biolocal:GridUse
From Wiki CEINGE
Setup the access to the grid
The bioinfoaccess server can be used to access the SCOPE grid, by using the personal certificate, properly installed and initialized. If you have your personal certificate already installed in your browser, export it as file and save it in your home directory, under the .globus directory.
In the image, a certificate file will be generated and should be uploaded on the bioinfoaccess server:
scp myCertificate.p12 gianluca@bioinfoaccess.ceinge.unina.it:
On the bioinfo access server, some commands should still be used to have the personal certificate installed correctly:
mkdir .globus cd .globus openssl pkcs12 -nocerts -in ../myCertificate.p12 -out userkey.pem openssl pkcs12 -clcerts -nokeys -in ../myCertificate.p12 -out usercert.pem chmod 400 userkey.pem chmod 600 usercert.pem
The two openssl command are needed to extract the private and public key from the pk12 certificate file. Don't forget to change the access mode of the files!
The account is now configured to provide the correct credentials when the access to the grid is requested.
Access and use the grid
Before start submitting jobs to the grid, a new proxy certificate should be created in the scope VO:
voms-proxy-init -voms scope
To get information about the proxy certificate, use the voms-proxy-info command. Particularly useful to know the remaining time of validity.
To execute a job a jdl file should be compiled as follows:
Executable = "/bin/echo";
Arguments = "Hello World";
StdOutput = "message.txt";
StdError = "stderror";
OutputSandbox = {"message.txt","stderror"};
To submit and view the state of the job use the command:
edg-job-submit test1.jdl edg-job-status https://scoperb01.dsf.unina.it:9000/DXWtFSVPAjfLeAIBlRcfdw
In the above example, after the submission a url is returned to refer to the submitted job. It is used to get the status.
When the state becomes "done", the result can be retreived with the command:
edg-job-get-output https://scoperb01.dsf.unina.it:9000/DXWtFSVPAjfLeAIBlRcfdw
