User:Troels Emtekær Linnet

Troels Emtekær Linnet PhD student Copenhagen University SBiNLab

Tests

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Test2

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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 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=5.1.0

# 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 alsp Installation linux

sudo apt-get -y install python-numpy

Then test relax

relax -i

Then install other packages Solve depencies. See alsp 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 and test relax installation

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'