Troels Emtekær Linnet PhD student Copenhagen University SBiNLab

Tests

Test2

Test DPL imagecontainer=Screenshots

[[%PAGE%|thumb|185px|A random relax screenshot. See Screenshots.]]

SeriesTab

ls -v -d -1 */*.ft2 > allplanes.list

cd analysis_FT/int_corr_ft_method_all_awk/coMDD
seriesTab -in peaks.dat
seriesTab -in ../../peaks.dat -out allplanes_coMDD_ser.ser -list allplanes_coMDD.list

Test randomimagebycategor

Test

from math import pi
from lib import nmr
from lib.physical_constants import return_gyromagnetic_ratio


id = 'test'
H_frq = 900.0e6
B0_tesla =  H_frq / return_gyromagnetic_ratio(nucleus='1H') * 2.0 * pi
print "B0 in Tesla:", B0_tesla
isotope = '15N'

yOBS_N15_rad_s = return_gyromagnetic_ratio(nucleus=isotope) * B0_tesla
yOBS_N15_ppm = nmr.frequency_to_ppm_from_rad(frq=yOBS_N15_rad_s, B0=H_frq, isotope=isotope)

print yOBS_N15_ppm

# Convert hz
offset_hz = 2100.
offset_ppm = nmr.frequency_to_ppm(frq=offset_hz, B0=H_frq, isotope=isotope)
print offset_ppm


#yOBS_rad_s = return_gyromagnetic_ratio(nucleus=isotope) * B0_tesla
#print yOBS_rad_s
#yOBS_ppm = nmr.frequency_to_ppm_from_rad(frq=yOBS_rad_s, B0=H_frq, isotope=isotope)
#print yOBS_ppm


# Center carriage In ppm
yCAR_ppm = 118.078

Google Cloud Computing

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

pricing

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

The pricing explained here: https://cloud.google.com/pricing/
A pricing calculator is here: https://cloud.google.com/products/calculator/

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.

The monthly price was of November 2015, $32.26.

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

Note, there are some limitations: https://cloud.google.com/free-trial/#/faq

Start free trial

Please first see this video:

https://cloud.google.com/compute/docs/linux-quickstart or https://www.youtube.com/watch?v=BnEhYaUY4sA

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

Go to https://console.developers.google.com/compute
In the line of relax, click SSH
This should open a browser terminal window

Get relax and unpack

v=5.0.0

# 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-5.0.0.GNU-Linux.x86_64.tar.bz2
rm relax-5.0.0.GNU-Linux.x86_64.tar.bz2
ln -s $HOME/relax-5.0.0/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

https://cloud.google.com/compute/docs/tutorials/transfer-files

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:

https://console.developers.google.com/compute
In the line of relax, click SSH, and drop down to: View gcloud command.

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

#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:

https://console.developers.google.com/compute
Tick the relax project and click the "Stop" button.

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

User:Troels Emtekær Linnet

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