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Computational Biology Application Suite for High Performance Computing
 
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Installing  BioHPC on server(s)
  • If not yet done, copy the distribution network_drive directory to the H: network drive.

  • Edit H:\CBSU\clusters. This directory contains text files, each file corresponds to a cluster and lists all its nodes.

  • Copy your BLAST databases to the appropriate H:\CBSU subdirectories (optional). You can download databases later, see documentation for more details.

  • Edit H:\CBSU\updates\tasks and H:\CBSU\updates\tasks.repeat. These files define scripts that are executed on each node before BioHPC calculations start. The first script runs only once on a node, the other each time when a job starts.

  • Install SQLExpress Advanced, choose mixed mode of authentication (Windows and server/local) for database access.

  • Copy  CBSUJOBS database from installation to the local data directory of your SQL server. Attach this database.

  • Create an account for database access (recommended name biohpcsql) with local SQL server authorization, set password (later needed in setup.aspx).

  • Allow biohpcsql to write data to database and execute stored procedures newdb, newjob, newrtjob.

  • Install Perl.

  • Install Visual Studio 2008 (optional). You will need Visual Studio if you want to recompile programs or interface.

  • Install Windows SDK and .NET 3.5 runtime

  • On the web server Install client for Microsoft Windows Compute Cluster Server 2003 and client for Microsoft Windows HPC Server 2008. You need to install at least the one that corresponds to the cluster scheduler you will be using, you may install both.

  • Set up IIS virtual directory (recommended name BioHPC) for BioHPC with ASP.NET and a special Application Pool running as IDU

  • Enable ASP .NET Web Extension in IIS

  • Sometimes there are problems deploying ASP.NET on the server when it is the first ASP.NET site on the server. You may need CleanIISScriptMaps.exe if there are problems with registering BioHPC with .NET 2. Check .NET registration status in "Properties" of the virtual directory.

  • Enable SQL Express TCP/IP channel (if using SQL Express)

  • Enable mixed authorization modes in SQL (local and Windows, parameter LoginMode 2). You will need to do it only if you forgot to select this option during installation. You can do it via SQL Server configuration utility, or directly in the registry. After the changes are done SQL services have to be restarted, especially SQL Agent.

  • Set up virtual directories JOBS (pointing to H:\CBSU\JOBS) and CBSUFTP (optional), setup them to display various file types other than html or aspx as text (MIME: .* text/plain)

  • Add IDU to iis_wpg group on web server (Windows Server 2003). Add IDU to iis_usrs group on web server (Windows Server 2008).

  • Make web.config file fully readable/writable by IDU

  • Make sure all directories in BioHPC web site are accessible to IDU

  • Create file H:\CBSU\BioHPC_url readable/writable to IDU with full INTERNAL (from CCS/HPC cluster) url to BioHPC web server.

  • Create echeck.log with full control for IDU in BioHPC web directory.

  • Make sure local drives T: from the nodes are exported as t-drive with full control access for IDU

  • Make messages subdirectory in BioHPC web directory with full control access for IDU

  • Open file web.config (in a text editor like notepad) from directory BioHPC and change

    • <add key="WebDir" value="H:\Inetpub\wwwroot\BioHPC\" />
      such that value points to the directory where web server files for BioHPC are installed

    • <add key="HDriveUnc" value="\\fileserver\share" />
      such that value points to a share on the fileserver which is supposed to host BioHPC network drives (H:\CBSU). If there is a local H: drive and BioHPC files are installed in H:\CBSU directory do nothing, server always checks this directory existence first.

    • Leave other tags unchanged, they will be modified later.

  •  On the web server, open http://localhost/BioHPC/setup.aspx (use appropriate path to BioHPC virtual directory) and set local parameters. This file won't open outside the server.

  • If using SQL Express locally, the server name is server\SQLEXPRESS

  • Login as admin@biohpc with initial password BioHPC4All . Change initial administrator id to a valid e-mail address and change the password.

  • Set up ftp server for BioHPC (optional). Create JOBS and PBLAST directories at ftproot, writable to IDU locally. Create virtual directories JOBS and PBLAST readable to IDU. Export JOBS and PBLAST as UNC from the server, full access for IDU. If the FtpJobsUnc parameter in setup.aspx is empty, the it is assumed that the ftp server is not installed.

  • Modify acknowledgemnt.htm

  • Recompile ptools if necessary (present in H:\CBSU\src). Update binaries at H:\CBSU\ptools\mpims and H:\CBSU\bin_x64 using files from ptools\debug.

  • Set up automated tasks in Task Scheduler.

    • JSDLupdate. This service is required for JSDL clusters. Add a task (as IDU) for web_dir\JSDLupdate\bin\Debug\JSDLupdate.exe, running every 3 minutes, with no timeout (i.e. 72 hrs timeout). This task may take long when downloading files from JSDL cluster, but new task won't start until the previous one finishes.

    • StarDaemon. This service will update job information in BioHPC database, send required e-mail to the users without need of administrator action. Add a task (as IDU) for web_dir\StarDaemon\bin\Debug\StarDaemon.exe, running every 30 minutes, with no timeout.

  • If you plan to use HPC Basic Profile in order to access remote clusters you will need to install a supplementary web service providing information about available resources that is missing in the HPC Basic Profile implementation. Otherwise BioHPC will not know how many nodes/cores are available at the moment and it will not be able to submit jobs based on resource availability. Download the web service files and unzip them into a directory inside your web server. Create an active directory for the service and run it in the special Application Pool running as IDU.

Last revised 5/14/2009


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