Acces MySQL on titanic

Most of my databases are stored under user mpiblast. To access one, type mysql -d (e.g., test)

Manual proxy config for undergrad labs for Internet access

In Firefox: Under Tools->Options, General Tab, click Connection Settings and select Manual Proxy Configuration. Put in 138.26.65.1 for HTTP Proxy and 3128 for port number. Check "Use this proxy server for all protocols" and off to the Internet I go...

Trusting UAB CA on a UABGrid resource

There are four (4) things that need to be changed on every resource to get the UAB CA certificate where given resource can be used for job submission and as a job submission source (NOTE: all the steps except step 3 need to be done for every user on every resource):

1. Download userkey.pem and usercert.pem from http://uabgrid.uab.edu (click on Other Tools -> Manage Certificates)
2. Save these two files to given resource in ~/.globus directory and change userkey.pem permissions to read only.
3. As root, save the 56498486.signing_policy and UAB-root.crt
   to /etc/grid-security/certificates directory on given resource.
   Those files can be obtained with the following set of commands:
   cd /etc/grid-security/certificates
   wget http://webapp.lab.ac.uab.edu/UAB-root.crt
   wget https://www.pki.virginia.edu/nmi-bridge/certs/56498486.signing_policy
   ln -s UAB-root.crt 56498486.0
4. As root, add an entry to grid-mapfile - this entry can be obtained by executing grid-proxy-info by particular user (after the previous steps have been completed) and then copy the issuer line into grid-mapfile (e.g.: /C=US/ST=Alabama/L=Birmingham/O=University of Alabama at Birmingham/OU=UABgrid/CN=afgane/emailAddress=afgane@uab.edu)

Submit a simple WS-GT4 job

Must have valid proxy and execute the following command: globusrun-ws -s -submit -F olympus.cis.uab.edu -c /bin/date

Setting up GT4 MDS hierarchy

As user globus, edit file $GLOBUS_LOCATION/etc/globus_wsrf_mds_index/hierarchy.xml
to include the line with the server higher up in the hierarchy (i.e., below ...upstream... element). For example, to have olympus as head of the hierarchy, add the following line on everest:
https://olympus.cis.uab.edu:8443/wsrf/services/DefaultIndexService
This needs to be done on every machine you want to have register with the higher level resource.
There is also an option to register resources from higher levels and not have to edit files on all individual resources but rather only in one place. To use this option, add the following line (i.e., below ...downstream... element in above stated file) to the machine acting as the head of hierarchy (e.g., olympus): https://everest.cis.uab.edu:8443/wsrf/services/DefaultIndexService

Once the hierarchy file has been updated, globus needs to be restarted on that machine. To restart globus, as root, execute: /etc/init.d/globus-4.0.2 restart


To check if everything works, execute: wsrf-query -s https://olympus.cis.uab.edu:8443/wsrf/services/DefaultIndexService '/*' grep 138.26.64.200 wc -l7 as regular user from any machine (e.g., as user afgane - Note that grid-proxy must be valid to work!). Above command checks for everest's MDS report through olympus.

To check if WebMDS works too, as globus start tomcat on olympus: $CATALINA_HOME/bin/startup.sh and point the browser to: http://olympus.cis.uab.edu:8080/webmds/

Full information on how do to this can be obtained form here.

GridWay 5 installation procedure complement

Good instruction on installing GridWay 5 can be obtained from http://www.gridway.org/documentation/stable/installconfguide/

When executing 'globus-makefile-header -flavor gcc32dbg globus_gram_client \ globus_ftp_client globus_gass_copy > makefile-header' use the 'gcc64dbgpthr' flavor by executing the following command (on everest): 'globus-makefile-header -flavor gcc64dbgpthr globus_gram_client globus_ftp_client globus_gass_copy > makefile-header'

Once I got to the 'make' part, I got an error saying something about '...recompile with -fPIC flag...'. To correct this, I changed the Makefile where CFLAGS is defined to include -fPIC flag. The line should look like this: 'CFLAGS = -fPIC -Wall -g $(CFLAGS_SUNOS) $(DB4_FLAGS) $(DEBUG_FLAGS)'