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NCSA Blue Waters Examples

Examples of running basic jobs on NCSA's Blue Waters

Login Node Splash Screen

   ___  __           _      __     __
  / _ )/ /_ _____   | | /| / /__ _/ /____ ___  ___
 / _  / / // / -_)  | |/ |/ / _ `/ __/ -_) __)(_-<
/____/_/\_,_/\__/   |__/|__/\_,_/\__/\__/_/  /___/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Batch and Scheduler configuration.
  Queues:  normal (default), high, debug, noalloc
  Features:  "xe" (default), "xk", "x" (xe or xk non-specific)
             "xehimem" (128GB mem), "xkhimem" (64GB mem)
  30 min default wall time, 7 day maximum
  -lnodes=X:ppn=Y syntax supported.

All SSH traffic on this system is monitored.

Questions?  Mail [email protected] to create a support ticket.
For known issues:  https://bluewaters.ncsa.illinois.edu/known-issues
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Running a Job with Shifter

Most of this will follow the NCSA Blue Waters documentation on Shifter, but it will additionally give some further information and asides to get new users up to speed.

On Blue Waters, Shifter is provided as a module called shifter. Unlike other modules, it can only be loaded on a MOM node in a Shifter job, which is a job that requests shifter generic resource.

Note: A Machine Oriented Mini-server (MOM) node is a shared service resource that manages job execution, and on Blue Waters is accessed through starting an interactive session.

Example: Running a Docker image

From the Blue Waters login node start an interactive Shifter job on a single node with 32 processes per node (ppn) on an XE node (N.B. XK is required for GPUs) for a maximum of 1 hour

qsub -I -l gres=shifter -l nodes=1:ppn=32:xe -l walltime=01:00:00

The job will then be queued up

INFO: Job submitted to account: abcd
qsub: waiting for job 12345689.bw to start

and when it returns (which can take some time) the user will be on a MOM node. Once the job starts, load the shifter module

module load shifter

to start using the shifter and shifterimg commands.

aprun -b -N 1 -- shifter --image=centos:7 -- /bin/bash -i

N.B.: If you don't include the interactive flag -i shifter will run the image with no prompt, so you will have to guess when execution finishes in the interactive session.

Finding Docker images that can work with Blue Waters can be a bit tricky given

when you prepare a Docker image for your application, make sure to use a base image that provides glibc that supports the version of Linux kernel installed on Blue Waters, which is version 3.0.101. This requirement is tricky to check automatically because it depends on the version of glibc and --enable-kernel flag used at the time glibc is compiled. If glibc provided by the operating system in the image does not support the version of Linux kernel installed on Blue Waters, consider using a different base image.

From a NCSA help ticket, it was revealed that distributions with glibc v2.23 or older can be made compatible with the Linux kernel on Blue Waters (v3.0.101), whereas glibc v2.24 or newer can not. So before you try to use a Docker image on Blue Waters check it locally.

Examples:

The python:3.8 image can NOT be used

$ docker run --rm python:3.8 /bin/bash -c "ldd --version"
ldd (Debian GLIBC 2.28-10) 2.28
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

but the centos:7 image CAN be used

$ shifterimg pull centos:7
$ docker run --rm centos:7 /bin/bash -c "ldd --version"
ldd (GNU libc) 2.17
Copyright (C) 2012 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

If you tried to run an incompatible Docker image on Blue Waters you'd get a kernel fatal error like the following

$ shifterimg pull python:3.8
$ aprun -b -N 1 -cc none -- shifter --image=python:3.8 --entrypoint=/bin/bash
mount: warning: ufs seems to be mounted read-only.
mount: warning: dsl/opt seems to be mounted read-only.
FATAL: kernel too old
Application 96757362 exit codes: 127
Application 96757362 resources: utime ~0s, stime ~1s, Rss ~22900, inblocks ~40955, outblocks ~38774

Running a shifter job with GPUs

Running on a GPU with shifter requires using the XK nodes

qsub -I -l gres=shifter -l nodes=1:ppn=8:xk -l walltime=01:00:00

and then loading both the shifter and nvidia modules

module load shifter
module load craype-accel-nvidia35

then the NVIDIA drivers and CUDA libraries can be picked up

aprun -b -N 1 -- shifter --image=centos:7 -- /bin/bash -c "nvidia-smi && nvcc --version"
mount: warning: ufs seems to be mounted read-only.
mount: warning: dsl/opt seems to be mounted read-only.
Thu Jan 14 23:28:33 2021
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 390.46                 Driver Version: 390.46                    |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  Tesla K20X          On   | 00000000:02:00.0 Off |                    0 |
| N/A   32C    P8    17W / 225W |      0MiB /  5700MiB |      0%   E. Process |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID   Type   Process name                             Usage      |
|=============================================================================|
|  No running processes found                                                 |
+-----------------------------------------------------------------------------+
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2017 NVIDIA Corporation
Built on Fri_Nov__3_21:07:56_CDT_2017
Cuda compilation tools, release 9.1, V9.1.85

Note that given that Blue Waters has CUDA 9 installed, and CUDA 10 will not be installed given that Blue Waters is entering end-of-life operations, modern machine learning frameworks like JAX, PyTorch (v1.X), and TensorFlow (v2.X) can not use the GPUs.

Blue Waters does have the Blue Waters Python software stack (bwpy), which can be loaded with

module load bwpy/<version you want here> # example bwpy/2.0.4

which includes PyTorch and TensorFlow, but quite old releases (torch v0.X and tensorflow v1.X) that are compatible with CUDA v9 only.