For application users

From PRAGMAgridWIKI

This is a quick start guide to use Gfarm on the PRAGMA testbed. If you need detailed information about Gfarm, you had better check the original documents.

1 Initial setup
2 How to use GfarmFS-FUSE
3 Share your application data
4 Share your software
- 4.1 Compilation

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Initial setup

Set up the path environment variable.
Generate your proxy certificate.
Create your home directory in the Gfarm filesystem.
Prepare a mount point, e.g. /tmp/$USER in a local file system.

$ Inform your GLOBAL username in Gfarm file system and your Subject DN to Gfarm administrators.
$ export PATH=/opt/gfarm_v2/bin:$PATH
$ grid-proxy-init
$ mkdir /tmp/$USER

If you fail the above commands, please ask the site administrator. Your Gfarm environment may not be properly configured.

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How to use GfarmFS-FUSE

Do the initial setup if you use Gfarm first time.

Generate your proxy certificate

$ grid-proxy-init

Mount the Gfarm filesystem by 'gfarm2fs' command.

$ gfarm2fs /tmp/$USER
cd /tmp/$USER
ls -al

Unmount the Gfarm filesystem by 'fusermount' command after you finish your work.

$ fusermount -u /tmp/$USER

If you don't want to run the commands everytime, add these lines to your ~/.bash_profile file. Of course you can modify the lines as you want. Note that you still need to run grid-proxy-init when you access any files on the gfarm filesystem.

timeleft=`grid-proxy-info -timeleft 2> /dev/null`
if [ $? -ne 0 ] ; then
    grid-proxy-init
else
   if [ $timeleft -eq 0 ] ; then
       grid-proxy-init
   fi
fi
mount | awk '{ print $3 }' | grep /tmp/$USER >&/dev/null
if [ ! $? -eq 0 ]; then
    gfarm2fs /tmp/$USER
fi

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Share your application data

You can just save your data in the file under /tmp/$USER/home/$USER directory after you mount the Gfarm filesystem. The file can be accessed wherever you can mount the Gfarm filesystem on the PRAGMA testbed.

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Share your software

Make sure that the software package is actually sharable by having the proper license agreements.

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Compilation

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Inside Gfarm/FUSE

Currently this is still experimental, and performance needs to be improved.

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Compile using Local Filesystem

Community Software Area (CSA) is a shared space for the PRAGMA community. Applications, libraries, scripts and etc. can be shared by all PRAGMA users. Once a software is installed in this space by an user, all PRAGMA testbed users can access the software from any testbed cluster with Gfarm installed.

However, application users must understand the limitation and take responsibility for the portability of your binaries. Here is an example of binary portability issue in running application FMO.

The shared directory is "~/gfs/share/" when you mount the Gfarm file system under ~/gfs.

Shared software MUST be installed on "~/gfs/share/$CLUSTER_NAME." $CLUSTER_NAME indicates where you built the software and tested it works correctly. In addition, a person who installed the software MUST leave notes for the installation, in order to distinguish software installations for different architecture, os, globus flavors, compiler versions etc., please add detail into ~/gfs/$CLUSTER_NAME/NOTES file.

We have created some initial subdirectories at the $CLUSTER_NAME level. You can create an application directory under $CLUSTER_NAME.

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