Getting Started on Blue Gene
System Access
UNIX Login
To log onto Blue Gene from a UNIX machine, use Secure Shell (SSH) with the hostname bglogin.sdsc.edu.
ssh username@bglogin.sdsc.edu
or
ssh –l username bglogin.sdsc.edu
For more information on using SSH, see the ssh man pages.
PC or Mac Login
To log onto Blue Gene from a PC or Mac, download an SSH client from the OpenSSH page for Windows or Mac. PuTTY is another simple, free SSH client. Click here to download the latest version. WinSCP is a scp(1) program for Windows, with PuTTY integrated into it.
Moving Files to Blue Gene
For transferring files to Blue Gene from a UNIX system, secure copy (scp) is recommended. The following is an example scp command from a local machine to Blue Gene:
scp original_file username@bglogin.sdsc.edu:/to_dir/copied_file
To use secure copy from a Windows platform, download a copy of WinSCP (freeware).
File Systems & Disk Storage
WARNING: It is your responsibility to back up critical data! Please maintain your own copy of important data stored on SDSC file systems.
Currently there are three user-accessible file systems on BlueGene. These file systems are NFS-mounted and accessible by all runs.
| File System | Characteristics |
| /users | All of the user home directories are located on this file system, which is backed up regularly. However, given its limited size (currently only 1.1 TB), you should minimize your usage of this file system. |
| /bggpfs | The /bggpfs file system is about 20 TB in size. It should be your preferred location for large files and is not backed up. It is part of all the predefined partitions and can be used for all user jobs. |
| /gpfs-wan | The /gpfs-wan file system is 225 TB and accessible from DataStar, BlueGene, and TeraGrid. It is part of all the predefined partitions and can be used for all I/O-intensive jobs. |
File Storage: Archival
WARNING: It is your responsibility to back up critical data! Please maintain your own copy of important data stored in SDSC archival systems. Because of the enormous amount of data involved, SDSC does not back up files in archival storage. Although the SDSC storage systems are very reliable, data can be lost or damaged due to media failures, system software bugs, hardware failures, and user mistakes.
Archival storage for SDSC production systems is provided through SDSC's High Performance Storage System (HPSS).
The recommended interface to HPSS is HSI. HSI supports wildcards for local and HPSS pathname pattern matching and provides recursion for many commands, including the ability to store, retrieve, and list entire directory tress, or change permissions on entire trees. It may be used interactively or in batch mode and may be included in UNIX pipes. HSI is also especially useful for SDSC users with accounts on multiple platforms, as it provides an interface to the SDSC HPSS system from most SDSC machines.
The default authentication method for hsi is specified in a .hsirc file in each user's home directory. HSI uses Distributed Computing Environment (DCE) keytabs as the default authentication method. You can verify that the DCE keytab installed and available for your login by issuing the hsi command to access HPSS. If you do not have a DCE keytab you can set one up by running the following command:
/usr/local/bin/get_hpss_keytab
The following example illustrates a directory move from a local machine to Blue Gene via HPSS:
- create a copy of the local directory with tar (the time to do this depends upon the sizes and number of files, etc.):
tar -cf your_tar_file .
- compress tar file with gzip (this step may not be necessary if your tar file is small). This creates a tar file with the name your_tar_file.gz:
gzip your_tar_file
- access HPSS from local machine with HSI (client binaries are available for download at the HSI site):
hsi
- store the compressed file in HPSS:
put your_tar_file.gz
- login to Blue Gene and access HPSS with HSI:
ssh bglogin.sdsc.edu
/usr/local/apps/hsi/bin/hsi - download compressed tar file from HPSS:
get your_tar_file.gz
- uncompress tar file:
gunzip your_tar_file.gz
- move tar file to the desired location on DataStar and untar:
tar -xf your_tar_file
For more details on using HPSS, refer to the HPSS User Guide. In addition, Lawrence Livermore National Laboratory has developed the HPSS Tape Archiver (HTAR). HTAR is a file-bundling and storage utility designed to efficiently transfer a very large number of (related) files in the form of a manageable archive or library such as HPSS. For more information, please visit the HTAR Reference Manual.
