Mascot

General

Mascot (physical server) runs software called Mascot (database application) - this, and storing of research data related to this is the sole purpose of this server.

Mascot software is provided and licensed via SynthSys locally (smartin8/tlebihan). The software itself is provided on CD, currently kept by Sarah Martin.

In short, Mascot reads mass-spec data and tries to match it to known sequences from within its database.

/disk/data/mascot contains the software itself and its databases (~500GB circa 2012)

/disk/data/ms-data contains the instrument readings that is searched (~4TB circa 2012)

tlebihan is the "owner" of the machine

smartin8 is the "manager" of the machine

Only these users have SSH access to the machine. Access is provided by role 'mascot'. Access is not to be granted to others and the server is not to be used by others without permission from the above.

Startup procedure (Should be automatic on boot)

om apache start

nsu

cd /disk/data/mascot/bin/

./ms-monitor.exe

Apache

Note: Mascot software runs as perl scripts in apache, and creates files/folders under the apache account.

We need the workaround script in /disk/data/start_httpd because of this, it overrides umask and starts httpd with umask 0002 (equivalent to chmod 775). The mascot directories are group mascot and setgid enabled.

These two together mean files created by httpd are owner apache, group mascot, and permissions 755 thus allowing users to modify files/folders created via the web interface under /disk/data/mascot.

This file is executed as root on startup so make sure its permissions remain secure!

Starting Apache

om apache start

Startup script

#!/bin/bash
umask 0002
/usr/sbin/httpd $@

Mascot

Accounts

See accounts sheet

Locations

/disk/data/mascot

URLs

http://mascot.inf.ed.ac.uk/mascot/cgi/login.pl

Starting Mascot Manually

nsu

cd /disk/data/mascot/bin/

./ms-monitor.exe

Install requirements/notes:

Apache

Perl

Perl GD libraries

Perl XML libraries

(All provided via LCFG components now)

Note: Mascot expects Perl in /usr/bin/local/perl so you have to ln -s /usr/bin/perl /usr/bin/local/perl after OS (re)installation.

If symlink /disk/data/mascot/bin/auto/msparser/msparser.so exists, it needs to be removed

Backups

It's complicated. See RT#57680

/disk/data/ is mirrored, but excluding the larger, static directories namely:

/ms-data/2008 /ms-data/2009 /ms-data/2010 /ms-data/2011 (These are in a static tape backup, see below)

/yhuang (unimportant stuff)

/mascot/data (These are covered by the TiBS tape backup)

The following are backed up daily direct to tape (TiBS client installed by neilb):

/disk/data/ms-data/2012

/disk/data/ms-data/backups

/disk/data/mascot

We have one off full tape backups of:

/disk/data/ms-data/2008

/disk/data/ms-data/2009

/disk/data/ms-data/2010

/disk/data/ms-data/2011

Hardware

Dell PowerEdge R710

1x Intel Xeon X5550 2.66Ghz Quad-core CPU

16GB (4x4GB) RAM

PERC 6/I RAID controller PCIe w/256MB cache

16x SATA DVD-ROM

4-port GBE NIC

iDRAC6 Enterprise BMC (with dedicated port)

Originally 4x1TB SATA 7200RPM HDDs in RAID1+0 now upgraded to 6x2TB SATA 7200RPM RAID6

Topic revision: r2 - 06 Sep 2012 - 13:08:02 - YanHuang
 
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