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Introduction to HPC Workshop
October 9 2014
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Introduction
Rob Lane
HPC Support
Research Computing Services
CUIT
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Introduction
HPC Basics
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Introduction
First HPC Workshop
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Yeti
• 2 head nodes
• 101 execute nodes
• 200 TB storage
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Yeti
• 101 execute nodes–38 x 64 GB–8 x 128 GB–35 x 256 GB–16 x 64 GB + Infiniband–4 x 64 GB + nVidia K20 GPU
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Yeti
• CPU– Intel E5-2650L–1.8 GHz–8 Cores–2 per Execute Node
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Yeti
• Expansion Round–66 new systems–Faster CPU–More Infiniband–More GPU (nVidia K40)–ETA January 2015
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Yeti
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HP S6500 Chassis
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HP SL230 Server
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Job Scheduler
• Manages the cluster
• Decides when a job will run
• Decides where a job will run
• We use Torque/Moab
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Job Queues
• Jobs are submitted to a queue
• Jobs sorted in priority order
• Not a FIFO
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Access
Mac Instructions
1. Run terminal
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Access
Windows Instructions
1. Search for putty on Columbia home page
2. Select first result
3. Follow link to Putty download page
4. Download putty.exe
5. Run putty.exe
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Work Directory
$ cd /vega/free/users/your UNI
• Replace “your UNI” with your UNI
$ cd /vega/free/users/hpc2108
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Copy Workshop Files
• Files are in /tmp/workshop
$ cp /tmp/workshop/* .
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Editing
No single obvious choice for editor
• vi – simple but difficult at first• emacs – powerful but complex• nano – simple but not really standard
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nano
$ nano hellosubmit
“^” means “hold down control”
^a : go to beginning of line
^e : go to end of line
^k: delete line
^o: save file
^x: exit
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hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
# Set output and error directories
#PBS -o localhost:/vega/free/users/UNI#PBS -e localhost:/vega/free/users/UNI
# Print "Hello World"
echo "Hello World"
# Sleep for 10 seconds
sleep 10
# Print date and time
date
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hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
# Set output and error directories
#PBS -o localhost:/vega/free/users/UNI#PBS -e localhost:/vega/free/users/UNI
# Print "Hello World"
echo "Hello World"
# Sleep for 10 seconds
sleep 10
# Print date and time
date
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hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
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hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
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hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
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hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
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hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
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hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
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hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
![Page 30: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/30.jpg)
hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
![Page 31: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/31.jpg)
hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
![Page 32: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/32.jpg)
hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
![Page 33: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/33.jpg)
hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m n#PBS -V
![Page 34: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/34.jpg)
hellosubmit
#!/bin/sh
# Directives
#PBS -N HelloWorld#PBS -W group_list=yetifree#PBS -l nodes=1:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m n#PBS -V
![Page 35: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/35.jpg)
hellosubmit
# Set output and error directories
#PBS -o localhost:/vega/free/users/UNI#PBS -e localhost:/vega/free/users/UNI
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hellosubmit
# Set output and error directories
#PBS -o localhost:/vega/free/users/UNI#PBS -e localhost:/vega/free/users/UNI
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hellosubmit
# Print "Hello World"
echo "Hello World"
# Sleep for 10 seconds
sleep 10
# Print date and time
date
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hellosubmit
$ qsub hellosubmit
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hellosubmit
$ qsub hellosubmit298151.elk.cc.columbia.edu$
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hellosubmit
$ qsub hellosubmit298151.elk.cc.columbia.edu$
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qstat
$ qsub hellosubmit298151.elk.cc.columbia.edu$ qstat 298151Job ID Name User Time Use S Queue---------- ------------ ---------- -------- - -----298151.elk HelloWorld hpc2108 0 Q batch1
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hellosubmit
$ qsub hellosubmit298151.elk.cc.columbia.edu$ qstat 298151Job ID Name User Time Use S Queue---------- ------------ ---------- -------- - -----298151.elk HelloWorld hpc2108 0 Q batch1
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hellosubmit
$ qsub hellosubmit298151.elk.cc.columbia.edu$ qstat 298151Job ID Name User Time Use S Queue---------- ------------ ---------- -------- - -----298151.elk HelloWorld hpc2108 0 Q batch1
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hellosubmit
$ qsub hellosubmit298151.elk.cc.columbia.edu$ qstat 298151Job ID Name User Time Use S Queue---------- ------------ ---------- -------- - -----298151.elk HelloWorld hpc2108 0 Q batch1
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hellosubmit
$ qsub hellosubmit298151.elk.cc.columbia.edu$ qstat 298151Job ID Name User Time Use S Queue---------- ------------ ---------- -------- - -----298151.elk HelloWorld hpc2108 0 Q batch1
![Page 46: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/46.jpg)
hellosubmit
$ qsub hellosubmit298151.elk.cc.columbia.edu$ qstat 298151Job ID Name User Time Use S Queue---------- ------------ ---------- -------- - -----298151.elk HelloWorld hpc2108 0 Q batch1
![Page 47: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/47.jpg)
hellosubmit
$ qsub hellosubmit298151.elk.cc.columbia.edu$ qstat 298151Job ID Name User Time Use S Queue---------- ------------ ---------- -------- - -----298151.elk HelloWorld hpc2108 0 Q batch1$ qstat 298151qstat: Unknown Job Id Error 298151.elk.cc.columbia.edu
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hellosubmit
$ ls -ltotal 4-rw------- 1 hpc2108 yetifree 398 Oct 8 22:13 hellosubmit-rw------- 1 hpc2108 yetifree 0 Oct 8 22:44 HelloWorld.e298151-rw------- 1 hpc2108 yetifree 41 Oct 8 22:44 HelloWorld.o298151
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hellosubmit
$ ls -ltotal 4-rw------- 1 hpc2108 yetifree 398 Oct 8 22:13 hellosubmit-rw------- 1 hpc2108 yetifree 0 Oct 8 22:44 HelloWorld.e298151-rw------- 1 hpc2108 yetifree 41 Oct 8 22:44 HelloWorld.o298151
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hellosubmit
$ ls -ltotal 4-rw------- 1 hpc2108 yetifree 398 Oct 8 22:13 hellosubmit-rw------- 1 hpc2108 yetifree 0 Oct 8 22:44 HelloWorld.e298151-rw------- 1 hpc2108 yetifree 41 Oct 8 22:44 HelloWorld.o298151
![Page 51: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/51.jpg)
hellosubmit
$ ls -ltotal 4-rw------- 1 hpc2108 yetifree 398 Oct 8 22:13 hellosubmit-rw------- 1 hpc2108 yetifree 0 Oct 8 22:44 HelloWorld.e298151-rw------- 1 hpc2108 yetifree 41 Oct 8 22:44 HelloWorld.o298151
![Page 52: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/52.jpg)
hellosubmit
$ ls -ltotal 4-rw------- 1 hpc2108 yetifree 398 Oct 8 22:13 hellosubmit-rw------- 1 hpc2108 yetifree 0 Oct 8 22:44 HelloWorld.e298151-rw------- 1 hpc2108 yetifree 41 Oct 8 22:44 HelloWorld.o298151
![Page 53: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/53.jpg)
hellosubmit
$ cat HelloWorld.o298151Hello WorldThu Oct 9 12:44:05 EDT 2014
![Page 54: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/54.jpg)
hellosubmit
$ cat HelloWorld.o298151Hello WorldThu Oct 9 12:44:05 EDT 2014
Any Questions?
![Page 55: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/55.jpg)
Interactive
• Most jobs run as “batch”• Can also run interactive jobs• Get a shell on an execute node• Useful for development, testing,
troubleshooting
![Page 56: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/56.jpg)
Interactive
$ cat interactiveqsub -I -W group_list=yetifree -l walltime=5:00,mem=100mb
![Page 57: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/57.jpg)
Interactive
$ cat interactiveqsub -I -W group_list=yetifree -l walltime=5:00,mem=100mb
![Page 58: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/58.jpg)
Interactive
$ cat interactiveqsub -I -W group_list=yetifree -l walltime=5:00,mem=100mb
![Page 59: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/59.jpg)
Interactive
$ cat interactiveqsub -I -W group_list=yetifree -l walltime=5:00,mem=100mb
![Page 60: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/60.jpg)
Interactive
$ cat interactiveqsub -I -W group_list=yetifree -l walltime=5:00,mem=100mb
![Page 61: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/61.jpg)
Interactive
$ cat interactiveqsub -I -W group_list=yetifree -l walltime=5:00,mem=100mb
![Page 62: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/62.jpg)
Interactive
$ qsub -I -W group_list=yetifree -l walltime=5:00,mem=100mbqsub: waiting for job 298158.elk.cc.columbia.edu to start
![Page 63: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/63.jpg)
Interactive
qsub: job 298158.elk.cc.columbia.edu ready
.--. ,-,-,--(/o o\)-,-,-,. ,' // oo \\ ', ,' /| __ |\ ', ,' //\,__,/\\ ', , /\ /\ , , /'`\ /' \ , | /' `\ /' '\ | | \ ( ) / | ( /\| /' '\ |/\ ) \| /' /'`\ '\ |/ | /' `\ | ( ( ) ) `\ \ /' /' `\ \ /' /' / / \ \ v v v v v v +--------------------------------+ | | | You are in an interactive job. | | | | Your walltime is 00:05:00 | | | +--------------------------------+
![Page 64: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/64.jpg)
Interactive
$ hostnamecharleston.cc.columbia.edu
![Page 65: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/65.jpg)
Interactive
$ exitlogout
qsub: job 298158.elk.cc.columbia.edu completed$
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GUI
• Can run GUI’s in interactive jobs
• Need X Server on your local system
• See user documentation for more information
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User Documentation
• hpc.cc.columbia.edu
• Go to “HPC Support”
• Click on Yeti user documentation
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Job Queues
• Scheduler puts all jobs into a queue
• Queue selected automatically
• Queues have different settings
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Queue Time Limit Memory Limit
Max. User Run
Batch 1 12 hours 4 GB 512
Batch 2 12 hours 16 GB 128
Batch 3 5 days 16 GB 64
Batch 4 3 days None 8
Interactive 4 hours None 4
Job Queues
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qstat -q
$ qstat -q
server: elk.cc.columbia.edu
Queue Memory CPU Time Walltime Node Run Que Lm State---------------- ------ -------- -------- ---- --- --- -- -----batch1 4gb -- 12:00:00 -- 42 15 -- E Rbatch2 16gb -- 12:00:00 -- 129 73 -- E Rbatch3 16gb -- 120:00:0 -- 148 261 -- E Rbatch4 -- -- 72:00:00 -- 11 12 -- E Rinteractive -- -- 04:00:00 -- 0 1 -- E Rinterlong -- -- 48:00:00 -- 0 0 -- E Rroute -- -- -- -- 0 0 -- E R ----- ----- 330 362
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yetifree
• Maximum processors limited–Currently 4 maximum
• Storage quota–16 GB
• No email support
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yetifree
$ quota -sDisk quotas for user hpc2108 (uid 242275): Filesystem blocks quota limit grace files quota limit gracehpc-cuit-storage-2.cc.columbia.edu:/free/ 122M 16384M 16384M 8 4295m 4295m
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yetifree
$ quota -sDisk quotas for user hpc2108 (uid 242275): Filesystem blocks quota limit grace files quota limit gracehpc-cuit-storage-2.cc.columbia.edu:/free/ 122M 16384M 16384M 8 4295m 4295m
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from: root <[email protected]>to: [email protected]: Wed, Oct 8, 2014 at 11:41 PMsubject: PBS JOB 298161.elk.cc.columbia.edu
PBS Job Id: 298161.elk.cc.columbia.eduJob Name: HelloWorldExec host: dublin.cc.columbia.edu/4Execution terminatedExit_status=0resources_used.cput=00:00:02resources_used.mem=8288kbresources_used.vmem=304780kbresources_used.walltime=00:02:02Error_Path: localhost:/vega/free/users/hpc2108/HelloWorld.e298161Output_Path: localhost:/vega/free/users/hpc2108/HelloWorld.o298161
![Page 75: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/75.jpg)
from: root <[email protected]>to: [email protected]: Wed, Oct 8, 2014 at 11:41 PMsubject: PBS JOB 298161.elk.cc.columbia.edu
PBS Job Id: 298161.elk.cc.columbia.eduJob Name: HelloWorldExec host: dublin.cc.columbia.edu/4Execution terminatedExit_status=0resources_used.cput=00:00:02resources_used.mem=8288kbresources_used.vmem=304780kbresources_used.walltime=00:02:02Error_Path: localhost:/vega/free/users/hpc2108/HelloWorld.e298161Output_Path: localhost:/vega/free/users/hpc2108/HelloWorld.o298161
![Page 76: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/76.jpg)
from: root <[email protected]>to: [email protected]: Wed, Oct 8, 2014 at 11:41 PMsubject: PBS JOB 298161.elk.cc.columbia.edu
PBS Job Id: 298161.elk.cc.columbia.eduJob Name: HelloWorldExec host: dublin.cc.columbia.edu/4Execution terminatedExit_status=0resources_used.cput=00:00:02resources_used.mem=8288kbresources_used.vmem=304780kbresources_used.walltime=00:02:02Error_Path: localhost:/vega/free/users/hpc2108/HelloWorld.e298161Output_Path: localhost:/vega/free/users/hpc2108/HelloWorld.o298161
![Page 77: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/77.jpg)
from: root <[email protected]>to: [email protected]: Wed, Oct 8, 2014 at 11:41 PMsubject: PBS JOB 298161.elk.cc.columbia.edu
PBS Job Id: 298161.elk.cc.columbia.eduJob Name: HelloWorldExec host: dublin.cc.columbia.edu/4Execution terminatedExit_status=0resources_used.cput=00:00:02resources_used.mem=8288kbresources_used.vmem=304780kbresources_used.walltime=00:02:02Error_Path: localhost:/vega/free/users/hpc2108/HelloWorld.e298161Output_Path: localhost:/vega/free/users/hpc2108/HelloWorld.o298161
![Page 78: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/78.jpg)
from: root <[email protected]>to: [email protected]: Wed, Oct 8, 2014 at 11:41 PMsubject: PBS JOB 298161.elk.cc.columbia.edu
PBS Job Id: 298161.elk.cc.columbia.eduJob Name: HelloWorldExec host: dublin.cc.columbia.edu/4Execution terminatedExit_status=0resources_used.cput=00:00:02resources_used.mem=8288kbresources_used.vmem=304780kbresources_used.walltime=00:02:02Error_Path: localhost:/vega/free/users/hpc2108/HelloWorld.e298161Output_Path: localhost:/vega/free/users/hpc2108/HelloWorld.o298161
![Page 79: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/79.jpg)
from: root <[email protected]>to: [email protected]: Wed, Oct 8, 2014 at 11:41 PMsubject: PBS JOB 298161.elk.cc.columbia.edu
PBS Job Id: 298161.elk.cc.columbia.eduJob Name: HelloWorldExec host: dublin.cc.columbia.edu/4Execution terminatedExit_status=0resources_used.cput=00:00:02resources_used.mem=8288kbresources_used.vmem=304780kbresources_used.walltime=00:02:02Error_Path: localhost:/vega/free/users/hpc2108/HelloWorld.e298161Output_Path: localhost:/vega/free/users/hpc2108/HelloWorld.o298161
![Page 80: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/80.jpg)
from: root <[email protected]>to: [email protected]: Wed, Oct 8, 2014 at 11:41 PMsubject: PBS JOB 298161.elk.cc.columbia.edu
PBS Job Id: 298161.elk.cc.columbia.eduJob Name: HelloWorldExec host: dublin.cc.columbia.edu/4Execution terminatedExit_status=0resources_used.cput=00:00:02resources_used.mem=8288kbresources_used.vmem=304780kbresources_used.walltime=00:02:02Error_Path: localhost:/vega/free/users/hpc2108/HelloWorld.e298161Output_Path: localhost:/vega/free/users/hpc2108/HelloWorld.o298161
![Page 81: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/81.jpg)
from: root <[email protected]>to: [email protected]: Wed, Oct 8, 2014 at 11:41 PMsubject: PBS JOB 298161.elk.cc.columbia.edu
PBS Job Id: 298161.elk.cc.columbia.eduJob Name: HelloWorldExec host: dublin.cc.columbia.edu/4Execution terminatedExit_status=0resources_used.cput=00:00:02resources_used.mem=8288kbresources_used.vmem=304780kbresources_used.walltime=00:02:02Error_Path: localhost:/vega/free/users/hpc2108/HelloWorld.e298161Output_Path: localhost:/vega/free/users/hpc2108/HelloWorld.o298161
![Page 82: Introduction to HPC Workshop October 9 2014. Introduction Rob Lane HPC Support Research Computing Services CUIT](https://reader038.vdocuments.us/reader038/viewer/2022103122/56649d0a5503460f949dc148/html5/thumbnails/82.jpg)
Intern
• Research Computing Services (RCS) is looking for an intern
• Paid position• ~10 hours a week• Will be on LionShare next week
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MPI
• Message Passing Interface
• Allows applications to run across multiple computers
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MPI
• Edit MPI submit file
• Load MPI environment module
• Compile sample program
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MPI
#!/bin/sh
# Directives
#PBS -N MpiHello#PBS -W group_list=yetifree#PBS -l nodes=3:ppn=1,walltime=00:01:00,mem=20mb#PBS -M [email protected]#PBS -m abe#PBS -V
# Set output and error directories
#PBS -o localhost:/vega/free/users/UNI#PBS -e localhost:/vega/free/users/UNI
# Load mpi module.
module load openmpi
# Run mpi program.
mpirun mpihello
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MPI
$ module load openmpi$ which mpicc/usr/local/openmpi/bin/mpicc$ mpicc -o mpihello mpihello.c
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MPI
$ qsub mpisubmit298501.elk.cc.columbia.edu
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Questions?
Any questions?