Troels Emtekær Linnet

Troels Emtekær Linnet PhD student Copenhagen University SBiNLab

Tests

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<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/cyspka.py" />

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

run relax at cloud.sagemath.com

Try relax at cloud.sagemath.com

This tutorial shows how to get relax running at cloud.sagemath.com.

cloud.sagemath.com is optimal for

• fully functional linux and python environment
• online accessibility
• rapid installation of relax
• testing purposes
• teaching

cloud.sagemath.com is not the optimal for

• long-time calculations stretching over several days
• multiple CPU's (above 4 CPU's )

pricing

• The benefits are well explained here: http://www.sagemath.org/library-why.html
• The pricing is here: https://cloud.sagemath.com/policies/pricing.html
• For the FAQ of sagemath, visit: https://github.com/sagemathinc/smc/wiki/FAQ
• Miling list: https://groups.google.com/forum/?fromgroups#!forum/sage-cloud

The meanings are

• 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).
• 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.
• 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.
• 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.

Sign-up and ssh to account

Do the following

• Go to https://cloud.sagemath.com/
• Sign-up for account. Note, you don't even need a "working e-mail", as no confirmation mail is send. It just works.

Establish file access over SSH

At your own computer, create a SSH-keypair.

tlinnet@linmac:.ssh$ ssh-keygen

Click here to see the input to ssh-keygen:

Generating public/private rsa key pair.
Enter file in which to save the key (/Users/tlinnet/.ssh/id_rsa): id_sage
Enter passphrase (empty for no passphrase): 
Enter same passphrase again: 
Your identification has been saved in id_sage.
Your public key has been saved in id_sage.pub.
The key fingerprint is:
SHA256:SqvIflxxxxx/xxxxxxxxxxxxx/XXXX tlinnet@linmac
The key's randomart image is:
+---[RSA 2048]----+
xxxxx
+----[SHA256]-----+

Then load your key and copy the content the public-key to clipboard

tlinnet@linmac:~$ ssh-add $HOME/.ssh/id_sage

Click here to see the input to ssh-keygen:

Enter passphrase for /Users/tlinnet/.ssh/id_sage: 
Identity added: /Users/tlinnet/.ssh/id_sage (/Users/tlinnet/.ssh/id_sage)

tlinnet@linmac:~$ ssh-add -l

Then copy the content of the public key to clipboard

cat $HOME/.ssh/id_sage.pub
# On a mac, one can copy directly to the the clipboard of the computer
cat $HOME/.ssh/id_sage.pub | pbcopy
# On linux

Then create a project at cloud.sagemath.com

• https://cloud.sagemath.com/projects
• Click at the project, and click then on the settings wrench.
• Under the info box Project control, there is a button to >_ SSH into your project...
• Then click on the link to ~/.ssh/authorized_keys,
• In the next window, paste in the line from before of cat $HOME/.ssh/id_sage.pub
• Save and close the tab of ~/.ssh/authorized_keys, .
• Click again on the settings wrench.
• Again under the info box Project control, there is a button to >_ SSH into your project...
• Here comes the USER@HOST info you need

It could look like this:

79688471c8704aa2b7b0be59d626e9cf@compute2-us.sagemath.com 

From you own terminal at your computer, try

ssh 79688471c8704aa2b7b0be59d626e9cf@compute2-us.sagemath.com

To make things easier, you can but this in your SSH config file

bash
SAGEUSER=79688471c8704aa2b7b0be59d626e9cf
SAGEHOST=compute2-us.sagemath.com

cat <<EOF >> $HOME/.ssh/config

Host sage
User $SAGEUSER
HostName $SAGEHOST
Compression yes
ForwardX11 yes
Port 22
EOF

cat $HOME/.ssh/config

Then try the connection

ssh sage

Inspect the cloud.sagemath.com

When ssh connected to your project, try some of the following commands:

uptime
whoami
lscpu
htop -u `whoami`