Run relax at Google Cloud Computing

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Background

This follows the same idea as from Run relax at cloud.sagemath.com

Make a rapid deployment of relax on a computer cluster


pricing

For this example of Google Cloud Computing, we wan't to have access to as many computer cores as possible

For the price calculation of:

  • 1 server
  • using Free: Debian, CentOS, ...
  • with a regular VM Class
  • Instance type of (HIGH CPU) n1-highcpu-32 (vCPUs: 32, RAM: 28.80 GB)
  • 0 SSD
  • Datacenter location Europe
  • Average days per month each server is running: 1 days, per month.

This 1 day price was of November 2015, $32.26. Constantly running is $686.78 per month.

At November 2015, google give free trial of 300$. https://cloud.google.com/free-trial/

Note, there are some limitations:

For this time, the most important limitation is 8 CPUs. For the price calculation of:

  • 1 server
  • using Free: Debian, CentOS, ...
  • with a regular VM Class
  • Instance type of (HIGH CPU) n1-highcpu-8 (vCPUs: 8, RAM: 7.20 GB)
  • 0 SSD
  • Datacenter location Europe
  • Average days per month each server is running: 1 days, per month.

This 1 day price was of November 2015, $8.06. Constantly running is $171.70 per month.

'This essentially gives you 2 months of free computation with 8 CPU's.

Start free trial

Please first see this video:

Go to: https://cloud.google.com/free-trial/ and click Start your free trial.

You need to sign up with a credit card. To prevent mis-abuse from robots and hackers.

Then go to: https://console.developers.google.com

  • You should already have a project called My First Project.
  • Create a new project in top right corner of the browser under the dropdown of My First Project.
  • Call the new project relax with App Engine location at europe-west

Create a Virtual Machine instance

  • Click then at Try Compute Engine or go to https://console.developers.google.com/compute
  • Click Create instance
  • Name: relax
  • Zone: Don't change this. As of Nov 2015, it seems that if you change this, you cannot select more than 2 vCPU's
  • Machine type: From the very bottom, create 8 vCPUs. 32 cores need an upgrade to you account, and the free trial only allows for 8 vCPU's.
  • Boot disk: 10 GB of Ubuntu 14.04 LTS
  • Zone: Now change this to: europe-west1-c
  • Let the rest be default and click Create.

Access Virtual Machine instance

Get relax and unpack

v=5.1.0

# Get relax
curl http://download.gna.org/relax/relax-$v.GNU-Linux.x86_64.tar.bz2 -o relax-$v.GNU-Linux.x86_64.tar.bz2

# Make home bin
mkdir -p $HOME/bin
tar xvjf relax-5.1.0.GNU-Linux.x86_64.tar.bz2
rm relax-5.1.0.GNU-Linux.x86_64.tar.bz2
ln -s $HOME/relax-5.1.0/relax $HOME/bin

# Add $HOME/bin to PATH
echo '' >> $HOME/.bashrc
echo 'export PATH=$PATH:$HOME/bin' >> $HOME/.bashrc
source $HOME/.bashrc

Solve depencies. See also Installation linux 

sudo apt-get -y install python-numpy

Then test relax 

relax -i

Then install other packages Solve depencies. See also Installation linux 

sudo apt-get -y install python-scipy python-matplotlib python-pip
sudo apt-get -y install openmpi-bin openmpi-doc libopenmpi-dev
sudo pip install mpi4py
sudo pip install epydoc

# Check installation
relax -i

Inspect server

Install these very good server packages Solve depencies. See alsp Installation linux 

sudo apt-get -y install htop

Then check server 

uptime
whoami
lscpu
htop -u `whoami`

Then check mpirun 

mpirun --version
mpirun --report-bindings -np 4 echo "hello world"
mpirun --np 8 relax --multi='mpi4py'

Install trunk of relax

Solve dependencies.

See alsp Installation linux 

sudo apt-get -y install subversion scons grace

Checkout relax and build.

svn co svn://svn.gna.org/svn/relax/trunk relax_trunk

# Build
cd relax_trunk
scons
 
# Link to executable
cd $HOME
mkdir -p $HOME/bin
ln -s $HOME/relax_trunk/relax $HOME/bin/relax_trunk
 
# See relax info
relax_trunk -i

install Minfx

See Minfx 

v=1.0.12

mkdir -p $HOME/Downloads
cd $HOME/Downloads
curl http://download.gna.org/minfx/minfx-$v.tar.gz -o minfx-$v.tar.gz
tar -xzf minfx-$v.tar.gz
cd minfx-$v
sudo pip install .
cd $HOME

# Test relax
relax_trunk -i

install Bmrblib

See Bmrblib 

v=1.0.4

mkdir -p $HOME/Downloads
cd $HOME/Downloads
curl http://download.gna.org/bmrblib/bmrblib-$v.tar.gz -o bmrblib-$v.tar.gz
tar -xzf bmrblib-$v.tar.gz
cd bmrblib-$v
sudo pip install .
cd $HOME

# Test relax
relax_trunk -i

Check installation of relax

relax_trunk --time -x

Transfer files back and forth to the server

Se

Install gcloud

See https://cloud.google.com/sdk/

On your own computer 

cd $HOME/Downloads
curl https://sdk.cloud.google.com | bash
source $HOME/.bash_profile
gcloud init

This will start a browser to authenticate you. When it ask for a ID, just write "test" and say no to cloning.

Then go to:

It could look like this. Try this in your own terminal. This should make some SSH keys and bring you to the server 

gcloud compute --project "relax-1143" ssh --zone "europe-west1-c" "relax"

This should bring you to the google server. 

lscpu
cat $HOME/.ssh/authorized_keys 
exit

# At your own computer
ls -l $HOME/.ssh/google*
cat $HOME/.ssh/config
ssh-add -l
ssh-add $HOME/.ssh/google_compute_engine
ssh-add -l

Copy files

See: https://cloud.google.com/sdk/gcloud/reference/compute/copy-files

The ssh command was 

gcloud compute --project "relax-1143" ssh --zone "europe-west1-c" "relax"

We make a test file and copy it 

touch test.txt
gcloud compute --project "relax-1143" copy-files test.txt relax:~ --zone "europe-west1-c"

# Try a directory
mkdir testdir
cp test.txt testdir
gcloud compute --project "relax-1143" copy-files testdir relax:~ --zone "europe-west1-c"

# Back again
cd testdir
gcloud compute --project "relax-1143" copy-files relax:~/testdir . --zone "europe-west1-c"

ssh-config with gcloud

See https://cloud.google.com/sdk/gcloud/reference/compute/config-ssh

gcloud compute config-ssh makes SSHing to virtual machine instances easier by adding an alias for each instance to the user SSH configuration (~/.ssh/config) file. 

gcloud compute --project "relax-1143" config-ssh
cat $HOME/.ssh/config

# ssh in
ssh relax.europe-west1-c.relax-1143
exit

# Use sed to change value of your local computes ssh config file
grep 'relax.europe-west1-c.relax-1143' $HOME/.ssh/config
sed 's/relax.europe-west1-c.relax-1143/gcc_relax/g' $HOME/.ssh/config
sed -i.bak 's/relax.europe-west1-c.relax-1143/gcc_relax/g' $HOME/.ssh/config
ls -l $HOME/.ssh/config*
grep 'gcc_relax' $HOME/.ssh/config
ssh gcc_relax

Use scp and rsync when gcloud has been ssh-config configured

#First fast check
touch test2.txt
scp test2.txt  gcc_relax:
ssh gcc_relax
ls
exit

# Or use rsync
mkdir dirtest
rsync --progress -avzhe ssh ./dirtest gcc_relax:
ssh gcc_relax
ls
rmdir dirtest
exit

STOP the google instance after test to stop the billing of computation

By browser

Go to:

By terminal

# Get at list of projects
gcloud compute --project "relax-1143" instances list

# Start it, it takes 30 seconds.
gcloud compute --project "relax-1143" instances start --zone "europe-west1-c" "relax"
ssh gcc_relax
exit

# Stop it through terminal
gcloud compute --project "relax-1143" instances stop --zone "europe-west1-c" "relax"
# This should now not work
ssh gcc_relax

See also

Retrieved from "http://wiki.nmr-relax.com/wiki/index.php?title=Run_relax_at_Google_Cloud_Computing&oldid=6524"