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High Level Differences from ikt

  1. You only get what you ask for, regardless of the resources available on the node. If you ask for 1 CPU, you'll only get one. If you ask for 1GB of RAM, you'll only get 1GB.
  2. An allocation won't get the same set of nodes all the time, just access to the particular number of nodes to which they're entitled.
  3. No occasional preemption in ckpt (formerly bf queue) for the moment.
  4. Preempted jobs get 30s to do something smart before being killed and requeued.
  5. Mox isn't monitored yet. Please report any problems to help@uw.edu with Hyak as the first word in the subject.

Connecting

SSH = mox.hyak.uw.edu

BBCP = mox1.hyak.uw.edu

File Transfers

Internal to Hyak systems

You can copy files at high speed without a password between the Hyak systems using commands like the ones below.

From ikt to mox

ikt1$ hyakbbcp myfile mox1.hyak.uw.edu:/gscratch/MYGROUP/
ikt1$ hyakbbcp -r mydirectory mox1.hyak.uw.edu:/gscratch/MYGROUP/

From mox to ikt

mox1$ hyakbbcp myfile ikt1.hyak.uw.edu:/gscratch/MYGROUP/
mox1$ hyakbbcp -r mydirectory ikt1.hyak.uw.edu:/gscratch/MYGROUP/

Slurm Primer

Show Queue

All Jobs
squeue
Jobs in Allocation
squeue -p <my short group>
All Jobs in ckpt (was bf)
squeue -p ckpt
Jobs in ckpt from Allocation
squeue -A <my short group>-ckpt

Submit

Own Allocation

Like ikt you're limited to the number of nodes your group purchased for your allocation.

sbatch -p <my short group> -A <my short group> test-job.sh

Checkpoint Allocation (formerly bf queue)

If you want access to all the nodes in the cluster, you need to use the ckpt partition.

sbatch -p ckpt -A <my short group>-ckpt test-job.sh

Interactive Session

Build Allocation - usage limited by core count and time

srun -p build --pty /bin/bash

Own Allocation

srun -p <my short group name> --pty /bin/bash

See Node Counts per Allocation

sacctmgr show qos format=name,grptres

Show Job Info

scontrol show job <jobid>

Show Node Info

scontrol show node <node>

Sample Job Script

Change items that are bold and red.

#!/bin/bash
## Job Name
#SBATCH --job-name=test-job
## Resources
## Nodes
#SBATCH --nodes=2   
## Walltime (ten minutes)
#SBATCH --time=10:00
## Memory per node

#SBATCH --mem=2G
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/MYGROUP/MYUSER/MYRUN

module load icc_<version>-impi_<VERSION>
mpirun /gscratch/MYGROUP/MYMODEL/MYMODEL-BIN


Other documentation:

See articles on mox at below link:

Hyak HOWTO

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