理化学研究所計算科学研究センター(R-CCS) | RIKEN R-CCS...Command ~/sim_ns_model/run.sh Input Type Argument Executable_on localhost Key Type Default Val l Integer 200

RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE

Computer simulations create the future

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http://crest-cassia.github.io/oacis/en/configuring_simulator.html

http://crest-cassia.github.io/oacis/ja/configuring_simulator.html


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1. Work directory and shell script are created.Jobs are submitted to the scheduler.

2. Jobs are executed by the job scheduler.Current directory is set to the work directory.

3. Results are downloaded to OACIS server.The files are parsed and the records are updated.

database

job scheduler

(ex. Torque)

OACIS Computational Host

qsubSSH login

sh

execute in the work directory

the work directory is compressed into a single file.tar

download (scp)& expand

parse job status &update the record


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wrap script

simulation program

run.py

_input.json

a.out

1. Input parameters given by OACIS

2. parse command line args and make an XML file

3. launch the simulation program as a subprocess

RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE �

http://crest-cassia.github.io/oacis/en/configuring_simulator.htmlOther samples for these scripts are found in our doc page.

Load the input JSON file

Make an XML file

Spawn a subprocess


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Simulator name

Definition of Parametersname, type, default value

preprocess command�optional�

command of Simulator

JSON or Argument input

A note of the Simulator

List of executable hosts


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Duplicating Simulator

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Simulator name

Definition of Parametersname, type, default value

“echo”

Select “Argument”

Select “localhost”


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Key Description

l Road length

v Maximum velocity

rho Car density

p deceleration probability

t_init initialization steps

t_measure measurement steps

mkdir temp && cd temp~/sim_ns_model/run.sh 200 5 0.3 0.1 100 300 12345

docker exec -it -u oacis my_oacis bash -l


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Item Contents

Name MySimulator

Definition of Parameters L, v, rho, p, t_init, t_measure

Command ~/sim_ns_model/run.sh

Input Type Argument

Executable_on localhost

Key Type Default Val

l Integer 200

v Integer 5

rho Float 0.3

p Float 0.1

t_init Integer 100

t_measure Integer 300

Click

“Add Parameter”

to increase the

number of

parameters.


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(At OACIS host)ssh-keygen -t rsa # ~/.ssh/id_rsa ~/.ssh/id_rsa.pub are createdscp ~/.ssh/id_rsa.pub [USER]@[HOST_NAME]:~

# copy your public key to the remote host(At Computational host)cat ~/id_rsa.pub >> ~/.ssh/authorized_keys && chmod 600 ~/.ssh/authorized_keys

# add your public key to the list of authorized keys(At OACIS host)eval `ssh-agent` # launch SSH agentssh-add ~/.ssh/id_rsa # add key to agent. Enter your passphrase.ssh [USER]@[HOST_NAME] # verify that you don’t need to enter the passphrase

bundle exec rake daemon:restart # launch OACIS


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Host my_serverHostName my_server.example.comPort 22User muraseIdentityFile ~/.ssh/id_rsa

Host my_server2HostName 127.0.0.1Port 22User muraseIdentityFile ~/.ssh/id_rsa


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Refer to https://github.com/crest-cassia/xsub


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export PATH="$HOME/xsub/bin:$PATH"export XSUB_TYPE="none"

https://github.com/crest-cassia/xsub.git


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host information for SSH connection

Directory used for running jobs. OACIS will create sub

directories under this.Maximum number of

concurrent jobs.Worker checks the status of

the remote host with this interval.

The available range of the number of MPI processes and

threads.

List of executable simulators on that host.

http://crest-cassia.github.io/oacis/en/tutorial.html#registering-a-host


Parameters required by XSUB (Host Parameters)

are automatically set.


Host Parameters are required when creating a PS.


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docker exec -u oacis my_oacis cat /home/oacis/.ssh/id_rsa.pub >> ~/.ssh/authorized_keyschmod 600 ~/.ssh/authorized_keys

# testing connectiondocker exec -it -u oacis my_oacis bash –l# edit (~/.ssh/config file)ssh my_hostexit # logout from computational hostexit # logout from container

# installing xsub on computational hostgit clone https://github.com/crest-cassia/xsub.git ~/xsub

# edit ~/.bash_profile. Add the following two lines.export PATH="$HOME/xsub/bin:$PATH"export XSUB_TYPE="none"

https://github.com/crest-cassia/xsub.git


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We can define a HostGroup, a group of Hosts.When creating a job, HostGroup can be specified as a destination of the submission. The jobs are submitted to one of the hosts in the HostGroup.


click Hosts

click “New Host Group”

We can select a HostGroup as the place to which jobs are submitted.


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Documents

理化学研究所 計算科学研究センター(R-CCS) | RIKEN R-CCS...Command ~/sim_ns_model/run.sh Input Type Argument Executable_on localhost Key Type Default Val l Integer 200

理化学研究所計算科学研究センター(R-CCS) | RIKEN R-CCS...Command ~/sim_ns_model/run.sh Input Type Argument Executable_on localhost Key Type Default Val l Integer 200