + fabric variant and network selection environment variables must defined together in a partition.
• Because we use spack and/or easybuild to install packages, and the generated module names encode the compiler + MPI library chain, the application module names must be defined in the environment.
• The tests themselves can then be fully generic, without having to include logic for specific systems/partitions/environments.

Adding a new system

Modify the following aspects of reframe_config.py - use the config for "alaska" as an example and follow ReFrame's configuration documentation:

• Add a new system into the "systems" key.
• Add partitions to this system as required to cover your test matrix. Within each partition:
  • The "modules" defined here should be sufficent to load an MPI library (whether a compiler module must be specified to do that depends on how your module hierarchy is configured).
  • Define any environment variables required to get the scheduler and MPI library combination to function properly. The program and slurm sbatch scripts provided in helloworld/ may be helpful in testing this.
• In the "environments" section, for each test you want to run on this system copy an existing test environment definition and change:
  • "target_systems" to list the "system:partition" combintations you want to run on
  • "modules" to specify the module(s) needed to run the appropriate benchmark within the specified partition. Note that depending on how benchmark modules are named, you may need to specify multiple environments with different partitions in "target_systems".

You also need to update various files in 'systems':

• sysinfo.json defines some properties for tested systems
• Other application/benchmark-specific files should be placed in a system-named directory - see the relevant README.

Usage

Setup your environment:

cd /projects/benchmarks
spack load reframe
spack load miniconda3
conda activate hpc-tests

Firstly, run tests for one of the applications installed via spack:

# Intel MPI Benchmarks:
reframe -C reframe_config.py -c apps/imb/ --run --performance-report

# CP2K:
reframe -C reframe_config.py -c apps/cp2k/ --run --performance-report

Note some tests also have tags which can be used to filter tests - see the appropriate README.

• ReFrame will generate two types of output for each test:

  • Test outputs, including stdout, stderr and any results files which should be retained. These are copied to the output/ directory tree, and overwritten each time a test is re-run.
  • "Performance variables", i.e. metrics extracted or computed from test outputs. These are defined in the tests themselves, and saved by ReFrame into a "performance log" in the perflog/ directory tree. A performance log is a record-structured file with each line containing data for one performance variable from a run.

  Both of these use the same directory structure:

    <system>/<partition>/<environment>/test_directory/test/
  

Secondly, create/update plots for this system:

• Start the jupyter server:

  cd /projects/benchmarks
  jupyter notebook
  

• Then browse to https://<login-node-ip>:<port> where port is given in the output from above, and login using the password you specified above (note: the notebook command output will include the hostname but you will have to use the IP).

• You will now see a file browser. Navigate to apps/<application>/<application>.ipynb.

• Step through the notebook using the play buttons.

• Once happy with results, commit to a branch.

• NB: Notebooks in the master branch should not contain outputs, only plotting code. This makes merging between branches easier. The script tools/plots.py script may be useful to clear or refresh notebook outputs.

Spack

Spack setup is non-trivial and the docs/tutorials are somewhat out-of-date / missing info in places (details in this bug). This section will therefore try to describe how to get a working spack setup from scrach on an OpenHPC system using tmod for modules. However you should probably read the "basic use" section for concepts. The quick version is that spack installs packages as described by a "spec" which (as well as the version) can optionally describe the compiler and any dependencies (such as MPI libraries). Multiple specs of the same package may be installed at once.

Setup

First, install:

cd ~
git clone https://github.com/spack/spack.git

Modify ~/.bashrc to contain:

export SPACK_ROOT=~/spack
. $SPACK_ROOT/share/spack/setup-env.sh

This makes spack commands available in your shell, but does not integrate spack with your module system if that is lmod - contrary to what the documentation says.

Run:

spack compiler list

and check a useful compiler is shown. If not, load the appropriate module, run:

spack compiler find

and check it gets added.

Check if patch is available on your system. If not, install it using spack:

spack install patch

Then load it - you will have to do this every time before running spack install (or add it to your .bashrc):

spack load patch

At this point you could install other compilers using Spack if required - not shown here but essentially the same as the package install instructions below, plus the spack compiler ... commmands shown above.

Finally, as ReFrame cannot use spack load directly we need to enable spack's support for lmod:

• Firstly, modify ~/.spack/modules.yaml to e.g.:

  modules:
    enable::
      - lmod
    <snip>
    lmod:
      core_compilers:
        - gcc@7.3.0
      hierarchy:
        - mpi
  

  This:

  • Tells spack to use lmod as the module system (the "::" means only use this)
  • Lists the compiler(s) to use as the entry point to the module tree.
  • Tells spack to base the tree on the mpi library dependency for packages.

• Rebuild any existing modules:

  spack module lmod refresh --delete-tree -y
  

  This only needs to be done once after modifying modules.yaml, all subsequent package installations will use these settings.

• Tell lmod where to find the module tree root, e.g.:

  module use $SPACK_ROOT/share/spack/lmod/linux-centos7-x86_64/Core/
  

• Add the module use ... command to your ~/.bashrc.

Installing Packages

Spack installs packages using a spec, for example to install openmpi integrated with the system slurm and using the ucx transport layer:

spack install openmpi@4.0.3 fabrics=ucx schedulers=auto

Note that slurm integration - via pmix - appears to need openmpi v4 or greater. See this PR for details.)

Confirm the slurm integration using:

spack load openmpi@4.0.3 # assuming this is the only spack-provided openmpi4 build
ompi_info | grep slurm # should show various MCA components for slurm

For full details of spack spec formats see the documentation but in brief:

• The "@" suffix gives a version, and can be e.g. "@4" for latest v4, "@4:" for latest after v4 (e.g. possibly v5).
• The "a=b" portions are called "variants" - spack list <package> will show what defaults are.
• A compilier can optionally be specified too as e.g. "%gcc@9.0.3".

We can now install packages depending on this openmpi installation.

First, find the hash of the relevant openmpi installation, e.g. for the above:

spack find -l openmpi@4.0.3

will return something like ziwdzwh.

Install a package using this MPI library, e.g.::

spack spec -I gromacs@2016.4 ^openmpi/ziwdzwh

The ^ provides a spec for a dependency - normally this can just be another spack spec e.g. openmpi@4: but here we use /<hash> to ensure spack reuses the library we previously built, rather than building another openmpi package. This shouldn't generally be necessary but appears to be in this case due to some subtleties in how Spack handles dependencies with non-default options.

Note that before actually installing a package, you can use spack spec -I to process dependencies and see what is already installed, e.g.:

spack spec -I gromacs@2016.4 %gcc@9: ^openmpi/qpsxmnc

Adding a test

Some things which might help:

• tools/report.py is a CLI tool to interrogate performance logs.

Synthetic benchmarks will all be different, but application benchmarks should follow these conventions:

• Run under time and extract a performance variable 'runtime_real' giving the end-to-end wallclock time (see e.g. reframe_gromacs.py).
• Scale the test across numbers of nodes - this can be done using modules.reframe_extras.scaling_config(), see apps/castep/reframe_castep.py for an example.
• Add tags 'num_procs=%i' and 'num_nodes=%i'. This allows modules.utils.tabulate_last_perf() to automatically generate scaling plots (e.g. see gromacs or castep examples).