Mist
Mist | |
---|---|
Installed | Dec 2019 |
Operating System | Red Hat Enterprise Linux 7.6 |
Number of Nodes | 54 IBM AC922 |
Interconnect | Mellanox EDR |
Ram/Node | 256 GB |
GPUs/Node | 4 V100-SMX2-32GB |
Login/Devel Node | mist.scinet.utoronto.ca |
Vendor Compilers | IBM XL |
Queue Submission | Slurm |
Warning
Mist is in early users/beta testing phase. All instructions below are temporary and subject to change.
Specifications
The Mist cluster is a GPU cluster of 54 IBM AC922 servers each with 32 IBM Power9 cores with 4 NVIDIA V100-SMX2-32GB GPU and NVLINKs in between. Each node of the cluster has 256GB RAM. It has InfiniBand EDR interconnection providing GPU-Direct RMDA capability.
Getting started on Mist
Currently Mist is under testing phase. Mist login node mist-login01 can be accessed via Niagara cluster.
ssh -Y MYCCUSERNAME@niagara.scinet.utoronto.ca ssh -Y mist-login01
Storage
The filesystem for Mist is shared with Niagara cluster. See Niagara Storage for more details.
Loading software modules
You have two options for running code on Mist: use existing software, or compile your own. This section focuses on the former.
Other than essentials, all installed software is made available using module commands. These modules set environment variables (PATH, etc.), allowing multiple, conflicting versions of a given package to be available. A detailed explanation of the module system can be found on the modules page.
Common module subcommands are:
module load <module-name>
: load the default version of a particular software.module load <module-name>/<module-version>
: load a specific version of a particular software.module purge
: unload all currently loaded modules.module spider
(ormodule spider <module-name>
): list available software packages.module avail
: list loadable software packages.module list
: list loaded modules.
Along with modifying common environment variables, such as PATH, and LD_LIBRARY_PATH, these modules also create a SCINET_MODULENAME_ROOT environment variable, which can be used to access commonly needed software directories, such as /include and /lib.
There are handy abbreviations for the module commands. ml
is the same as module list
, and ml <module-name>
is the same as module load <module-name>
.
Tips for loading software
- We advise against loading modules in your .bashrc. This can lead to very confusing behaviour under certain circumstances. Our guidelines for .bashrc files can be found here.
- Instead, load modules by hand when needed, or by sourcing a separate script.
- Load run-specific modules inside your job submission script.
- Short names give default versions; e.g.
cuda
→cuda/10.1.243
. It is usually better to be explicit about the versions, for future reproducibility. - Modules often require other modules to be loaded first. Solve these dependencies by using
module spider
.
Available compilers and interpreters
- cuda module has to be loaded first for GPU softwares.
- For most compiled software, one should use the GNU compilers (gcc for C, g++ for C++, and gfortran for Fortran). Loading an at ( IBM Advance Toolchain) or gcc module makes these available.
- The IBM XL compiler suite (xlc_r, xlc++_r, xlf_r) is also available, if you load one of the xl modules.
- To compile mpi code, you must additionally load an openmpi or spectrummpi module.
CUDA
The current installed CUDA Tookits are 10.1.243 and 10.2.89
module load cuda/<version>
The current NVIDIA driver version is 440.33.01
Documentation and API reference information for the CUDA Toolkit can be found here: http://docs.nvidia.com/cuda/index.html
GNU Compilers
A GCC-7.4.0 will be loaded automatically when loading CUDA module. More recent versions of the GNU Compiler Collection (C/C++/Fortran) are provided in the IBM Advance Toolchain and GCC modules with enhancements for the POWER9 CPU. Module at/11.0 provides GCC-7.4.1. Module at/12.0 provides GCC-8.3.1. A gcc/9.2.0 module is also available for newest GCC. A CUDA module should be loaded before loading IBM Advance Toolchain GCC modules.
More information about the IBM Advance Toolchain can be found here: https://developer.ibm.com/linuxonpower/advance-toolchain/
IBM XL Compilers
To load the native IBM xlc/xlc++ and xlf (Fortran) compilers, run
module load xl/16.1.1
IBM XL Compilers are enabled for use with NVIDIA GPUs, including support for OpenMP GPU offloading and integration with NVIDIA's nvcc command to compile host-side code for the POWER9 CPU. Information about the IBM XL Compilers can be found at the following links:IBM XL C/C++, IBM XL Fortran
OpenMPI
openmpi/<version> module is avaiable with different compilers including GCC and XL. spectrummpi/<version> module provides IBM Spectrum MPI.
PGI
To load PGI compiler and its own OpenMPI environment, run:
module load pgi/19.10 module load openmpi/3.1.3-pgi-19.10
Softwares
Anaconda (Python)
Anaconda is a popular distribution of the Python programming language. It contains several common Python libraries such as SciPy and NumPy as pre-built packages, which eases installation. Anaconda is provided as modules: anaconda3
To install Anaconda locally, user need to load the module and create a conda environment:
module load anaconda3 conda create -n myPythonEnv python=3.7
- Note: By default, conda environments are located in $HOME/.conda/envs. Downloaded tarballs and packages are under $HOME/.conda/pkgs. User may run into problem with disk quota if there are too many environments created. To clean conda cache, please run: "conda clean -y --all" and/or "rm -rf $HOME/.conda/pkgs/*" after installation of packages.
To activate the conda environment: (should be activated before running python)
source activate myPythonEnv
Once the environment is activated, user can update or install packages via conda or pip
conda install <package_name> (preferred way to install packages) pip install <package_name>
To deactivate:
source deactivate
To remove a conda enviroment:
conda remove --name myPythonEnv --all
To verify that the environment was removed, run:
conda info --envs
IBM Watson Machine Learning Community Edition (PowerAI)
IBM Watson Machine Learning Community Edition (PowerAI) contains many popular ML packages including TensorFlow and PyTorch. It is distributed through IBM Conda channel. To install packages from PowerAI, user needs to specify IBM Conda channel when using Anaconda.
module load anaconda3 conda create --name wmlce_env -c https://public.dhe.ibm.com/ibmdl/export/pub/software/server/ibm-ai/conda <package_name> (e.g. powerai, tensorflow-gpu, keras, pytorch, powerai-rapids, etc) source activate wmlce_env
NAMD
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
v2.13
module load cuda/10.1.243 at/11.0 fftw/3.3.8 spectrummpi/10.03 namd/2.13
Running with one process per node
An example of the job script (using 1 node, one process per node, 32 CPU threads per process + 4 GPUs per process):
#!/bin/bash #SBATCH --time=20:00 #SBATCH --gpus-per-node=4 #SBATCH --ntasks=1 #SBATCH --nodes=1 #SBATCH -p compute_full_node module load cuda/10.1.243 at/11.0 fftw/3.3.8 spectrummpi/10.03 namd/2.13 scontrol show hostnames > nodelist-$SLURM_JOB_ID `which charmrun` -npernode 1 -hostfile nodelist-$SLURM_JOB_ID `which namd2` +setcpuaffinity +pemap 0-127:4 +idlepoll +ppn 32 +p $((32*SLURM_NTASKS)) stmv.namd
Running with one process per GPU
NAMD may scale better if using one process per GPU. Please do your own benchmark. An example of the job script (using 1 node, one process per GPU, 8 CPU threads per process + 1 GPUs per process):
#!/bin/sh #SBATCH --time=20:00 #SBATCH --gpus-per-node=4 #SBATCH --ntasks=4 #SBATCH --nodes=1 #SBATCH -p compute_full_node module load cuda/10.1.243 at/11.0 fftw/3.3.8 spectrummpi/10.03 namd/2.13 scontrol show hostnames > nodelist-$SLURM_JOB_ID `which charmrun` -npernode 4 -hostfile nodelist-$SLURM_JOB_ID `which namd2` +setcpuaffinity +pemap 0-127:4 +idlepoll +ppn 8 +p $((8*SLURM_NTASKS)) stmv.namd
Submitting jobs
Once you have compiled and tested your code or workflow on the Mist login nodes, and confirmed that it behaves correctly, you are ready to submit jobs to the cluster. Your jobs will run on some of Mist's 53 compute nodes. When and where your job runs is determined by the scheduler.
Mist uses SLURM as its job scheduler. It is configured to allow only Single-GPU jobs and Full-node jobs (4 GPUs per node).
You submit jobs from a login node by passing a script to the sbatch command:
mist-login01:scratch$ sbatch jobscript.sh
This puts the job in the queue. It will run on the compute nodes in due course. In most cases, you should not submit from your $HOME directory, but rather, from your $SCRATCH directory, so that the output of your compute job can be written out (as mentioned above, $HOME is read-only on the compute nodes).
Example job scripts can be found below. Keep in mind:
- Scheduling is by single gpu or by full node, so you ask only 1 gpu or 4 gpus per node.
- Your job's maximum walltime is 24 hours.
- Jobs must write their output to your scratch or project directory (home is read-only on compute nodes).
- Compute nodes have no internet access.
- Your job script will not remember the modules you have loaded, so it needs to contain "module load" commands of all the required modules (see examples below).
Single-GPU job script
For a single GPU job, each will have a quarter of the node which is 1 GPU + 8/32 CPU Cores/Threads + ~58GB CPU memory. Users should never ask CPU or Memory explicitly. If running MPI program, user can set --ntasks to be the number of MPI ranks. It is suggested to use NVIDIA Multi-Process Service (MPS) if running multiple MPI ranks on one GPU.
#!/bin/bash #SBATCH --nodes=1 #SBATCH --gpus-per-node=1 #SBATCH --time=1:00:0 module load anaconda3 source activate conda_env python code.py ...
Full-node job script
Multi-GPU job should ask for a minimum of one full node. User need to specify "compute_full_node" partition in order to get all resource on a node.
- An example for a 2-node, 8-rank OpenMPI job: (Each rank binds to 1 GPU and 8 physical CPU cores in this case)
#!/bin/bash #SBATCH --nodes=2 #SBATCH --gpus-per-node=4 #SBATCH --ntasks=8 #SBATCH --time=1:00:00 #SBATCH -p compute_full_node module load cuda/10.1.243 at/11.0 openmpi/4.0.2 mpirun -bind-to core -map-by slot:PE=8 -report-bindings ./program