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LapDevelopment_ServerDeployment
This is the version from 10.03.2016
The instructions on this page are intended to provide a step by step installation of a lap+galaxy instance with:
- Abel Cluster Support
- FEIDE Authetification
- POSTGRES Data Storage
- Gold Accounting
In this section I will briefly describe the preparation of the server in term of additional services that are not related to Galaxy and LAP. This services must be present in order to do various actions like HTTP Proxy and connection to Abel.
PostgresSQL is the database used to store users data. The database is provided by UIO DB Hotell
To install Postgres on Fedora/Redhat use the following command:
yum install postgresql postgresql-server postgresql-devel postgresql-contrib
For test purposes you can initialize postgres server on local machine that can be used by galaxy. This server will be replaced in the production and development version of LAP. The local installation of posgres should have an enabled ssl.
The Apache server serves as a proxy and aggregate for both galaxy and gold interfaces. It is used also from the module for Feide authentication.
1. Install apache server and appropriate mods.
yum install httpd mod_ssl mod_auth_kerb mod_nss mod_proxy_html
Node.js is the library used by Galaxy to compile Javascript files. The library verifies the dependencies downloads javascripts and creates a compact version of the scripts in the /static folder of Galaxy.
sudo yum install npm
sudo npm install -g grunt grunt-cli
The slurm library is used to send jobs to the cluster. Prerequisites: your server should have a network card with the appropriate submit network.
1. Download and install the latest libraries provided by USIT admins. Go to the nh machine. Get the following rpms:
#In the directory /export/rocks/install/contrib/
munge-<version>.x86_64.rpm
munge-libs-<version>.x86_64.rpm
munge-devel-<version>.x86_64.rpm
slurm-<version>.x86_64.rpm
slurm-munge-<version>.x86_64.rpm
slurm-plugins-<version>.x86_64.rpm
slurm-perlapi-<version>.x86_64.rpm
N.B. I think that maybe you should have an USIT account to do this. I will verify this. If needed this libraries can be put in our SVN.
2. Download configuration files from /etc/munge and /etc/slurm. And start munge
service munge start
3. Ensure that the lap user and the slurm user have the same UID and GUD as on Abel. The easy way is to copy the corresponding lines from /etc/shadow
4. Download and install drma-slurm. This version is modified to include additional parameter working directory.
yum install gperf
git clone https://<username>@bitbucket.usit.uio.no/scm/ft/drmaa.git
cd drmaa
yum install ragel-6.6-2.3.x86_64.rpm
cd slurm-drmaa-1.0.6
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/slurm/lib64
./configure --with-slurm-inc=/opt/slurm/include/ --with-slurm-lib=/opt/slurm/lib64/ --prefix=/site/drmaa/ --enable-debug
make
make install
5. Modify the network resolve files
In resolve.conf add:
nameserver 10.110.1.1
In hosts add:
10.110.1.1 nielshenrik.local nielshenrik
6. Test the connection with the following script:
open (OUT, ">$ARGV[0]");
system("sleep 60");
my $time = localtime();
print OUT "The time is $time\n";
close( OUT );
# End of script
In order the test to work create the following file /etc/slurm_drmaa.conf
job_categories: {
default: "--account=staff --time=00:01:00 --mem-per-cpu=1000 --comment=hello",
},
Run the test:
export SLURM_DRMAA_CONF=/etc/slurm_drmaa.conf
/site/drmaa/bin/drmaa-run test.pl output
Download the local copy of modified Gold software from: https://bitbucket.usit.uio.no/scm/ft/gold-usit-repository.git.
1. Compile Gold.
yum install libpqxx-devel.x86_64 libpqxx.x86_64
yum install perl-DBD-Pg.x86_64
cd gold-usit-repository
chmod +x usit/bin/*
usit/bin/create-empty-dirs.sh
./configure --prefix=/opt/gold --with-db=Pg --with-log-dir=/opt/gold/log --with-perl-libs=local --with-gold-libs=local --with-cgi-bin=/var/www/cgi-bin/gold
make
2. Install Gold. Supper User account is required.
sudo su
make deps
make gui
make install
make install gui
3. Edit the configuration files. Go to the directory /opt/gold/etc/. In the file goldd.conf:
super.user = root
database.datasource = DBI:Pg:dbname=<DATABASE_NAME>;host=<DATABASE_HOST>
database.user = <USERNAME>
database.password = <PASSWORD>
In file gold.conf. Un comment the following fragment.
# account.show = Id,Name,Amount,Projects,Users,Machines,Description
# allocation.show = Id,Account,Active,StartTime,EndTime,Amount,CreditLimit,Deposited
# balance.show = Id,Name,Amount,Reserved,Balance,CreditLimit,Available
# job.show = Id,JobId,User,Project,Machine,Queue,QualityOfService,Stage,Charge,Processors,Nodes,WallDuration,StartTime,EndTime,Description
# machine.show = Name,Active,Architecture,OperatingSystem,Description
# project.show = Name,Active,Users,Machines,Description
# quotations.show = Id,Amount,Job,Project,User,Machine,StartTime,EndTime,WallDuration,Uses,ChargeRates,Description
# reservation.show = Id,Name,Amount,StartTime,EndTime,Job,User,Project,Machine,Accounts,Description
# transaction.show = Id,Object,Action,Actor,Name,Child,JobId,Amount,Delta,Account,Project,User,Machine,Allocation,Count,Description
# user.show = Name,Active,CommonName,PhoneNumber,EmailAddress,DefaultProject,Description
4. Initialize the database
psql -d <DATABASE> -h <DBHOSTNAME> -U <DBUSERNAME> < /installation-path/bank.sql
5. Create virtual host for gold in httpd. Make Gold authentication keys.
make auth_key
# Generate private key
openssl genrsa -out ca.key 1024
# Generate CSR
openssl req -new -key ca.key -out ca.csr
# Generate Self Signed Key
openssl x509 -req -days 365 -in ca.csr -signkey ca.key -out ca.crt
# Move the files to the correct locations
mkdir /etc/httpd/conf.d/gold_keys/
mv ca.crt /etc/httpd/conf.d/gold_keys/gold.crt
mv ca.key /etc/httpd/conf.d/gold_keys/gold.key
Open ssl.conf and add the following fragment:
<VirtualHost *:443>
DocumentRoot /var/www/cgi-bin/gold/
DirectoryIndex index.cgi
ServerName gold.<HOSTNAME>
ServerAdmin <YOUR EMAIL>
ErrorLog logs/gold-error_log
TransferLog logs/gold-access_log
SSLEngine on
SSLCertificateFile /etc/httpd/conf.d/gold_keys/gold-server.crt
SSLCertificateKeyFile /etc/httpd/conf.d/gold_keys/gold-server.key
SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown
</VirtualHost>
Open httpd.conf and add the following fragment:
Alias /cgi-bin/gold "/var/www/cgi-bin/gold"
<Directory "/var/www/cgi-bin">
AllowOverride None
Options +ExecCGI
AddHandler cgi-script .cgi .pl
Order allow,deny
Allow from all
</Directory>
6. Allow the default user for Galaxy to run GOLD scripts. Create the file /etc/sudoers.d/lap
#
# the LAP system user can issue GOLD commands without password and tty
#
Defaults:<USER> !requiretty
Cmnd_Alias GOLD = /opt/gold/bin/*
laportal <HOSTNAME>=(root) NOPASSWD: GOLD
7. Initialize Gold for usage.
Create a default machine
./gmkmachine -d "Linux Cluster at UiO" Abel-Galaxy
Create the Organization (project owner) for the default Galaxy project - root@laporal
./goldsh Organization Create Name='root@laportal'
Create the default project - gx_default
./gmkproject -d "Galaxy Default Project" gx_default --createAccount=False -o root@laportal
Crate a test user
./gmkuser -u kouylekov@gmail.com -d "test user" -p gx_default
N.B. The user must have the same email as the user in galaxy.
Add the created user to the default project gx_default
./gchproject --addUsers kouylekov@gmail.com -p gx_default
Create an account for the user
./gmkaccount -p gx_default -u kouylekov@gmail.com
Deposit 200 hours in the account. The a parameter is determined by the output of the previous command.
./gdeposit -a 1 -h 200
As a prerequisite to LAP installation, there must be a MongoDB database available for access by the LAP user. Some notes on how MongoDB is configured on the LAP servers is available on the LapDevelopment/MongoDB, but for local installations
-
Install MongoDB via your package manager, e.g.
yum install mongodb-server -
Confirm that the database directory (/var/lib/mongodb/ by default) is available;
-
Optionally, review MongoDB settings (e.g. in /etc/mongodb.conf and /etc/sysconfig/mongod);
-
Start the server and optionally enable automated start-up, e.g.
/etc/init.d/mongodb start
By default, MongoDB initially allocates database space relatively generously (at around three gigabytes, it appears). If disk space is at a premium (as can be the case on a laptop :-), consider adding the --smallfiles option to the start-up sequence of the MongoDB server.
On the (non-Galaxy) LAP side, the following components are required: the LAP Tree, Library, tool descriptions, and (optionally) operational scripts.
cd /home/laportal
svn co http://user@svn.emmtee.net/lap/trunk/tree
cd
svn co http://user@svn.emmtee.net/lap/trunk/tools
svn co http://user@svn.emmtee.net/lap/trunk/operation
Create a file with the name env.sh in /home/laportal that contains all the environment variables needed to run LAP
export LAPTREE=/home/laportal/tree
export LAPLIBRARY=/home/laportal/library
export LAPSTORE=mongodb://127.0.0.1:27017/lapstore
In early 2016, there are several versions of Galaxy in use with LAP. However, development focus now shifts towards the 2015.03 release, and there is a pre-configured snapshot available in SVN with local extensions (e.g. custom datatypes) and the basic configuration to use the LAP Tool descriptions (assuming the above locations):
cd /home/laportal
svn co http://svn.emmtee.net/lap/trunk/local/galaxy
When using this version, no symbolic links should be required (assuming the LAP components reside in the recommended location), i.e. config/galaxy.ini already points to the LAP tool configuration:
tool_config_file = /home/laportal/tools/config.xml
tool_path = /home/laportal/tools
To start Galaxy:
cd /home/laportal/galaxy
./run.sh > main.log
At this point, with a bit of luck, the built-in Galaxy web server will be listening at http://localhost:8080.
Except for (currently, a small number of) LAP-specific extensions, this Galaxy version corresponds to the following release:
git clone https://github.com/galaxyproject/galaxy/
cd galaxy
git checkout release_15.03
The following commands are used to enable SSL connection in Galaxy. This connection is required by the Hotell database servers. To do this you must recompile the module psycopg2. The recompilation is done with the following procedure.
1. Install the postgresql client and server (we need the server only to compile the postgresql ssl module!! Don't start the server)
yum install postgresql-server.x86_64 postgresql-devel.x86_64 postgresql.x86_64
2. Install also the following libraries to in order to compile the module
yum install gcc redhat-rpm-config python-devel.x86_64 python27-python-setuptools.noarch
3. Download the psycog python pack needed for the SSL connection with the DB. It might already exist but it is not compiled for SSL. The package is available at: http://initd.org/psycopg. (Verified version is 2.6.1. the current release)
4. Modify the setup.py as follows: just before the line
from distutils.core import setup, Extension
add the following lines
import pkg_resources
from scramble_lib import *
5. Compile the package.
#Indicates the path of the scaramble lib
export PYTHONPATH=/home/laportal/galaxy/scripts/scramble/lib
python setup.py bdist_egg
6. The compilation creates an pscyog2-<VERSION-ARCH>.egg in the dist folder. The egg must be placed in Galaxy default egg directory galaxy/eggs/.
7. Update the file egs.ini with the correct versions of psycopg2
The Apache server serves as a proxy and aggregate for both galaxy and gold interfaces. It is used also from the module for Feide authentication.
1. Edit the file /etc/httpd/conf/httpd.conf. Redirect the root to SSL 443 port.
<VirtualHost _default_:80>
RewriteEngine on
ReWriteCond %{SERVER_PORT} !^443$
RewriteRule ^/(.*) https://%{HTTP_HOST}/$1 [NC,R,L]
</VirtualHost>
Allow static pages to be loaded by apache.
<Directory /home/laportal/galaxy/static/>
Options Indexes FollowSymLinks
AllowOverride None
Require all granted
</Directory>
Update the CGI section.
Alias /cgi-bin/gold "/var/www/cgi-bin/gold"
ScriptAlias /cgi-bin/ "/var/www/cgi-bin/"
<Directory "/var/www/cgi-bin">
AllowOverride None
Options +ExecCGI
AddHandler cgi-script .cgi .pl
Order allow,deny
Allow from all
</Directory>
2. Add the following rewrite rules to the virtual host in /etc/httpd/conf.d/ssl.conf
<VirtualHost _default_:443>
...
RewriteEngine on
RewriteRule ^/static/style/(.*) /home/laportal/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*) /home/laportal/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /home/laportal/galaxy/static/$1 [L]
RewriteRule ^/favicon.ico /home/laportal/galaxy/static/favicon.ico [L]
RewriteRule ^/robots.txt /home/laportal/galaxy/static/robots.txt [L]
RewriteRule ^(.*) http://127.0.0.1:8080$1 [P]
...
4. Optionally you can generate SSL keys for the certificate check if mod_ssl and open_ssl are installed, if not install them.
yum install mod_ssl
yum install openssl.x86_64
Create keys and certificates
# Generate private key
openssl genrsa -out ca.key 1024
# Generate CSR
openssl req -new -key ca.key -out ca.csr
# Generate Self Signed Key
openssl x509 -req -days 365 -in ca.csr -signkey ca.key -out ca.crt
# Move the files to the correct locations
cp ca.crt /etc/pki/tls/certs/galaxy.server.crt
cp ca.key /etc/pki/tls/private/galaxy.server.key
cp ca.csr /etc/pki/tls/private/galaxy.server.csr
To use them appropriately modify the ssl.conf file.
For the time being, at least, we assume that all annotations (by all LAP users) share one database and one database user; to initially create the database and user:
mongo --verbose -u laportal -p '????????' admin
use lapstore
db.addUser({ user: "lapstore", pwd: "????????", roles: [ "readWrite" ] })
To connect to the LAP Store using the MongoDB Shell:
mongo --verbose -u lapstore -p '????????' lapstore
To inspect the contents of a specific collection (use show collections or db.getCollectionNames() for the selection):
db[db.getCollectionNames()[0]].find().pretty()
To drop all collections, i.e. free up storage space; this will render all Galaxy files in all user histories (i.e. receipts, referring to collections) useless, thus must only be used on development instances:
db.getCollectionNames().forEach(function(foo) { if (foo.indexOf("system.") == -1) db[foo].drop(); })
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