Grid computing is different from computing on a server or cluster. The main difference is that the focus of grid computing is to provide a way to access available resources from a wide pool of resources. As a result, one usually does not obtain a standard account that has an e-mail box and home directory associated with it. One gets access to the resource and can store files, but these files in general are visible to othr grid users, and one should not count on the file baing private or permanent.

The way to use grids is to prepare input files, start intense computation, wait for completion of the computation, and retrieve the result files.

More sophisticated uses of the UF grid will be supported later on, but in this initial project, we only support simple runs as above with one application, gaussian 03.

Obtaining UF Grid Certificates

To use the UF Grid, you must obtain a certificate. This certificate will be granted to you based on the existence of a valid GatorLink account. Follow the following steps to create a certificate.

Go to HPC web site Go to the HPC portal https://hpc1.hpc.ufl.edu/portal. In the upper left corner, you will see a button create new account. Click on it. A series of fields will appear.
The three top rows relate to obtaining certificate. They must all be filled out and you should not press return before you are done! The fields are

Gatorlink Username

Gatorlink Password

Email address

Fill in the fields and press the Create New Grid credentials button.
from here you can continue on and immediately create a Gridport account

Store certificates You will receive an e-mail with two attachments, called yourid_cert.pem and yourid_key.pem. Save these files for future use as usercert.pem and userkey.pem. On UNIX systems, save them in .globus. On Windows systems, save them somewhere safe.
You will not need to manipulate the certificates yourself when you are using the gridport interface explained below. But more sophisticated access to the grid is possible and will be explained in the future.

Creating a UF Gridport account

One way to interact with the grid and make it do useful work is to use the Gridport interface. Another, more powerful interface is In-VIGO; it will be available soon. A third interface, for geeks and grid experts, is to use the grid command directly.

Go to HPC web site Go to the HPC portal https://hpc1.hpc.ufl.edu/portal. In the upper left corner, you will see a button create new account. Click on it. A series of fields will appear.
The six bottom rows relate to creating a Gridport account. They must all be filled out and you should not press return before you are done! The fields are

Username that you want to account to have, can be the same as the GatorlLink id or different.

Password for the new account

Password (confirm)

First Name

Last Name

Email:

Fill in the fields and press the Create New Account button

Guassian license Only if you have signed a Gaussian license agreement (contact Erik Deumens, NPB 2334, deumens@qtp.ufl.edu), will the Gridport account provide access to the Gaussian 03 software. If there is no license agreement on file, the database will provide the Gridport account only standard privileges, such as to run Amber.

File Management Once you are logged in to the Gridport interface a list of options becomes available underneath the UF logo. The first useful option is file management. Click on the text and bottom of the screen shows three new options

Transfer and List Files

Upload Files

Download Files

and a button labeled list files. Click on this button and a list of all files in the /home/gaussian directory will appear. If you did not sign the Gaussian license, the files in /home/griduser will be listed.
You can click on any file name to show its content, if it is text, or to download it using HTTP, if it is not.
You can shift-click to force download of a text file.
The top of the file listing shows a Source host and a Source Directory. You can change the source directory and click on the List files -Est Xfer and then the new directry will be listed.

Upload Files The option upload files under File Management brings a panel with four fields

Resource is the host holding the home directory hpcio1

Input File is the file to upload with a browse button, which starts a file manage window on the host that is running the browser you are using, such as your laptop

Directory is the directory where you want to put the file; the default is "tilde", which is the UNIX home directory

Filename is the name you want to give the file on the grid system.

Command Execution The top level option Command Execution allows you to execute simple commands like ls, mkdir, etc. There are four fields, and two have good defaults.

Host the command will be executed on this host, the default hpc1.hpc.ufl.edu is fine

Port the number 15080 is fine

Command this must be typed with the correct Linux path name, e.g. /bin/ls

Arguments to the command; you cannot use wildcards or spaces; /bin/mkdir with argument test01 works fine; but /bin/cp wih arguments a b does not.

Batch Job Submission The option Batch Job Submission allows you to submit a job file to the PBS job manager.

Host, Port, Executable are fine as they are

Arguments must be at least the job file name and can contains other legal PBS qsub options.

Standard Output and Standard Error are the output of the qsub, not of the job. The job output is best given inside the job file as in the example below

Directory and CPU Count are also best given in the job file.

PBS example job
#!/bin/sh #PBS -N g03-h20 #PBS -o h2o.out #PBS -e h2o.err #PBS -m abe #PBS -M deumens@qtp.ufl.edu #PBS -q workq #PBS -l nodes=1 echo Running g03...
This job send e-mail at job beginning and end and in case of job abort. It asks for 1 node and the workq queue.

Available software on the UF Grid

Gaussian03 The Gaussian 03 program system for ab-initio electronic structure calculations created by John Pople and his collaborators.
The directory /home/gaussian contains an example input file h2o.inp and PBS job file h2o.job
Every user of Gaussian should first make a subdirectory for permanent and scratch files, using the Command Execution
Command /bin/mkdir Arguments your_name /scratch/gaussian/your_name
Then download the h2o.job file and edit it to reflect your computation. Call is your_label.job. Also prepae the Gaussian input file and call it your_label.inp.
Then upload the new job file to the sub directory just created with File Management - Upload Files.
Also upload the Gaussian input file.
Next submit the job with Batch Job Submission specifying the Argument your_name/your_label.job
Your will receive e-mails when the jobs starts and finishes. Then you can log in to Grid Port again and check the output file your_label.log in the subdirectory your_name
Your can submit several Gaussian jobs and have all of them running at the same time, as long as you maek sure each job has a unique label.
Example PBS job file for a 1-node 2-CPU parallel run of g03
#!/bin/sh #PBS -N g03-h20 #PBS -o deumens/h2o.out #PBS -e deumens/h2o.err #PBS -m abe #PBS -M deumens@qtp.ufl.edu #PBS -q workq #PBS -l nodes=1 echo Running g03... g03root=/apps/gaussian export g03root . $g03root/g03/bsd/g03.profile USER=deumens LABEL=h2o PERM=$HOME/$USER GAUSS_SCRDIR=/scratch/gaussian/$USER/$LABEL export GAUSS_SCRDIR mkdir -p $GAUSS_SCRDIR cp $PERM/$LABEL.inp $GAUSS_SCRDIR/$LABEL.inp cd $GAUSS_SCRDIR g03 $LABEL.inp > $LABEL.log cp $LABEL.log $PERM cd $PERM rm -fr $GAUSS_SCRDIR echo done

Amber 8.0 Making this software available on the grid will be the next project of the UF HPC team.

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Last Updated 12/15/07