Grace:QuickStart

Grace Quick Start Guide

Grace Usage Policies

Access to Grace is granted with the condition that you will understand and adhere to all TAMU HPRC and Grace-specific policies.

General policies can be found on the HPRC Policies page.

Grace-specific policies, which are similar to Terra, can be found on the Grace Policies page.

Accessing Grace

Most access to Grace is done via a secure shell session. In addition, two-factor authentication is required to login to any cluster.

Users on Windows computers use either PuTTY or MobaXterm. If MobaXterm works on your computer, it is usually easier to use. When starting an ssh session in PuTTY, choose the connection type 'SSH', select port 22, and then type the hostname 'Grace.tamu.edu'. For MobaXterm, select 'Session', 'SSH', and then remote host 'Grace.tamu.edu'. Check the box to specify username and type your NetID. After selecting 'Ok', you will be prompted for Duo Two Factor Authentication. For more detailed instructions, visit the Two Factor Authentication page.

Users on Mac and Linux/Unix should use whatever SSH-capable terminal is available on their system. The command to connect to Grace is as follows. Be sure to replace [NetID] with your TAMU NetID.

[user1@localhost ~]$ ssh [NetID]@Grace.tamu.edu

Note: In this example [user1@localhost ~]$ represents the command prompt on your local machine.
Your login password is the same that used on Howdy. You will not see your password as your type it into the login prompt.

Off Campus Access

Please visit this page to find information on accessing Grace remotely.

For more detailed instructions on how to access our systems, please see the HPRC Access page.

Navigating Grace & Storage Quotas

When you first access Grace, you will be within your home directory. This directory has smaller storage quotas and should not be used for general purpose.

You can navigate to your home directory with the following command:

[NetID@Grace1 ~]$ cd /home/NetID

Your scratch directory has more storage space than your home directory and is recommended for general purpose use. You can navigate to your scratch directory with the following command:

[NetID@Grace1 ~]$ cd /scratch/user/NetID

You can navigate to scratch or home easily by using their respective environment variables.

Navigate to scratch with the following command:

[NetID@Grace1 ~]$ cd $SCRATCH

Navigate to home with the following command:

[NetID@Grace1 ~]$ cd $HOME

Your scratch directory is restricted to 1TB/250,000 files of storage. This storage quota is expandable upon request. A user's scratch directory is NOT backed up.

Your home directory is restricted to 10GB/10,000 files of storage. This storage quota is not expandable. A user's home directory is backed up on a nightly basis.

You can see the current status of your storage quotas with:

[NetID@Grace1 ~]$ showquota

If you need a storage quota increase, please contact us with justification and the expected length of time that you will need the quota increase.

The Batch System

The batch system is a load distribution implementation that ensures convenient and fair use of a shared resource. Submitting jobs to a batch system allows a user to reserve specific resources with minimal interference to other users. All users are required to submit resource-intensive processing to the compute nodes through the batch system - attempting to circumvent the batch system is not allowed.

On Grace, Slurm is the batch system that provides job management. More information on Slurm can be found in the Grace Batch page.

Managing Project Accounts

The batch system will charge SUs from the either the account specified in the job parameters, or from your default account (if this parameter is omitted). To avoid errors in SU billing, you can view your active accounts, and set your default account using the myproject command.

Finding Software

Software on Grace is loaded using modules.

A list of the most popular software on our systems is available on the HPRC Available Software page.

To find most available software on Grace, use the following command:

[NetID@Grace1 ~]$ module avail

To search for particular software by keyword, use:

[NetID@Grace1 ~]$ module spider keyword

To load a module, use:

[NetID@Grace1 ~]$ module load moduleName

To list all currently loaded modules, use:

[NetID@Grace1 ~]$ module list

To remove all currently loaded modules, use:

[NetID@Grace1 ~]$ module purge

If you need new software or an update, please contact us with your request.

There are restrictions on what software we can install. There is also regularly a queue of requested software installations.

Please account for delays in your installation request timeline.

Running Your Program / Preparing a Job File

In order to properly run a program on Grace, you will need to create a job file and submit a job.

The simple example job file below requests 1 core on 1 node with 2.5GB of RAM for 1.5 hours. Note that typical nodes on Grace have 28 cores with 120GB of usable memory and ensure that your job requirements will fit within these restrictions. Any modules that need to be loaded or executable commands will replace the "#First Executable Line" in this example.

#!/bin/bash
##ENVIRONMENT SETTINGS; CHANGE WITH CAUTION
#SBATCH --export=NONE        #Do not propagate environment
#SBATCH --get-user-env=L     #Replicate login environment
  
##NECESSARY JOB SPECIFICATIONS
#SBATCH --job-name=JobExample1     #Set the job name to "JobExample1"
#SBATCH --time=01:30:00            #Set the wall clock limit to 1hr and 30min
#SBATCH --ntasks=1                 #Request 1 task
#SBATCH --ntasks-per-node=1        #Request 1 task/core per node
#SBATCH --mem=2560M                #Request 2560MB (2.5GB) per node
#SBATCH --output=Example1Out.%j    #Send stdout/err to "Example1Out.[jobID]"

#First Executable Line

Note: If your job file has been written on an older Mac or DOS workstation, you will need to use "dos2unix" to remove certain characters that interfere with parsing the script.

[NetID@Grace1 ~]$ dos2unix MyJob.slurm

More information on job options can be found in the Building Job Files section of the Grace Batch page.

More information on dos2unix can be found on the dos2unix section of the HPRC Available Software page.

Submitting and Monitoring Jobs

Once you have your job file ready, it is time to submit your job. You can submit your job to slurm with the following command:

[NetID@Grace1 ~]$ sbatch MyJob.slurm
Submitted batch job 3606

After the job has been submitted, you are able to monitor it with several methods. To see the status of all of your jobs, use the following command:

[NetID@Grace1 ~]$ squeue -u NetID
JOBID       NAME                USER                    PARTITION   NODES CPUS STATE       TIME        TIME_LEFT   START_TIME           REASON      NODELIST            
3606        myjob2              NetID                   short       1     3    RUNNING     0:30        00:10:30    2016-11-27T23:44:12  None        tnxt-[0340]  

To see the status of one job, use the following command, where XXXX is the JobID:

[NetID@Grace1 ~]$ squeue --job XXXX
JOBID       NAME                USER                    PARTITION   NODES CPUS STATE       TIME        TIME_LEFT   START_TIME           REASON      NODELIST            
XXXX        myjob2              NetID                   short       1     3    RUNNING     0:30        00:10:30    2016-11-27T23:44:12  None        tnxt-[0340]  

To cancel a job, use the following command, where XXXX is the JobID:

[NetID@Grace1 ~]$ scancel XXXX

More information on Job Submission and Job Monitoring Slurm jobs can be found at the Grace Batch System page.

tamubatch

tamubatch is an automatic batch job script that submits jobs for the user without the need of writing a batch script on the Terra and Grace clusters. The user just needs to provide the executable commands in a text file and tamubatch will automatically submit the job to the cluster. There are flags that the user may specify which allows control over the parameters for the job submitted.

tamubatch is still in beta and has not been fully developed. Although there are still bugs and testing issues that are currently being worked on, tamubatch can already submit jobs to both the Terra and Grace clusters if given a file of executable commands.

For more information, visit this page.

Additional Topics

Translating Ada/LSF <--> Grace/Slurm

The HPRC Batch Translation page contains information on converting between LSF, PBS, and Slurm.

Our staff has also written some example jobs for specific software. These software-specific examples can be seen on the Individual Software Pages where available.

Finding Software

Software on Grace is loaded using modules.

You can see the most popular software on the HPRC Available Software page.

You can find most available software on Grace with the following command:

[NetID@Grace1 ~]$ module avail

You can search for particular software by keyword using:

[NetID@Grace1 ~]$ module spider keyword

You can load a module using:

[NetID@Grace1 ~]$ module load moduleName

You can list all currently loaded modules using:

[NetID@Grace1 ~]$ module list

You can remove all currently loaded modules using:

[NetID@Grace1 ~]$ module purge

If you need new software or an update, please contact us with your request.

There are restrictions on what software we can install. There is also regularly a queue of requested software installations.

Please account for delays in your installation request timeline.

Transferring Files

Files can be transferred to Grace using the scp command or a file transfer program.

Our users most commonly utilize:

• WinSCP - Straightforward, legacy
• FileZilla Client - Easy to use, additional features, available on most platforms
• MobaXterm Graphical SFTP - Included with MobaXterm

See our [Grace-Filezilla example video] for a demonstration of this process.

Advice: while GUIs are acceptable for file transfers, the cp and scp commands are much quicker and may significantly benefit your workflow.

Reliably Transferring Large Files

For files larger than several GB, you will want to consider the use of a more fault-tolerant utility such as rsync.

[NetID@Grace1 ~]$ rsync -av [-z] localdir/ userid@remotesystem:/path/to/remotedir/

An rsync example can be seen on the Ada Fast Transfer page.

Graphic User Interfaces (Visualization)

The use of GUIs on Grace is a more complicated process than running non-interactive jobs or doing resource-light interactive processing.

You have two options for using GUIs on Grace.

The first option is to run on the login node. When doing this, you must observe the fair-use policy of login node usage. Users commonly violate these policies by accident, resulting in terminated processes, confusion, and warnings from our admins.

The second option is to use a VNC job. This method is outside the scope of this guide. See the Grace Remote Visualization page for more information.