Difference between revisions of "Run relax at Google Cloud Computing"
(Switch to the {{relax source}} and {{relax url}} templates for the code URLs.) |
|||
(21 intermediate revisions by one other user not shown) | |||
Line 66: | Line 66: | ||
# Create instance | # Create instance | ||
− | gcloud compute instances create relax --zone us-central1-f --machine-type n1-highcpu- | + | gcloud compute instances create relax --zone us-central1-f --machine-type n1-highcpu-4 --image ubuntu-14-04 --boot-disk-size 10GB |
gcloud compute instances list | gcloud compute instances list | ||
# Or | # Or | ||
− | gcloud compute instances create relax --zone us-central1-f --machine-type n1-highcpu- | + | gcloud compute instances create relax --zone us-central1-f --machine-type n1-highcpu-4 --image rhel-6-v20160921 --boot-disk-size 10GB |
</source> | </source> | ||
Line 94: | Line 94: | ||
For '''rapid deployment''' use this command. This will install current version of relax and trunk. | For '''rapid deployment''' use this command. This will install current version of relax and trunk. | ||
− | + | See the list of deploy scripts here | |
− | + | * {{relax url|path=devel_scripts/deploy_scripts/}} | |
− | + | ||
− | # | + | Then download the script that matches the system. |
− | + | {{#tag: source| | |
− | source | + | # Select a version script |
+ | # Redhat Version 6 | ||
+ | VERS=deploy_google_computing_redhat_6_86_x64.sh | ||
+ | VERS=deploy_google_computing_redhat_6_86_x64_upgrade_python.sh | ||
+ | # Centos Version 6 | ||
+ | VERS=deploy_google_computing_centos_6_86_x64_upgrade_python.sh | ||
+ | # Redhat Version 7 | ||
+ | VERS=deploy_google_computing_redhat_7_86_x64.sh | ||
+ | # Ubuntu | ||
+ | VERS=deploy_google_computing_ubuntu_14-04_86_x64.sh | ||
+ | |||
+ | # Then set download URL | ||
+ | URL={{relax url|path=devel_scripts/deploy_scripts/$VERS|view=raw}} | ||
+ | |||
+ | # Download and readl | ||
+ | sudo yum -y install wget | ||
+ | wget $URL $VERS | ||
+ | mv $VERS* $VERS | ||
+ | cat $VERS | ||
+ | |||
+ | # Load functions | ||
+ | source $VERS | ||
− | # | + | # Do installation |
− | |||
installandcheck | installandcheck | ||
− | + | | lang="bash" | |
+ | }} | ||
+ | |||
'''Check installation of relax''' | '''Check installation of relax''' | ||
{{#tag:source| | {{#tag:source| | ||
− | mpirun --np | + | mpirun --np 2 relax_trunk --multi='mpi4py' |
relax_trunk --time -x | relax_trunk --time -x | ||
|lang="bash" | |lang="bash" | ||
}} | }} | ||
+ | |||
+ | == Test openmpi == | ||
+ | |||
+ | For BASH shell<br> | ||
+ | {{relax source|path=devel_scripts/openmpi_test_install_bash.sh|view=raw|text=See the script here}} | ||
+ | {{#tag: source| | ||
+ | URL={{relax url|path=devel_scripts/openmpi_test_install_bash.sh|view=raw}} | ||
+ | wget $URL | ||
+ | mv openmpi_test_install_bash.sh* openmpi_test_install_bash.sh | ||
+ | |||
+ | # Source functions | ||
+ | source openmpi_test_install_bash.sh | ||
+ | testopenmpi | ||
+ | | lang="bash" | ||
+ | }} | ||
+ | |||
+ | For TCSH shell<br> | ||
+ | {{relax source|path=devel_scripts/openmpi_test_install_tcsh.sh|view=raw|text=See the script here}} | ||
+ | {{#tag: source| | ||
+ | alias get 'set noglob; wget {{relax url|path=devel_scripts/openmpi_test_install_tcsh.sh|view=raw}}; mv openmpi_test_install_tcsh.sh* openmpi_test_install_tcsh.sh;unset noglob' | ||
+ | get | ||
+ | |||
+ | # Source functions | ||
+ | source openmpi_test_install_tcsh.sh | ||
+ | | lang="bash" | ||
+ | }} | ||
+ | |||
==Transfer files back and forth to the server== | ==Transfer files back and forth to the server== | ||
Line 178: | Line 227: | ||
This follows some example data from the tutorial here [[Tutorial_for_sorting_data_stored_as_numpy_to_on-resonance_R1rho_analysis|Tutorial for sorting data stored as numpy to on resonance R1rho_analysis]] | This follows some example data from the tutorial here [[Tutorial_for_sorting_data_stored_as_numpy_to_on-resonance_R1rho_analysis|Tutorial for sorting data stored as numpy to on resonance R1rho_analysis]] | ||
− | + | {{relax source|path=test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov|text=Overview of directory}} | |
Copy data to local dir | Copy data to local dir | ||
Line 189: | Line 238: | ||
− | + | {{relax source|path=test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov/1_tutorial_prepare_data.py|text=Prepare data}} | |
{{#tag:source| | {{#tag:source| | ||
cat 1_tutorial_prepare_data.py | cat 1_tutorial_prepare_data.py | ||
Line 197: | Line 246: | ||
}} | }} | ||
− | + | {{relax source|path=test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov/2_tutorial_load_data.py|text=Run analysis}} | |
{{#tag:source| | {{#tag:source| | ||
cat 2_tutorial_load_data.py | cat 2_tutorial_load_data.py | ||
− | mpirun --np | + | mpirun --np 2 relax_trunk --multi='mpi4py' 2_tutorial_load_data.py |
ls -latr | ls -latr | ||
|lang="bash" | |lang="bash" | ||
}} | }} | ||
− | + | {{relax source|path=test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov/3_tutorial_clustered.py|text=Run clustered analysis}} | |
{{#tag:source| | {{#tag:source| | ||
cat 3_tutorial_clustered.py | cat 3_tutorial_clustered.py | ||
− | mpirun --np | + | mpirun --np 2 relax_trunk --multi='mpi4py' 3_tutorial_clustered.py |
ls -latr | ls -latr | ||
|lang="bash" | |lang="bash" |
Latest revision as of 12:47, 27 October 2017
The Google Cloud Platform is a cloud computing platform that can be used for cheaply running relax on a cluster.
Contents
- 1 Background
- 2 Pricing
- 3 Start free trial
- 4 Create a Virtual Machine instance
- 5 Access Virtual Machine instance
- 6 Install packages at server
- 7 Test openmpi
- 8 Transfer files back and forth to the server
- 9 Use relax on a test dataset from a tutorial
- 10 STOP the google instance after test to stop the billing of computation
- 11 Upgrade account
- 12 Deploy google datalab to your server
- 13 See also
Background
This follows the same idea as from Run relax at cloud.sagemath.com
Make a rapid deployment of relax on a google computer cluster, and calculate for 2 months with 8 CPU's, for free.
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/
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/docs/free-trial-quotas
- https://cloud.google.com/free-trial/#/faq
For this time, the most important limitation is 8 CPUs.
8 CPU's
For the price calculation of:
- 1 server
- using Free: Debian, CentOS, ...
- with a regular VM Class
- Instance type of (HIGH CPU) n1-highcpu-8 (vCPUs: 8, RAM: 7.20 GB)
- 0 SSD
- Datacenter location United States
- Average days per month each server is running: 1 days, per month.
This 1 day price was of November 2015, $8.06. Constantly running is $171.70 per month.
This essentially gives you 2 months of free computation with 8 CPU's.
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 name relax, Project ID relax-1, App Engine location at us-central. NOTE: App engine HAS TO BE located in united states, if datalab should be enabled later.
Create a Virtual Machine instance
- Go to https://console.developers.google.com/home
- In the top right corner, there is a link to Activate Google Cloud Shell.
- Clicking this should start a terminal in half the window.
Links
# List all compute instances in the project
gcloud compute instances list
gcloud compute zones list
gcloud compute machine-types list | grep us-central1-f
gcloud compute machine-types list | grep us-central1-f | sort -k3 -n
gcloud compute images list
# Create instance
gcloud compute instances create relax --zone us-central1-f --machine-type n1-highcpu-4 --image ubuntu-14-04 --boot-disk-size 10GB
gcloud compute instances list
# Or
gcloud compute instances create relax --zone us-central1-f --machine-type n1-highcpu-4 --image rhel-6-v20160921 --boot-disk-size 10GB
Then you can SSH into the instance
PROJ=relax-1
ZONE=us-central1-f
PRID=instance-1
GCC=gcc
gcloud compute --project $PROJ ssh --zone $ZONE $PRID
gcloud compute --project "relax-1" ssh --zone "us-central1-f" "instance-1"
Access Virtual Machine instance
- Go to https://console.developers.google.com/compute
- In the line of relax, click SSH
- This should open a browser terminal window
Install packages at server
For rapid deployment use this command. This will install current version of relax and trunk.
See the list of deploy scripts here
Then download the script that matches the system.
# Select a version script
# Redhat Version 6
VERS=deploy_google_computing_redhat_6_86_x64.sh
VERS=deploy_google_computing_redhat_6_86_x64_upgrade_python.sh
# Centos Version 6
VERS=deploy_google_computing_centos_6_86_x64_upgrade_python.sh
# Redhat Version 7
VERS=deploy_google_computing_redhat_7_86_x64.sh
# Ubuntu
VERS=deploy_google_computing_ubuntu_14-04_86_x64.sh
# Then set download URL
URL=https://sourceforge.net/p/nmr-relax/code/ci/master/tree/devel_scripts/deploy_scripts/$VERS?format=raw
# Download and readl
sudo yum -y install wget
wget $URL $VERS
mv $VERS* $VERS
cat $VERS
# Load functions
source $VERS
# Do installation
installandcheck
Check installation of relax
mpirun --np 2 relax_trunk --multi='mpi4py'
relax_trunk --time -x
Test openmpi
For BASH shell
See the script here
URL=https://sourceforge.net/p/nmr-relax/code/ci/master/tree/devel_scripts/openmpi_test_install_bash.sh?format=raw
wget $URL
mv openmpi_test_install_bash.sh* openmpi_test_install_bash.sh
# Source functions
source openmpi_test_install_bash.sh
testopenmpi
For TCSH shell
See the script here
alias get 'set noglob; wget https://sourceforge.net/p/nmr-relax/code/ci/master/tree/devel_scripts/openmpi_test_install_tcsh.sh?format=raw; mv openmpi_test_install_tcsh.sh* openmpi_test_install_tcsh.sh;unset noglob'
get
# Source functions
source openmpi_test_install_tcsh.sh
Transfer files back and forth to the server
See here
Install gcloud on your local computer
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.
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.
PROJ=relax-1
ZONE=us-central1-f
PRID=relax
GCC=gcc
gcloud compute --project $PROJ config-ssh
cat $HOME/.ssh/config
# Use sed to change value of your local computes ssh config file
sed -i.bak "s/$PRID.$ZONE.$PROJ/$GCC/g" $HOME/.ssh/config
ls -l $HOME/.ssh/config*
grep "$GCC" $HOME/.ssh/config
ssh $GCC
exit
Use scp and rsync when gcloud has been ssh-config configured
#First fast check
cd $HOME/Downloads
touch test2.txt
scp test2.txt $GCC:
ssh $GCC
ls
rm test2.txt
exit
rm test2.txt
# Or use rsync
mkdir deletethisdir
rsync --progress -avzhe ssh ./deletethisdir $GCC:
ssh $GCC
ls
rmdir deletethisdir
exit
rmdir deletethisdir
Use relax on a test dataset from a tutorial
This follows some example data from the tutorial here Tutorial for sorting data stored as numpy to on resonance R1rho_analysis
Copy data to local dir
cd $HOME
cp -r $HOME/relax_trunk/test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov .
cd Paul_Schanda_2015_Nov
cat 1_tutorial_prepare_data.py
python 1_tutorial_prepare_data.py
ls -latr
cat 2_tutorial_load_data.py
mpirun --np 2 relax_trunk --multi='mpi4py' 2_tutorial_load_data.py
ls -latr
cat 3_tutorial_clustered.py
mpirun --np 2 relax_trunk --multi='mpi4py' 3_tutorial_clustered.py
ls -latr
See results
cd results_cluster/final
ls -latr
cat phi_ex.out
cat kex.out
STOP the google instance after test to stop the billing of computation
See: https://cloud.google.com/compute/docs/instances/stopping-or-deleting-an-instance
By browser
Go to:
- https://console.developers.google.com/compute
- Tick the relax project and click the "Stop" button.
By terminal
PROJ=relax-1
ZONE=us-central1-f
PRID=relax
GCC=gcc
# Get at list of projects
gcloud compute --project $PROJ instances list
# Start it, it takes 30 seconds.
gcloud compute --project $PROJ instances start --zone $ZONE $PRID
ssh $GCC
exit
# Stop it through terminal
gcloud compute --project $PROJ instances stop --zone $ZONE $PRID
# This should now not work
ssh $GCC
Upgrade account
To use 32 CPU's you need to upgrade your account
See
- https://cloud.google.com/free-trial/docs/upgrade-paid-account
- https://console.developers.google.com/compute/quotas
- https://cloud.google.com/free-trial/docs/free-trial-quotas
Deploy google datalab to your server
Warning This does not work |
Read more here: http://techcrunch.com/2015/10/13/google-launches-cloud-datalab-an-interactive-tool-for-exploring-and-visualizing-data
Note: Cloud Datalab uses AppEngine and Managed VMs beta, which is available in the US region only.
You cannot change the location after the project has been created.
See Location at: https://appengine.google.com/
Stop your server:
gcloud compute --project $PROJ instances stop --zone $ZONE $PRID
Cloud Datalab is deployed as an Google App Engine application module in a Google Developers Console project.
Click here to → Enable the Google Compute Engine API.
Visit:
Do the following
- Launch datalab
- Sign in
- Deploy to your project.