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| | yCAR_ppm = 118.078 | | yCAR_ppm = 118.078 |
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| − | = Google Cloud Computing =
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| − | This follows the same idea as from [[Run_relax_at_cloud.sagemath.com|Run relax at cloud.sagemath.com]]
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| − |
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| − | == pricing ==
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| − | For this example of '''Google Cloud Computing''', we wan't to have access to as many computer cores as possible
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| − |
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| − | * The pricing explained here: https://cloud.google.com/pricing/
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| − | * A pricing calculator is here: https://cloud.google.com/products/calculator/
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| − |
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| − | '''For the price calculation of:'''
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| − | * '''1''' server
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| − | * using '''Free: Debian, CentOS, ...'''
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| − | * with a '''regular''' VM Class
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| − | * Instance type of (HIGH CPU) '''n1-highcpu-32 (vCPUs: 32, RAM: 28.80 GB)'''
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| − | * 0 '''SSD'''
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| − | * Datacenter location '''Europe'''
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| − | * Average days per month each server is running: '''1''' days, per month.
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| − | The '''monthly''' price was of November 2015, '''$32.26'''.
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| − |
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| − | At November 2015, google give free trial of '''300$'''. https://cloud.google.com/free-trial/
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| − |
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| − | Note, there are some limitations: https://cloud.google.com/free-trial/#/faq
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| − |
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| − | == Start free trial ==
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| − | Please first see this video:
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| − | * https://cloud.google.com/compute/docs/linux-quickstart or https://www.youtube.com/watch?v=BnEhYaUY4sA
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| − |
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| − | Go to: https://cloud.google.com/free-trial/ and click '''Start your free trial'''.
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| − |
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| − | You need to sign up with a credit card. To prevent mis-abuse from robots and hackers.
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| − |
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| − | '''Then go to: https://console.developers.google.com'''
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| − | * You should already have a project called '''My First Project'''.
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| − | * '''Create a new project''' in top right corner of the browser under the dropdown of '''My First Project'''.
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| − | * Call the new project '''relax''' with '''App Engine location''' at '''europe-west'''
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| − |
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| − | == Create a Virtual Machine instance ==
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| − | * Click then at '''Try Compute Engine''' or go to https://console.developers.google.com/compute
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| − | * Click '''Create instance'''
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| − | * '''Name:''' relax
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| − | * '''Zone:''' Don't change this. As of Nov 2015, it seems that if you change this, you cannot select more than 2 vCPU's
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| − | * '''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.]
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| − | * '''Boot disk:''' 10 GB of Ubuntu 14.04 LTS
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| − | * '''Zone:''' Now change this to: europe-west1-c
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| − | * Let the rest be default and click '''Create'''.
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| − |
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| − | == Access Virtual Machine instance ==
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| − | * Go to https://console.developers.google.com/compute
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| − | * In the line of '''relax''', click '''SSH'''
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| − | * This should open a '''browser terminal window'''
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| − |
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| − | == Get relax and unpack ==
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| − |
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| − | {{#tag:source|
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| − | v={{current version relax}}
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| − |
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| − | # Get relax
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| − | curl http://download.gna.org/relax/relax-$v.GNU-Linux.x86_64.tar.bz2 -o relax-$v.GNU-Linux.x86_64.tar.bz2
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| − |
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| − | # Make home bin
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| − | mkdir -p $HOME/bin
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| − | tar xvjf relax-{{current version relax}}.GNU-Linux.x86_64.tar.bz2
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| − | rm relax-{{current version relax}}.GNU-Linux.x86_64.tar.bz2
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| − | ln -s $HOME/relax-{{current version relax}}/relax $HOME/bin
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| − |
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| − | # Add $HOME/bin to PATH
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| − | echo '' >> $HOME/.bashrc
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| − | echo 'export PATH=$PATH:$HOME/bin' >> $HOME/.bashrc
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| − | source $HOME/.bashrc
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| − | |lang="bash"
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| − | }}
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| − |
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| − | Solve depencies. See also [[Installation_linux|Installation linux]]
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| − | {{#tag:source|
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| − | sudo apt-get -y install python-numpy
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| − | |lang="bash"
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| − | }}
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| − |
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| − | Then test relax
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| − | {{#tag:source|
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| − | relax -i
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| − | |lang="bash"
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| − | }}
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| − |
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| − | Then install other packages
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| − | Solve depencies. See also [[Installation_linux|Installation linux]]
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| − | {{#tag:source|
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| − | sudo apt-get -y install python-scipy python-matplotlib python-pip
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| − | sudo apt-get -y install openmpi-bin openmpi-doc libopenmpi-dev
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| − | sudo pip install mpi4py
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| − | sudo pip install epydoc
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| − |
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| − | # Check installation
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| − | relax -i
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| − | |lang="bash"
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| − | }}
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| − |
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| − | == Inspect server ==
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| − |
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| − | Install these very good server packages
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| − | Solve depencies. See alsp [[Installation_linux|Installation linux]]
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| − | {{#tag:source|
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| − | sudo apt-get -y install htop
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| − | |lang="bash"
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| − | }}
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| − |
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| − | Then check server
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| − | {{#tag:source|
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| − | uptime
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| − | whoami
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| − | lscpu
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| − | htop -u `whoami`
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| − | |lang="bash"
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| − | }}
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| − |
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| − | Then check mpirun
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| − | {{#tag:source|
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| − | mpirun --version
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| − | mpirun --report-bindings -np 4 echo "hello world"
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| − | mpirun --np 8 relax --multi='mpi4py'
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| − | |lang="bash"
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| − | }}
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| − |
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| − | ==Install trunk of relax==
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| − |
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| − | === Solve dependencies. ===
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| − | See alsp [[Installation_linux|Installation linux]]
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| − | {{#tag:source|
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| − | sudo apt-get -y install subversion scons grace
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| − | |lang="bash"
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| − | }}
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| − |
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| − | === Checkout relax and build. ===
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| − | {{#tag:source|
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| − | svn co svn://svn.gna.org/svn/relax/trunk relax_trunk
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| − |
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| − | # Build
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| − | cd relax_trunk
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| − | scons
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| − |
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| − | # Link to executable
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| − | cd $HOME
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| − | mkdir -p $HOME/bin
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| − | ln -s $HOME/relax_trunk/relax $HOME/bin/relax_trunk
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| − |
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| − | # See relax info
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| − | relax_trunk -i
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| − |
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| − | |lang="bash"
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| − | }}
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| − |
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| − | ===install Minfx===
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| − | See [[Minfx]]
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| − | {{#tag:source|
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| − | v={{current version minfx}}
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| − |
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| − | mkdir -p $HOME/Downloads
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| − | cd $HOME/Downloads
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| − | curl http://download.gna.org/minfx/minfx-$v.tar.gz -o minfx-$v.tar.gz
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| − | tar -xzf minfx-$v.tar.gz
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| − | cd minfx-$v
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| − | sudo pip install .
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| − | cd $HOME
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| − |
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| − | # Test relax
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| − | relax_trunk -i
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| − | |lang="bash"
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| − | }}
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| − |
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| − | ===install Bmrblib===
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| − | See [[Bmrblib]]
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| − | {{#tag:source|
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| − | v={{current version bmrblib}}
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| − |
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| − | mkdir -p $HOME/Downloads
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| − | cd $HOME/Downloads
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| − | curl http://download.gna.org/bmrblib/bmrblib-$v.tar.gz -o bmrblib-$v.tar.gz
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| − | tar -xzf bmrblib-$v.tar.gz
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| − | cd bmrblib-$v
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| − | sudo pip install .
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| − | cd $HOME
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| − |
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| − | # Test relax
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| − | relax_trunk -i
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| − | |lang="bash"
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| − | }}
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| − |
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| − | ==Check installation of relax==
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| − | {{#tag:source|
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| − | relax_trunk --time -x
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| − | |lang="bash"
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| − | }}
| |
Troels Emtekær Linnet
PhD student
Copenhagen University
SBiNLab
Tests
80px
80px
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/cyspka.py" />
Test2
<include src="http://www.ietf.org/rfc/rfc1945" />
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
