ChemWiki - User contributions [en]

IT:servers

2006-07-13T10:12:44Z

Adamd: /* [http://www.openafs.org openAFS] */

== Configuring Servers ==

The following is specified for the SGI-based argon server. The location of various library and include paths will vary from machine to machine. The current base for the SGI is argon.ch.ic.ac.uk and /var/www/ This contains Apache, php, MySQL, htDig and various other utilities. Contact Henry Rzepa (rzepa@ic.ac.uk) for further information about these systems.

The new system is to be migrated to neon.ch.ic.ac.uk. Current paths are /var/www/ for installations etc and /mpt/web/ for
htdocs. No decision on log files yet made.

==Apache==

Currently 2.055, but might be upgradable to 2.2
<pre> ./configure --prefix=/var/www/apache2055 \
--enable-dav --enable-ssl --enable-rewrite --enable-ldap \
--enable-auth-ldap --with-ldap --with-speling --libdir=/usr/lib \
--with-ldap-include=/usr/include \
--with-ldap-lib=/usr/lib/ \
--with-ssl-include=/usr/include/openssl/ \
--with-ssl-lib=/usr/lib/ \
--with-ssl \
CPPFLAGS=-I/usr/kerberos/include</pre>

#Configuration files for apache: [http://www.ch.ic.ac.uk/rzepa/config/httpd.conf httpd.conf], [http://www.ch.ic.ac.uk/rzepa/config/mime.types mime.types], [http://www.ch.ic.ac.uk/rzepa/config/ssl.conf ssl.conf],
# A SSL server certificate needs to be installed for the system.
# Authentication uses SSL and LDAP, as specified in the configuration files.
# Server started using <pre>./apachectl startssl</pre>
#Path to htdocs on new server <pre>/mpt/web/htdocs/</pre>

==MySQL==

Currently 4.0.13. Not tested at 4.1.18. The existing databases will have to be backed up using e.g.
<pre>mysqldump –u root –psecret --all-databases > all.sql</pre> and reloaded into the new MySQL.

Mysql server installed by Sam Sharpe at <pre>/usr/bin/nysql</pre>

Please contact HSR for MySQL root password.

GRANT ALL PRIVILEGES ON PSS.* TO pss@www2.imperial.ac.uk IDENTIFIED BY '*******'

Adding access privs for remote service.

==PHP ==

Currently 4.4.2, but will need to move to 5 at some stage.

<pre>./configure --with-mysql=/usr/bin/mysql --with-apxs2=/var/www/apache2055/bin/apxs\
--with-ldap --with-config-file-path=/mpt/web/htdocs/php/</pre>

#Configuration files for php: [http://www.ch.ic.ac.uk/php/php.ini php.ini]
#Admin utility for php: [http://www.ch.ic.ac.uk/php/phpMyAdmin-2.5.3/ phpMyAdmin]
# The current system configuration is summarised [http://www.ch.ic.ac.uk/php/ here]

==Wiki==

[http://meta.wikimedia.org/wiki/MediaWiki Mediawiki] is the current flavour.

#The local settings file is [http://www.ch.ic.ac.uk/wiki/LocalSettings.php here]
#A [http://wiki.jmol.org/index.php/MediaWiki Jmol extension] is loaded to enable molecule display within the wiki
#A local authentication module [http://www.ch.ic.ac.uk/wiki/LdapAuthentication.php has been added]

==[http://www.muquit.com/muquit/software/Count/Count.html Web page counter]==

Can be replaced by any suitable alternative.

<pre><nowiki><img src="http://origin.ch.ic.ac.uk/cgi-bin/Count.cgi?df=pericyclic.dat&dd=B" alt="counter" /></nowiki></pre>

== [http://www.htdig.org/install.html htDig 3.1.6] Index and Search Engine.==

It employs external parsers for chemical files. UltraSeek might be useable, but would need to be configured for these external file types. The output templates are also special, invoking the Jmol applet to display certain types of file found by the search. For an example of the latter, see [http://www.ch.ic.ac.uk/local/symmetry/ the symmetry site]. Invoke the default search, and select load molecule.

#Configuration file for building htdig [http://www.ch.ic.ac.uk/rzepa/config/CONFIG CONFIG]
#Configuration files for indexing entire server: [http://www.ch.ic.ac.uk/rzepa/config/origin.conf origin.conf] [http://www.ch.ic.ac.uk/rzepa/config/motm.conf motm.conf] [http://www.ch.ic.ac.uk/rzepa/config/sym.conf sym.conf] [http://www.ch.ic.ac.uk/rzepa/config/it.conf it.conf] [http://www.ch.ic.ac.uk/rzepa/config/pericyclic.conf pericyclic.conf]
#External parsers for htdig: [http://www.ch.ic.ac.uk/rzepa/config/runchemdig.sh runchemdig.sh] doc2html
#Output templates for htdig: [http://www.ch.ic.ac.uk/rzepa/config/header.html header.html] [http://www.ch.ic.ac.uk/rzepa/config/long.html long.html] [http://www.ch.ic.ac.uk/rzepa/config/nomatch.html nomatch.html] [http://www.ch.ic.ac.uk/rzepa/config/footer.html footer.html]

==[http://www.analog.cx/ Analog log file analyzer]==

Currently set up as a crontab job, to run weekly. Used in conjuction with ReportMagic to generate
reports.

==[http://tomcat.apache.org/ Tomcat]==

Currently not installed, but should be.

==[http://www.openrdf.org/ Sesame]==

Currently not installed, but should be.

--[[User:Rzepa|Rzepa]] 08:42, 19 April 2006 (bst)

== [http://www.openafs.org openAFS] ==

Install the openafs package

sudo edit /private/var/db/openAFS/etc/CellServDB and add the ic.ac.uk domain

>ic.ac.uk #Imperial College London
155.198.63.149 #icafs1.cc.ic.ac.uk
155.198.63.148 #icafs2.cc.ic.ac.uk

sudo edit /private/var/db/openAFS/etc/ThisCell and replace entry with
ic.ac.uk

sudo edit /etc/krb5.conf

[logging]
default = FILE:/var/log/krb5libs.log
kdc = FILE:/var/log/krb5kdc.log
admin_server = FILE:/var/log/kadmind.log

[libdefaults]
ticket_lifetime = 24000
default_realm = IC.AC.UK
dns_lookup_realm = false
dns_lookup_kdc = false
#supported_enctypes = des3-cbc-sha1:normal des-cbc-md5:normal des-cbc-crc:afs3

# default_tkt_enctypes = des-cbc-md5
# default_tgs_enctypes =des-cbc-md5
# default_etypes = des-cbc-md5
# default_etypes_des = des-cbc-md5

[realms]
IC.AC.UK = {
kdc = icads11.ic.ac.uk:88
# kdc = icafs2.cc.ic.ac.uk:88
}

[domain_realm]
.ic.ac.uk = IC.AC.UK
ic.ac.uk = IC.AC.UK

[kdc]
profile = /var/kerberos/krb5kdc/kdc.conf

[appdefaults]
pam = {
debug = false
ticket_lifetime = 3600000
renew_lifetime = 3600000
forwardable = true
krb4_convert = false
}

to login do
kinit username followed by aklog

to logout do kdestroy to destroy your kerberos ticket and unlog to drop your afs token

Brief list of useful commands.
-----------------------------------------------------
login
------
kinit <USERNAME> ## get kerberos tickets
kdestroy ## drop kerberos tickets
aklog ## get AFS token
unlog ## drop afs token

------------------------------------------------------

Setting up a group
---------------------
pts creategroup <groupname> ## create a group (will be a negative number)
pts chown <groupname> <username> ## change the owner of the group (you will be the owner by default)
pts listowned <username> ## list groups you own
pts adduser -user <name> -group <groupname> ## add another user to a group

-------------------------------------------------------

ACLS
-----

fs listacl /afs/ic.ac.uk/software ## list acls on a directory
fs setacl /afs/ic.ac.uk/software <user> none. ## remove user access to a folder
fs setacl /afs/ic.ac.uk/software <user> rl ## grant read and list permissions
fs setacl /afs/ic.ac.uk/software <user> all ## grant all permissions to a user.

IT:servers

2006-07-13T10:09:50Z

Adamd: /* [http://www.openafs.org openAFS] */

IT:servers

2006-07-13T10:03:12Z

Adamd: /* [http://www.openrdf.org/ Sesame] */