1. CDL for BLAST Deployment
Jun Tatemura
CDDLM WG /
NEC Laboratories America
March 29, 2006
CDDLM WG

2. What to Deploy You have a code (BLAST) and data (database for BLAST)
A data center provides
A (computation) server
That lets you deploy your code and mount a file system
A file server
That lets you deploy your data
Deployment = make your code ready to run
Assuming that provisioning is done (= you have reserved a server and a file server to use)
File servers
Server cluster
BLAST
DATA
CDDLM WG

3. Components A Server A File Server <Server> <FileServer>
Upload your file to a directory (that is referred to as “RootDir”)
Mount a file system (ID) to a directory (Dir)
Specify an environment variable
A File Server
Upload your data (that is referred to as “ID”)
<Server>
<cmp:CommandPath …/>
<cmp:CodeBase/>
<Hostname cdl:lazy=“true”/>
<RootDir cdl:lazy=“true”/>
<FileSystem>
<ID/> <Dir/>
</FileSystem>
<Env/>
</Server>
<FileServer>
<cmp:CommandPath …/>
<cmp:CodeBase/>
<ID cdl:lazy=“true”/>
</FileServer>
These components (Servers and File Servers) are virtual entities. We don’t care how servers and file servers are physically located. They may or may not be dedicated machines.
CDDLM WG

4. A BLAST System
Your code/data is specified at cmp:CodeBase (using ACS?)
Server has a reference to the file server,
which is mounted at $ROOT/data
After deployment,
you can refer to BLASTSystem/Server/Hostname to locate a server
You can run $ROOT/bin/blastall with –d $DATA/ncbiblast/nr
how to coordinate with JSDL?
<BLASTSystem>
<Server cdl:extends=“d:Server”/>
<cmp:CodeBase>blast.tar</cmp:CodeBase>
<d:FileSystem>
<d:ID cdl:ref=“/File/d:ID”/>
<d:Dir>data</d:Dir>
</d:FileSystem>
<d:Env name=“ROOT” cdl:ref=“/Server/RootDir”/>
<d:Env name=“DATA”>$ROOT/data</d:Env>
</Server>
<File cdl:extends=“d:FileSystem”>
<cmp:CodeBase>blastdb.tar</cmp:CodeBase>
</File>
</BLASTSystem>
CDDLM WG

5. A Template For BLAST
If you want to deploy BLAST many times with different data, you may want to create a template to reuse
<BLASTTmpl>
<DataFile/>
<Server cdl:extends=“d:Server”/>
<cmp:CodeBase>blast.tar</cmp:CodeBase>
<d:FileSystem …/>
<d:Env …/>
</Server>
<File cdl:extends=“d:FileSystem”>
<cmp:CodeBase cdl:ref=“/DataFile”/>
</File>
</BLASTTmpl>
<MyBLAST cdl:extends=“tmpl:BLASTTmpl”>
<tmpl:DataFile>blastdb.tar</tmpl:DataFile>
</MyBLAST>
CDDLM WG