Troels Emtekær Linnet

Latest revision as of 15:59, 28 November 2015

Troels Emtekær Linnet PhD student Copenhagen University SBiNLab

Tests

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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

@@ Line 70: / Line 70: @@
 yCAR_ppm = 118.078
 </source>
-= Google Cloud Computing =
-This follows the same idea as from [[Run_relax_at_cloud.sagemath.com|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, [https://cloud.google.com/free-trial/#/faq 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 ==
-{{#tag:source|
-v={{current version relax}}
-# 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-{{current version relax}}.GNU-Linux.x86_64.tar.bz2
-rm relax-{{current version relax}}.GNU-Linux.x86_64.tar.bz2
-ln -s $HOME/relax-{{current version relax}}/relax $HOME/bin
-# Add $HOME/bin to PATH
-echo '' >> $HOME/.bashrc
-echo 'export PATH=$PATH:$HOME/bin' >> $HOME/.bashrc
-source $HOME/.bashrc
-|lang="bash"
-}}
-Solve depencies. See also [[Installation_linux|Installation linux]]
-{{#tag:source|
-sudo apt-get -y install python-numpy
-|lang="bash"
-}}
-Then test relax
-{{#tag:source|
-relax -i
-|lang="bash"
-}}
-Then install other packages
-Solve depencies. See also [[Installation_linux|Installation linux]]
-{{#tag:source|
-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
-|lang="bash"
-}}
-== Inspect server ==
-Install these very good server packages
-Solve depencies. See alsp [[Installation_linux|Installation linux]]
-{{#tag:source|
-sudo apt-get -y install htop
-|lang="bash"
-}}
-Then check server
-{{#tag:source|
-uptime
-whoami
-lscpu
-htop -u `whoami`
-|lang="bash"
-}}
-Then check mpirun
-{{#tag:source|
-mpirun --version
-mpirun --report-bindings -np 4 echo "hello world"
-mpirun --np 8 relax --multi='mpi4py'
-|lang="bash"
-}}
-==Install trunk of relax==
-=== Solve dependencies. ===
-See alsp [[Installation_linux|Installation linux]]
-{{#tag:source|
-sudo apt-get -y install subversion scons grace
-|lang="bash"
-}}
-=== Checkout relax and build. ===
-{{#tag:source|
-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
-|lang="bash"
-}}
-===install Minfx===
-See [[Minfx]]
-{{#tag:source|
-v={{current version minfx}}
-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
-|lang="bash"
-}}
-===install Bmrblib===
-See [[Bmrblib]]
-{{#tag:source|
-v={{current version bmrblib}}
-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
-|lang="bash"
-}}
-==Check installation of relax==
-{{#tag:source|
-relax_trunk --time -x
-|lang="bash"
-}}
-==Transfer files back and forth to the server==
-See https://cloud.google.com/compute/docs/tutorials/transfer-files
-=== Install gcloud===
-See https://cloud.google.com/sdk/
-On your own computer
-{{#tag:source|
-cd $HOME/Downloads
-curl https://sdk.cloud.google.com | bash
-source $HOME/.bash_profile
-|lang="bash"
-}}