Difference between revisions of "User:Troels Emtekær Linnet"
| Line 284: | Line 284: | ||
* https://console.developers.google.com/compute | * https://console.developers.google.com/compute | ||
* In the line of relax, click SSH, and drop down to: '''View gcloud command'''. | * 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 | + | |
| + | 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"> | <source lang="text"> | ||
gcloud compute --project "relax-1143" ssh --zone "europe-west1-c" "relax" | gcloud compute --project "relax-1143" ssh --zone "europe-west1-c" "relax" | ||
| Line 291: | Line 292: | ||
This should bring you to the google server. | This should bring you to the google server. | ||
<source lang="text"> | <source lang="text"> | ||
| + | lscpu | ||
cat $HOME/.ssh/authorized_keys | cat $HOME/.ssh/authorized_keys | ||
exit | exit | ||
| + | |||
| + | # At your own computer | ||
ls -l $HOME/.ssh/google* | ls -l $HOME/.ssh/google* | ||
cat $HOME/.ssh/config | cat $HOME/.ssh/config | ||
Revision as of 14:51, 28 November 2015
Troels Emtekær Linnet PhD student Copenhagen University SBiNLab
Contents
- 1 Tests
- 2 Test2
- 3 Test DPL imagecontainer=Screenshots
- 4 SeriesTab
- 5 Test randomimagebycategor
- 6 Test
- 7 Google Cloud Computing
Tests
<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
Google Cloud Computing
This follows the same idea as from 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, 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
v=5.1.0
# 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-5.1.0.GNU-Linux.x86_64.tar.bz2
rm relax-5.1.0.GNU-Linux.x86_64.tar.bz2
ln -s $HOME/relax-5.1.0/relax $HOME/bin
# Add $HOME/bin to PATH
echo '' >> $HOME/.bashrc
echo 'export PATH=$PATH:$HOME/bin' >> $HOME/.bashrc
source $HOME/.bashrc
Solve depencies. See also Installation linux
sudo apt-get -y install python-numpy
Then test relax
relax -i
Then install other packages Solve depencies. See also Installation linux
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
Inspect server
Install these very good server packages Solve depencies. See alsp Installation linux
sudo apt-get -y install htop
Then check server
uptime
whoami
lscpu
htop -u `whoami`
Then check mpirun
mpirun --version
mpirun --report-bindings -np 4 echo "hello world"
mpirun --np 8 relax --multi='mpi4py'
Install trunk of relax
Solve dependencies.
See alsp Installation linux
sudo apt-get -y install subversion scons grace
Checkout relax and build.
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
install Minfx
See Minfx
v=1.0.12
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
install Bmrblib
See Bmrblib
v=1.0.4
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
Check installation of relax
relax_trunk --time -x
Transfer files back and forth to the server
Se
Install gcloud
See https://cloud.google.com/sdk/
On your own computer
cd $HOME/Downloads
curl https://sdk.cloud.google.com | bash
source $HOME/.bash_profile
gcloud init
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
gcloud compute --project "relax-1143" ssh --zone "europe-west1-c" "relax"
This should bring you to the google server.
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
