Using HPC for Ansys CFX and FluentJohn Zaitseff, April 2015

High Performance Computing

The problem in computer labs

• Multiple computers locked for long periods of time• Often just a handful of students• All computers running Ansys CFX or Fluent• Often randomly rebooted by

other students and/or staff

• Cannot get a computer whenyou need it

• Can lose results when you do

Image credit: John Zaitseff, UNSW

The solution: High Performance Computing

“High performance computing is used to solve real-world problems of significant scale or detail across a diverse range of disciplines including physics, biology, chemistry, geosciences, climate sciences, engineering and many others.”

— Intersect Australiahttp://www.intersect.org.au/content/time-fast-computing

Image credit: IBM Blue Gene P supercomputer, Argonne National Laboratory

High Performance Computing architecture

Massively Parallel Distributed

Computational Clusters

• Many individual servers (“nodes”):dozens to thousands

• Multiple processors per node:between 8 and 64 cores

• Interconnected by fast networks• Almost always run Linux

– In our case: Rocks Linux Distributionon top of CentOS 6.x

The Leonardi cluster

Image credit: John Zaitseff, UNSW

High Performance Computing architecture

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Facilities for MECH students and staff

• The Newton cluster– For undergraduate students, postgraduates and staff– MECH9620, MECH4100, MMAN4010, MMAN4020, AERO4110 and

AERO4120 students already have an account!

• The Trentino cluster– For postgraduate students

and staff– By application

• The Leonardi cluster– For postgraduate students

and staff– By application

UNSW R1 Data Centre

Image credit: John Zaitseff, UNSW

The Newton cluster: newton.mech.unsw.edu.au• 10 × Dell R415 server nodes

– Head node: newton– Compute nodes: newton01 to newton09

• 160 × AMD Opteron 4386 3.1GHz processor cores– Two physical processors per node– Eight CPU cores per processor– Only four floating-point units per processor

• 320 GB of main memory (32 GB per node)• 12 TB of storage: 6 × 3 TB drives in RAID 6• 1Gb Ethernet network interconnect

http://cfdlab.unsw.wikispaces.net/

The Newton cluster

Image credit: John Zaitseff, UNSW

The Trentino cluster: trentino.mech.unsw.edu.au• 16 × Dell R815 server nodes

– Head node: trentino– Compute nodes: trentino01 to trentino15

• 1024 × AMD Opteron 6272 2.1GHz processor cores– Four physical processors per node– Sixteen CPU cores per processor– Only eight floating-point units per processor

• 2048 GB of main memory (128 GB per node)• 30 TB of storage: 12 × 3 TB drives in RAID 6• 4×1Gb Ethernet network interconnect

http://cfdlab.unsw.wikispaces.net/

The Trentino cluster

Image credit: John Zaitseff, UNSW

The Leonardi cluster: leonardi.eng.unsw.edu.au• 7 × HP BladeSystem c7000 blade enclosures• 1 × HP ProLiant DL385 G7 server: leonardi• 56 × HP BL685c G7 compute nodes

– Compute nodes: ec01b01-ec07b08• 2944 × AMD Opteron 6174 2.2GHz processor cores

and Opteron 6276 2.3GHz processor cores– Four physical processors per node– Twelve or sixteen CPU cores per processor

• 8448 GB of main memory (96–512 GB per node)• 93.5 TB of storage: 70 × 2 TB drives in RAID 6+0• 2×10Gb Ethernet network interconnect

http://leonardi.unsw.wikispaces.net/Nodes in the Leonardi cluster

Image credit: John Zaitseff, UNSW

• 3592 × Fujitsu blade server nodes• Multiple login nodes• Multiple management nodes• 57,472 Intel Xeon E5-2670 2.60GHz

processors• 160 TB of main memory• 10 PB of storage using the Lustre

distributed file system• 56Gb Infiniband FDR network

interconnect

http://nci.org.au/nci-systems/national-facility/peak-system/raijin/

The Raijin cluster: raijin.nci.org.au

Image credit: National Computational Infrastructure

Connecting to a HPC system

• Use the Secure Shell protocol (SSH)– Under Linux or Mac OS X: ssh username@hostname

(for example, ssh z9693022@newton.mech.unsw.edu.au)– Under Windows: PuTTY (Start » All Programs » PuTTY » PuTTY)– Can install Cygwin: “that Linux feeling under Windows”

• To connect to the Newton cluster:– Hostname: newton.mech.unsw.edu.au– Check RSA2 fingerprint: 69:7e:64:75:57:67:ad:4c:21:8e:90:7d:8e:97:70:ce

– User name: your zID– Password: your zPass

• You will get a command line prompt: something like• To exit, type exit and press ENTER.

z9693022@newton:~ $

Simple Linux commands

• List files in a directory: ls [options] [pathname ...]– [ ] indicates optional parameters, ... indicates one or more parameters– Italic fixed-width font indicates replaceable parameters– Options include “-l” (letter L) for a long (detailed) listing

• To show the current directory: pwd• To change directories: cd directory

– ~ is the home directory– . is the current directory– .. is the directory above the current one– ~user is the home directory of user user– Subdirectories are separated by “/”, e.g., /home/z9693022/src

• To create directories: mkdir directory• To remove an empty directory: rmdir directory• To get help for a command: man command

More simple Linux commands

• To output one or more file’s contents: cat filename ...• To view one or more files page by page: less filename ...

• To copy one file: cp source destination• To copy one or more files to a directory: cp filename ... dir• To preserve the “last modified” time-stamp: cp -p• To copy recursively: cp -pr source destination

• To move one or more files to a different directory: mv filename ... dir• To rename a file or directory: mv oldname newname• To remove files: rm filename ...

• Recommendation: use “ls filename ...” before rm or mv: what happens if you accidentally type “rm *”? or “rm * .c”? (note the space!)

Transferring files

• To copy files to a Linux or Mac OS X system: use scp, rsync or insync• To copy files to and from a Windows machine: use WinSCP (Start » All

Programs » WinSCP » WinSCP), or scp or rsync under Cygwin

• To copy files to and from the Newton cluster:– Host name newton.mech.unsw.edu.au– Check RSA2 fingerprint: 69:7e:64:75:57:67:ad:4c:21:8e:90:7d:8e:97:70:ce

– User name: your zID– Password: your zPass

• Using WinSCP, simply drag and drop files from one pane to the other.

Editing files

• Use an editor to edit text files• Many choices, leading to “religious wars”!• Some options: GNU Emacs, Vim, Nano

• Nano is very simple to use: nano filename– CTRL-X to exit (you will be asked to save any changes)

• GNU Emacs and Vim are highly customisable and programmable– For example, see the file ~z9693022/.emacs– Debra Cameron et al., Learning GNU Emacs, 3rd Edition, O’Reilly

Media, December 2004. ISBN 9780596006488, 9780596104184– Arnold Robbins et al., Learning the vi and Vim Editors, 7th Edition,

O’Reilly Media, July 2008. ISBN 9780596529833, 9780596159351

Running Ansys CFX jobs

1. Set up your job using Ansys CFX as per normal

2. Connect to the Newton cluster using PuTTY

3. Create a directory for this particular job

4. Transfer the .cfx and .def files to thatdirectory using WinSCP

5. Create an appropriate script file

6. Submit the job to the Newton queue

7. Periodically check the status of the job

8. Once finished, transfer the .out and.res files to your desktop computer

9. Check the results using the standardAnsys CFX tools

Image credit: The Ansys Blog at http://www.ansys-blog.com/

Steps 1 to 4: Setting up the job

1. Set up your job using Ansys CFX as per normal– May use the laboratory computers to do this

2. Connect to the Newton cluster using PuTTY– Connect to newton.mech.unsw.edu.au

3. Create a directory for this particular job– Use the mkdir directory command– Come up with a consistent naming scheme– Structure your directories; use subdirectories as required

4. Transfer the .cfx and .def files to that directory using WinSCP– Connect to newton.mech.unsw.edu.au as before

Step 5: Create a script file

a. Change to the newly-created directory: cd directoryb. Invoke the text editor to create a script file: nano filename.shc. Add the following text, replacing parameters as required:

#!/bin/bash#SBATCH --time=0-12:00:00 # for 0 days 12 hours#SBATCH --mem=30720 # 30GB memory#SBATCH --ntasks=1 # A single job#SBATCH --cpus-per-task=16 # 16 processor cores#SBATCH --mail-user=emailaddr@unsw.edu.au # or @student.unsw.edu.au#SBATCH --mail-type=ALL

cd $SLURM_SUBMIT_DIRmodule load cfx/15.0 # or cfx/14.5 as appropriatecfx5solve -batch -def filename.def -part 16 \ -start-method "Platform MPI Local Parallel"

d. Save the file by pressing CTRL-X and following the prompts

Steps 6 to 7: Submit and check on the job

6. Once you have created the filename.sh script file, submit it into the Newton queue:– Make sure you are in the correct directory– Submit the job: sbatch filename.sh– Take note of the job number: “Submitted batch job jobid”– Once submitted, you do not need to be connected to the cluster

7. Periodically check on the job status– The job will start as soon as resources are available for it to run– Emails will be sent to you on job start and completion

– Show queue status: squeue or squeue -l (letter L)– Show node status: sinfo– Cancel a running or queued job: scancel jobid

Running Ansys Fluent jobs

• Similar to running CFX jobs on the cluster• Different files need to be transferred to and from the cluster• Script file is also slightly different:

#!/bin/bash#SBATCH --time=0-12:00:00 # for 0 days 12 hours#SBATCH --mem=30720 # 30GB memory#SBATCH --ntasks=1 # A single job#SBATCH --cpus-per-task=16 # 16 processor cores#SBATCH --mail-user=emailaddr@unsw.edu.au # or @student.unsw.edu.au#SBATCH --mail-type=ALL

cd $SLURM_SUBMIT_DIRmodule load fluent/15.0 # or fluent/14.5 as appropriatefluent 3d -g -t16 -ssh <inputfilename.txt >outputfilename.txt # may replace “3d” with “2d” for two-dimensional meshes

Whom to ask for help?

1. Your colleagues

2. Your supervisor/lecturer

3. The HPC representative

John ZaitseffJ.Zaitseff@unsw.edu.au

Available for consultationson Tuesdays 9:30am–4pmby appointment only.

Getting help with HPC

Image credit: John Zaitseff, UNSW