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| | # Center carriage In ppm | | # Center carriage In ppm |
| | yCAR_ppm = 118.078 | | yCAR_ppm = 118.078 |
| − | </source>
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| − |
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| − | = run relax at cloud.sagemath.com =
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| − |
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| − | == Try relax at cloud.sagemath.com ==
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| − | This tutorial shows how to get relax running at cloud.sagemath.com.
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| − |
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| − | '''cloud.sagemath.com is optimal for'''
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| − | * fully functional linux and python environment
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| − | * online accessibility
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| − | * rapid installation of relax
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| − | * testing purposes
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| − | * teaching
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| − |
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| − | '''cloud.sagemath.com is not the optimal for'''
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| − | * long-time calculations stretching over several days
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| − | * multiple CPU's (above 4 CPU's )
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| − |
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| − | === pricing ===
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| − | * The benefits are well explained here: http://www.sagemath.org/library-why.html
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| − | * The pricing is here: https://cloud.sagemath.com/policies/pricing.html
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| − |
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| − | '''The meanings are'''
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| − | * '''Member hosting:''' This lets you move a project to a members-only server, which has much less load. If you have 16 of these, you can move 16 projects. You can change which projects you move at any time, though it can take a little while to move a project (depending on load).
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| − | * '''Network access:'''' This makes it so your project has 100% access to the whole internet, so you can connect to any external website. Otherwise, there is a small whitelist of sites (e.g., pypi, github) that a project may connect to.
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| − | * ''' Idle timeout''' You can allocate time between projects so that if you just shut your browser and come back (or aren't active), the project will continue running your code instead of just shutting down. By default, projects top running after 1 hour of not being actively used through a web browser.
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| − | * '''CPU shares:''' This allows you to increase your priority relative to other users on the same computer. So if the system is loaded, your code will run a bit faster than other users.
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| − |
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| − | == Sign-up and ssh to account ==
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| − |
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| − | Do the following
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| − | * Go to https://cloud.sagemath.com/
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| − | * Sign-up for account. Note, you don't even need a "working e-mail", as no confirmation mail is send. It just works.
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| − |
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| − | === Establish file access over SSH ===
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| − | At your own computer, create a SSH-keypair.
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| − |
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| − | <source lang="bash">
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| − | tlinnet@linmac:.ssh$ ssh-keygen
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| − | </source>
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| − |
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| − | {{collapsible script
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| − | | type = Click here to see the input to ssh-keygen
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| − | | lang = bash
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| − | | script =
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| − | Generating public/private rsa key pair.
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| − | Enter file in which to save the key (/Users/tlinnet/.ssh/id_rsa): id_sage
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| − | Enter passphrase (empty for no passphrase):
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| − | Enter same passphrase again:
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| − | Your identification has been saved in id_sage.
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| − | Your public key has been saved in id_sage.pub.
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| − | The key fingerprint is:
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| − | SHA256:SqvIflxxxxx/xxxxxxxxxxxxx/XXXX tlinnet@linmac
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| − | The key's randomart image is:
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| − | +---[RSA 2048]----+
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| − | xxxxx
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| − | +----[SHA256]-----+
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| − | }}
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| − |
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| − | Then load your key and copy the content the public-key to clipboard
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| − | <source lang="bash">
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| − | tlinnet@linmac:~$ ssh-add $HOME/.ssh/id_sage
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| − | </source>
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| − | {{collapsible script
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| − | | type = Click here to see the input to ssh-keygen
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| − | | lang = bash
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| − | | script =
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| − | Enter passphrase for /Users/tlinnet/.ssh/id_sage:
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| − | Identity added: /Users/tlinnet/.ssh/id_sage (/Users/tlinnet/.ssh/id_sage)
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| − | }}
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| − | <source lang="bash">
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| − | tlinnet@linmac:~$ ssh-add -l
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| − | </source>
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| − |
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| − | Then copy the content of the public key to clipboard
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| − | <source lang="bash">
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| − | cat $HOME/.ssh/id_sage.pub
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| − | # On a mac, one can copy directly to the the clipboard of the computer
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| − | cat $HOME/.ssh/id_sage.pub | pbcopy
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| − | # On linux
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| − | </source>
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| − |
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| − | Then create a project at cloud.sagemath.com
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| − | * https://cloud.sagemath.com/projects
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| − | * Click at the project, and click then on the '''settings''' wrench.
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| − | * Under the info box '''Project control''', there is a button to '''>_ SSH into your project...'''
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| − | * Then click on the link to '''~/.ssh/authorized_keys, '''
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| − | * In the next window, paste in the line from before of '''cat $HOME/.ssh/id_sage.pub'''
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| − | * Save and close the tab of '''~/.ssh/authorized_keys, '''.
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| − | * Click again on the '''settings''' wrench.
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| − | * Again under the info box '''Project control''', there is a button to '''>_ SSH into your project...'''
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| − | * Here comes the '''USER@HOST''' info you need
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| − |
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| − | It could look like this:
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| − | 79688471c8704aa2b7b0be59d626e9cf@compute2-us.sagemath.com
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| − |
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| − | From you own terminal at your computer, try
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| − | <source lang="bash">
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| − | ssh 79688471c8704aa2b7b0be59d626e9cf@compute2-us.sagemath.com
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| − | </source>
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| − |
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| − | To make things easier, you can but this in your SSH config file
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| − | <source lang="bash">
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| − | bash
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| − | SAGEUSER=79688471c8704aa2b7b0be59d626e9cf
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| − | SAGEHOST=compute2-us.sagemath.com
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| − |
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| − | cat <<EOF >> $HOME/.ssh/config
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| − |
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| − | Host sage
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| − | User $SAGEUSER
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| − | HostName $SAGEHOST
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| − | Compression yes
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| − | ForwardX11 yes
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| − | Port 22
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| − | EOF
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| − |
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| − | cat $HOME/.ssh/config
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| − | </source>
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| − |
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| − | Then try the connection
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| − | <source lang="bash">
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| − | ssh sage
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| | </source> | | </source> |
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
