1 Introduction
2 Allocation Information
3 System Architecture
4 Accessing the System
5 Computing Environment
6 Managing Files
7 Building Software
8 Software
9 Running Jobs
10 Sample Job Script
11 Help
12 References

Introduction

Scientific discovery today is being enabled through computational and data intensive research that exploit enormous amounts of available data.

The KyRIC cluster will advance several exciting research programs across many disciplines, such as Bioinformatics and System Biology Algorithms, Large Graph and Evolutionary Network Analysis, Image Processing, and Computational Modeling and Simulation.

The system is well suited for running computations in high-throughput genome sequencing, natural language processing of large datasets, and data scientists working on massive data graphs and big data analytics.

The KyRIC cluster has a hybrid architecture. It has large memory nodes that are increasingly needed by a wide range of ACCESS researchers, particularly researchers working with big data. Each of the KyRIC nodes in the cluster also has large 6TB SSD drives that are suitable to perform analytics on big data along with a traditional NFS mounted scratch.

Innovative Components: Large memory nodes with local SSD drives and NFS-mounted scratch.
Award Number: NSF MRI infrastructure award (ACI-1626364)
ACCESS hostname: kxc.ccs.uky.edu

Figure 1. LCC-KyRIC System

Allocation Information

As an ACCESS computing resource, KyRIC is accessible to ACCESS users who are given time on the system. To obtain an account, users may submit a proposal through the ACCESS Allocation Request System (XRAS) or request a Trial Account. Interested parties may contact ACCESS User Support for help with a KyRIC proposal.

System Architecture

The KyRIC hybrid cluster consists of two subsystems: a 5 nodes cluster, each with 4 10-core processors, 3TB RAM, and a 6TB SSD array; Each of these nodes have 40 cores (Broadwell class and lntel(R) Xeon(R) CPU E7-4820 v4 @ 2.00GHz with 4 sockets, 10 cores/socket). These 5 dedicated ACCESS nodes will have exclusive access to approximately 300 TB of network attached disk storage. All these compute nodes are interconnected through a 100 Gigabit Ethernet (l00GbE) backbone, and the cluster login and data transfer nodes will be connected through a 100Gb uplink to internet2 for external connections. Due to the use of the 100GbE network, this cluster is for single node jobs only and is not recommended for multi-node jobs, such as those using MPI.

Compute Nodes

These nodes are where jobs are actually executed after being submitted via the user-facing login nodes.

Table 1. Compute Node Specifications

MODEL	PowerEdge R930 Intel(R) Xeon(R) CPU E7-4820 v4 @ 2.00GHz
NUMBER OF NODES	5
TOTAL CORES PER NODE	40 cores 4 sockets; 10 cores/socket
THREADS PER CORE	2
THREADS PER NODE	80
CLOCK RATE	2.00
RAM	3TB
LOCAL STORAGE	6TB (SSD)
EXTENDED STORAGE	300 TB (NFS-mounted)

The login node is what users will directly access in order to submit jobs that will get forwarded to and executed in the compute nodes.

Table 2. Login Node Specifications

MODEL	Virtual Machines hosted in bare metal server PowerEdge R930 Intel(R) Xeon(R) CPU E7-4820 v4 @ 2.00GHz
NUMBER OF NODES	2
TOTAL CORES PER NODE	4
THREADS PER CORE	2
THREADS PER NODE	8
CLOCK RATE	2.00
RAM	16GB
EXTENDED STORAGE	300 TB (NFS-mounted)

Data Transfer Node

This node facilitates the transfer of data in and out of the KyRIC system. Users will log in to this node with the same credentials as for the login nodes. Also, Globus endpoints are available only on this node for parallel transfers.

Table 3. Data Node Specification

MODEL	Virtual Machines hosted in bare metal server PowerEdge R930 Intel(R) Xeon(R) CPU E7-4820 v4 @ 2.00GHz
NUMBER OF NODES	1
TOTAL CORES PER NODE	8
THREADS PER CORE	2
THREADS PER NODE	16
CLOCK RATE	2.00
RAM	32GB
EXTENDED STORAGE	300 TB (NFS-mounted)

Network

All nodes are interconnected through a 100 Gigabit Ethernet (l00GbE) backbone, and the cluster login and data transfer nodes will be connected through a 100Gb uplink to internet2 for external connections

Table 4. File Systems

FILE SYSTEM	QUOTA	FILE RETENTION

FILE SYSTEM	QUOTA	FILE RETENTION
`$HOME`	10GB	No file deletion policy applied on this partition
`$PROJECT`	500GB	No file deletion policy applied on this partition
`$SCRATCH`	10TB	30-day file deletion policy

Accessing the System

The login node for the cluster is kxc.ccs.uky.edu; authentication is now accomplished via SSH keys. Local password authentication is not supported; users must generate and install their own SSH keys. For help with either of these, see the Generating SSH Keys and Uploading Your Public Key pages.

If all else fails, you may ‘upload’ your public key by contacting us. Please send an email to help-hpc@hpc.uky.edu with the subject line that begins with "[KXC] (your_XSEDE/ACCESS username)".

After you have uploaded your public key, you should be able to connect to the KyRIC system using an SSH client. For example, from a computer running a Linux, MacOS, Windows Powershell, or Windows Subsystem for Linux, you may connect to KyRIC by opening a Terminal and entering:

ssh yourUserName@kxc.ccs.uky.edu

Third-party SSH clients that provide a GUI (e.g., Bitvise, MobaXterm, PuTTY) may also be used to connect to KyRIC.

When you log in to kxc.ccs.uky.edu, you will be assigned one of the two login nodes: kxc-login[1-2].ccs.uky.edu. These nodes are identical in both architecture and software environment. Users should normally log in through kxc.ccs.uky.edu but may specify one of the two nodes directly if they see poor performance.

Do not use the login nodes for computationally intensive processes. These nodes are meant for compilation, file editing, simple data analysis, and other tasks that use minimal compute resources. All computationally demanding jobs should be submitted and run through the batch queuing system.

Computing Environment

Modules

The Environment Modules package provides for dynamic modification of your shell environment. "module" commands set, change, or delete environment variables, typically in support of an application. They also let the user choose between different versions of the same software or different combinations of related codes. Several modules that determine the default KyRIC environment are loaded at login time.

Citizenship

You share KyRIC with other users, and what you do on the system affects others. Exercise good citizenship to ensure that your activity does not adversely impact the system and the research community with whom you share it. Here are some rules of thumb:

Don't run jobs on the login nodes.
Don't stress the filesystem.
Do use the debug partition to test out your job submission script.
Do submit an informative help-desk ticket.

Managing Files

No user data is backed up. Users are responsible for their own backups.

Each project and user is given a scratch space and home space. A good practice is to write your job's output into your scratch space. All compute nodes also have a local 5 TB SSD disk attached to it, but this local temporary space is shared among all jobs running on a single node and will be cleaned up (deleted) upon job completion.

Transferring your Files

KyRIC nodes support the following file transfer protocols.

scp ( if you have your SSH keys setup)
rsync (if you have your SSH keys setup)
Globus (only through DTN node)

Users are encouraged to transfer data using rclone, scp, globus, etc. through the high-speed data transfer node (DTN) and not through the login nodes.

Building Software

Singularity containers are supported. Building a Singularity container requires root access outside of the cluster. If you have a Singularity container ready, you can copy it into the cluster and run your jobs. Most of the software will be provided through singularity containers. Standard GNU and Intel compilers will be provided.

Software

Discover installed software by running "module avail".

Running Jobs

Job Accounting

KyRIC allocations are made in core-hours. The recommended method for estimating your resource needs for an allocation request is to perform benchmark runs. The core-hours used for a job are calculated by multiplying the number of processor cores used by the wall-clock duration in hours. KyRIC core-hour calculations should assume that all jobs will run in the regular queue and that they are charged for use of all 40 cores on each node.

The Slurm scheduler tracks and charges for usage to a granularity of a few seconds of wall clock time. The system charges only for the resources you use, not those you request. If your job finishes early and exits properly, Slurm will release the node back into the pool of available nodes. Your job will only be charged for as long as you are using the node.

Job Scheduler

KyRIC uses the Simple Linux Utility for Resource Management (SLURM) batch environment. When you run in batch mode, you submit jobs to be run on the compute nodes using the "sbatch" command as described below. Remember that computationally intensive jobs should be run only on the compute nodes and not the login nodes.

The user must create a Slurm submission job script ("jobscript") and the job can be executed by submitting a job to the queues:

login$ sbatch jobscript

Table 5. Common Slurm Commands

Command	Description
`sbatch script_file`	Submit SLURM job script
`scancel job_id`	Cancel job that has job_id
`squeue -u user_id`	Show jobs that are on queue for user_id
`sinfo`	Show partitions/queues, their time limits, number of nodes, and which compute nodes are running jobs or idle.

Table 6. sbatch Options

PROPERTY & DESCRIPTION	SYNTAX	EXAMPLE USE

PROPERTY & DESCRIPTION	SYNTAX	EXAMPLE USE
Job name custom-label (in addition to an integer id for the job automatically given by the program)	`#SBATCH –J jobname`	`#SBATCH --job-name=my_first_job`
Partition/queue specify where (queue) job is to run	`#SBATCH -p partition_id`	`#SBATCH -partition=normal` `#SBATCH -partition=debug`
Time limit job will be killed if it reaches time_limit specified.	`#SBATCH -t time_limit`	`#SBATCH --time=01:00:00 # one-hour limit` `#SBATCH --time=2-00:00:00 # 2-day limit`
Memory (RAM) The job will use up to the specified memory_amount.		`#SBATCH --mem=32g # request 32 GB ram`
Project account Run the job under this project account.	`#SBATCH -A account`	`#SBATCH --account=sampe_proj_acct`
Standard output filename specify stdout filename	`#SBATCH -o filename`	`#SBATCH --output=slurm%A_@a.out` `#SBATCH --output=prog_output.log`
Number of nodes and cores Always the number of nodes is 1 and cores can be upto 40	`#SBATCH --nodes=1` `#SBATCH -n X`	`#SBATCH --nodes=1` `#SBATCH -n 8`

Partitions (Queues)

Table 7. KyRIC Production Queues

QUEUE NAME	NODE TYPE	MAX NODES PER JOB (ASSOC'D CORES)*	MAX DURATION	MAX JOBS IN QUEUE*	CHARGE RATE (PER CORE-HOUR)

QUEUE NAME	NODE TYPE	MAX NODES PER JOB (ASSOC'D CORES)*	MAX DURATION	MAX JOBS IN QUEUE*	CHARGE RATE (PER CORE-HOUR)
normal	compute	1 node (40 cores)	72 hrs.	5*	1 SU

Interactive Sessions

You can also login to the compute node and run the jobs interactively if only the node is allocated to you.

Sample Job Script

#!/bin/bash
#SBATCH --time=00:15:00                  # Max run time
#SBATCH --job-name=my_test_job           # Job name
#SBATCH --ntasks=1                       # Number of cores for the job. Same as SBATCH -n 1
#SBATCH --partition=normal               # Specify partition/queue
#SBATCH -e slurm-%j.err                  # Error file for this job.
#SBATCH -o slurm-%j.out                  # Output file for this job.
#SBATCH -A <your project account>  # Project allocation account name (REQUIRED)

./myprogram   # This is the program that will be executed on the compute node. You will substitute this with your scientific application.

Help

Please submit tickets through the ACCESS portal with information detailing your problems.

ACCESS Documentation

KyRIC - Kentucky