Below are obsolete information for older HPC cloud. They are kept as reference.

Cloud template

change BUCKET_CLUSTER, BUCKET_DEFAULT, CLUSTER_NAME if a different bucket name is used at the cloudman script download site. For example https://cloudman-on.dtls.nl/cloudman-on
Once the hosting site of the bucket is moved, you also need to check/modify the following two variables in /opt/cloudman/pkg/ec2autorun.py

SERVICE_ROOT = 'http://cloudman-on.dtls.nl' 
DEFAULT_BUCKET_NAME = 'cloudman-on' # Ensure this bucket is accessible to anyone!

PASSWORD is set to have authentication on cloudman UI login. The default username is "admin"

CONTEXT=[
 BOOT_SCRIPT_NAME=cm_boot.py,
 BOOT_SCRIPT_PATH=/tmp/cm,
 BUCKET_CLUSTER=cloudman-on,
 BUCKET_DEFAULT=cloudman-on,
 CLOUDMAN_HOME=/mnt/cm,
 CLOUD_TYPE=opennebula,
 CLUSTER_NAME=cloudman-on,
 ON_HOST=http://one-xmlrpc.calligo.sara.nl:2633/RPC2,
 ON_PASSWORD=plain:row8inking,
 ON_PROXY=10.0.137.3:3128,
 ON_USERNAME=<username>,
 PASSWORD=<password>,
 ROLE=master,
 TESTFLAG=false ]
CPU=1
DISK=[
 BUS=virtio,
 IMAGE="GalaxyMaster_2012_10_18",
 IMAGE_UNAME=hailiang.mei@nbic.nl ]
GRAPHICS=[
 TYPE=vnc ]
MEMORY=8192
NAME="NBIC Galaxy"
NIC=[
 MODEL=e1000,
 NETWORK=internet,
 NETWORK_FILTER=226,
 NETWORK_UNAME=oneadmin ]
NIC=[
 MODEL=e1000,
 NETWORK=sombrerogalaxy-nbic,
 NETWORK_UNAME=hailiang.mei@nbic.nl ]
OS=[
 ARCH=x86_64,
 BOOT=hd ]
RAW=[
 TYPE=kvm ]
TEMPLATE_ID=2514
VCPU=1

VM Shutdown and Start Instructions

In order to stop the running VM at the SARA cloud and save it into a image file, we need to shutdown the VM and restart a new instance. Below are the steps:

Perform an update of the linux packages

sudo nbic-dist-upgrade
Save the logs printed by the update in the Server Logs
Log into cloud management console: https://ui.hpccloud.sara.nl/
Activate "save as" image of the current running VM, named with the current date e.g. "GalaxyMaster_2012_10_18"
Shutdown the VM
Go to the images section, and make the new image readable and writable for the group
Go to the templates section, update "IMAGE=GalaxyMaster_2012_10_18" in the template "NBIC Galaxy"
Unpack cm.tar.gz in the shared dropbox folder.
Update "IMAGE=GalaxyMaster_2012_10_18" in cm/clouds/opennebula.py

tar czf cm.tar.gz cm
In the cloud management console, create a new VM (in the "Virtual Machines" section, click "+New" in the upper right corner): name it as "nbicgalaxy" and select the "NBIC Galaxy" template.
- Note, make sure "nbicgalaxy" is spelled correctly as it is crucial to have the correct DNS name for our VM: nbicgalaxy.sombrerogalaxy-nbic.cloudlet.sara.nl
In the cloud management console, select the running VM, click button "Update Properties" and give the "group" access to "use" and "manage" the VM
Once the new VM is running, you could log into it and start the lanch of Cloudman service (including Galaxy)

Cloudman Startup Instructions

(Note: normally nginx should start automatically when the VM restarts. In case it is not the case, you can manually start it by executing: "sudo /opt/galaxy/pkg/nginx/sbin/nginx".)

You need to restart cloudman in case the VM is restarted.

stop the running cloudman process

sudo sh /mnt/cm/run.sh --stop-daemon

kill the hanging Galaxy process that still occupies the Galaxy port if necessary

sudo kill -9 `sudo fuser -n tcp 42284`

kill all running sge process (let cloudman handle the start of SGE)

sudo pkill -U sgeadmin

update /etc/hosts with master node's internal IP address

ifconfig eth1
sudo vim /etc/hosts and replace the line
10.0.137.xxx	ubuntu

if there are lines specifying worker nodes in /etc/hosts, remove them

if you updated the IP address in the previous step: restart rabbitmq server

sudo pkill -U rabbitmq
sudo /etc/init.d/rabbitmq-server start

start cloudman script

sudo sh /mnt/cm/run.sh --daemon

When cloudman is not working for the cloud middleware, some things need to be started by hand instead:

 sudo su postgres
 /usr/lib/postgresql/9.1/bin/postgres -D /mnt/galaxyData/pgsql/data -p 5840

 sudo /opt/galaxy/pkg/nginx/sbin/nginx

 sudo /bin/su - galaxy -c "export SGE_ROOT=/opt/sge; sh /mnt/galaxyTools/galaxy-central/run.sh --daemon"

go to http://galaxy.nbic.nl/cloud and login with admin/{default password} to initiate the launch of cloud Galaxy. When it asks you for the 'initial storage' just ignore this and click on the 'cloudman' button at the bottom of the pop-up.

Check the log file /mnt/cm/paster.log to see if cloudman services (including postgres, SGE, Galaxy) start successfully.

Galaxy Startup Instructions

Start and stop Galaxy only.

sudo /bin/su - galaxy -c "export SGE_ROOT=/opt/sge; sh /mnt/galaxyTools/galaxy-central/run.sh --stop-daemon"
sudo /bin/su - galaxy -c "export SGE_ROOT=/opt/sge; sh /mnt/galaxyTools/galaxy-central/run.sh --daemon"

Galaxy Update Instructions

When PennState Galaxy team releases new versions, we need to update our Galaxy codebase.

Stop the service

lock the job submission at the NBIC Galaxy server via the admin UI.
Stop the Galaxy daemon.

sudo /mnt/galaxyTools/galaxy-central/run.sh --stop-daemon

Download new release of Galaxy

Galaxy codebase is located at /mnt/galaxyTools (which is a NFSv4 mount of the cloud VM. All mount points are owned by user "postgres" as a workaround to support cloudman and postgres service)

go to the directory of /mnt/galaxyTools/sources/ and check out the latest code (central version) from Penn State:

hg clone https://bitbucket.org/galaxy/galaxy-central galaxy-<year>-<month>-<date>

Note: this is just a copy for reference. Do not modify this copy!

Copy this folder to /mnt/galaxyTools/. This will become the active installation with local mods.

cp /mnt/galaxyTools/sources/galaxy-<year>-<month>-<date> /mnt/galaxyTools/ -r

Update the Galaxy symbolic link

cd /mnt/galaxyTools
rm galaxy-central
ln -s galaxy-<year>-<month>-<date>/ galaxy-central

Backup the Galaxy DB

Start the database service if it is not running (e.g., stopped by the cloudman script.)

sudo su postgres
/usr/lib/postgresql/9.1/bin/postgres -D /mnt/galaxyData/pgsql/data -p 5840

Backup the current galaxy DB.

sudo su postgres
pg_dump -p 5840 galaxy > galaxyDB_backup.out

Update database

Configure the new galaxy: we keep the all the files (datasets) associated with histories stored in the Postgres database in a separate database folder outside the galaxy root folder.

cd /mnt/galaxyTools/galaxy-central
rmdir database 
# Note: make sure this is the EMPTY database folder of the new install and not 
# a symlink pointing to our data in /opt/galaxy/data/database/
ln -s /mnt/galaxyData/database database

Test starting up the cloudman/Galaxy server (and fetch/check eggs if necessary)

sudo /mnt/cm/run.sh --daemon

Copy NBIC tools and data

Customize the new Galaxy: We keep copies of modified (config) files in the conerice repository. You should diff our customized versions in the conerice repo with the new versions in Galaxy. When necessary merge updates from the Galaxy developers with our local customizations and commit a new version to the conerice repo. If there are no changes you can simply copy the files below:

cd /mnt/galaxyTools/sources/
svn update conerice
cp conerice/masterfiles/galaxy/sombrero/static/welcome.html              /mnt/galaxyTools/galaxy-central/static/
cp conerice/masterfiles/galaxy/sombrero/config/universe_wsgi.ini          /mnt/galaxyTools/galaxy-central/
cp conerice/masterfiles/galaxy/sombrero/config/tool_data_table_conf.xml          /mnt/galaxyTools/galaxy-central/
cp conerice/masterfiles/galaxy/sombrero/config/tool_conf.xml              /mnt/galaxyTools/galaxy-central/
cp conerice/masterfiles/galaxy/sombrero/config/shed_tool_conf.xml          /mnt/galaxyTools/galaxy-central/
cp conerice/masterfiles/galaxy/sombrero/config/datatypes_conf.xml          /mnt/galaxyTools/galaxy-central/
cp conerice/masterfiles/galaxy/sombrero/lib/galaxy/datatypes/registry.py  /mnt/galaxyTools/galaxy-central/lib/galaxy/datatypes/
cp conerice/masterfiles/galaxy/sombrero/tools/data_source/upload.py       /mnt/galaxyTools/galaxy-central/tools/data_source/

Create symlinks for our tools and datatypes from the NBIC Galaxy Module Repository

cd /mnt/galaxyTools/sources/galaxytools
svn update
svn export trunk /mnt/galaxyTools/nbic_gmr
cd /mnt/galaxyTools/galaxy-central/tools
ln -s /mnt/galaxyTools/nbic_gmr/ nbic_gmr
cd /mnt/galaxyTools/galaxy-central/static/images
ln -s /mnt/galaxyTools/nbic_gmr/data/image-links/ nbic_gmr
cd /mnt/galaxyTools/galaxy-central/lib/galaxy/datatypes/
for item in $(ls /mnt/galaxyTools/nbic_gmr/data/datatypes/); do ln -s /mnt/galaxyTools/nbic_gmr/data/datatypes/$item; done

Create symlinks for custom tool-data files in /mnt/galaxyTools/galaxy-central/tool-data/

cd /mnt/galaxyTools/galaxy-central/tool-data/
for item in $(ls /mnt/galaxyData/tool-data/); do ln -s /mnt/galaxyData/tool-data/$item; done

Restart the service

sudo /mnt/cm/run.sh --daemon

Check the log file /mnt/galaxyTools/galaxy-central/paster.log to see if Galaxy started (without errors).

Useful tips

Creating new user accounts

To keep the server safe it is important to have a policy on the user accounts.

Create a new user with the following command (replace group1,group2 and user with the correct values of course, if no special group memberships are necessary, you can omit the -G ...)

sudo useradd -G sudo -m -U -b /home -s /bin/bash -c 'Full name of the user' username

Always use a strong password on user accounts (8 or more characters and use letters, numbers and specials). Set the initial password with

sudo passwd user

When you create an account and have to e-mail the password to the user enforce a password change on first use with the following command:

sudo chage -d 0 user

When you are giving temporary access to someone set an expiration date for the account with the following command:

sudo chage -E YYYY-MM-DD user

make sure the user is member of the right groups. Users who need to have access to galaxy need to be in the devs group, but only give group membership if it is really necessary. Anyone who is member of the devs group can potentially break stuff...
To change the group memberships later on you can use the following command:

sudo usermod -a -G devs user

HPC cloud status

Sometimes it is handy to check the system status in the cloud.

The file-server that serves the virdirs (NFS): https://ganglia.surfsara.nl/?c=Calligo-Services&h=m-fileserver01.calligo.sara.nl&m=load_one&r=hour&s=by%20name&hc=4&mc=2

The file-server that serves the VM images: https://ganglia.surfsara.nl/?c=Calligo-Services&h=m-fileserver02.calligo.sara.nl&m=load_one&r=hour&s=by%20name&hc=4&mc=2

Obsolete instructions for Galaxy server on old HPC cloud

Contents

Below are obsolete information for older HPC cloud. They are kept as reference.

Cloud template

VM Shutdown and Start Instructions

Cloudman Startup Instructions

Galaxy Startup Instructions

Galaxy Update Instructions

Stop the service

Download new release of Galaxy

Backup the Galaxy DB

Update database

Copy NBIC tools and data

Restart the service

Useful tips

Creating new user accounts

HPC cloud status

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