Difference between revisions of "User:Troels Emtekær Linnet"

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yCAR_ppm = 118.078
 
yCAR_ppm = 118.078
 
</source>
 
</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==
 
Se
 
* https://cloud.google.com/compute/docs/tutorials/transfer-files
 
 
=== Install gcloud===
 
See https://cloud.google.com/sdk/
 
 
On your own computer
 
<source lang="python">
 
cd $HOME/Downloads
 
curl https://sdk.cloud.google.com | bash
 
source $HOME/.bash_profile
 
gcloud init
 
</source>
 
 
This will start a browser to authenticate you. When it ask for a ID, just write "test" and say no to cloning.
 
 
Then go to:
 
* https://console.developers.google.com/compute
 
* In the line of relax, click SSH, and drop down to: '''View gcloud command'''.
 
 
It could look like this. Try this in your own terminal. This should make some SSH keys and bring you to the server
 
<source lang="text">
 
gcloud compute --project "relax-1143" ssh --zone "europe-west1-c" "relax"
 
</source>
 
 
This should bring you to the google server.
 
<source lang="bash">
 
lscpu
 
cat $HOME/.ssh/authorized_keys
 
exit
 
 
# At your own computer
 
ls -l $HOME/.ssh/google*
 
cat $HOME/.ssh/config
 
ssh-add -l
 
ssh-add $HOME/.ssh/google_compute_engine
 
ssh-add -l
 
</source>
 
 
=== Copy files ===
 
See: https://cloud.google.com/sdk/gcloud/reference/compute/copy-files
 
 
The ssh command was
 
<source lang="bash">
 
gcloud compute --project "relax-1143" ssh --zone "europe-west1-c" "relax"
 
</source>
 
 
We make a test file and copy it
 
<source lang="bash">
 
touch test.txt
 
gcloud compute --project "relax-1143" copy-files test.txt relax:~ --zone "europe-west1-c"
 
 
# Try a directory
 
mkdir testdir
 
cp test.txt testdir
 
gcloud compute --project "relax-1143" copy-files testdir relax:~ --zone "europe-west1-c"
 
 
# Back again
 
cd testdir
 
gcloud compute --project "relax-1143" copy-files relax:~/testdir . --zone "europe-west1-c"
 
</source>
 
 
=== ssh-config with gcloud ===
 
See https://cloud.google.com/sdk/gcloud/reference/compute/config-ssh
 
 
gcloud compute config-ssh makes SSHing to virtual machine instances easier by adding an alias for each instance to the user SSH configuration (~/.ssh/config) file.
 
 
<source lang="bash">
 
gcloud compute --project "relax-1143" config-ssh
 
cat $HOME/.ssh/config
 
 
# ssh in
 
ssh relax.europe-west1-c.relax-1143
 
 
# Use sed to change value
 
grep 'relax.europe-west1-c.relax-1143' $HOME/.ssh/config
 
sed 's/relax.europe-west1-c.relax-1143/gcc_relax/g' $HOME/.ssh/config
 
sed -i.bak 's/relax.europe-west1-c.relax-1143/gcc_relax/g' $HOME/.ssh/config
 
ls -l $HOME/.ssh/config*
 
grep 'gcc_relax' $HOME/.ssh/config
 
ssh gcc_relax
 
</source>
 
 
=== Use scp and rsync  ===
 
 
{{#tag:source|
 
#First fast check
 
touch test2.txt
 
scp test2.txt  gcc_relax:
 
ssh gcc_relax
 
ls
 
exit
 
 
# Or use rsync
 
mkdir dirtest
 
rsync --progress -avzhe ssh ./dirtest gcc_relax:
 
ssh gcc_relax
 
ls
 
rmdir dirtest
 
exit
 
|lang="bash"
 
}}
 

Latest revision as of 15:59, 28 November 2015

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