Brutus - Complete User Guide

Brutus is an experimental FPGA resource provided by the Northwest Indiana Compuational Grid (NWICG) through the Rosen Center for Advanced Computing (RCAC). Brutus currently consists of an SGI Altix 450 with two SGI RC100 blades with two FPGAs each, for a total of 4 FPGAs. Using Brutus effectively requires careful code development in either VHDL or Mitrion-C, but can result in significant performance increases. BLAST has been benchmarked on Brutus at 70x typical general-purpose CPU performance.

Detailed Hardware Specification

Number of Nodes	Processor	Cores per Node	Memory per Node	Interconnect
2	Virtex 4 LX200 FPGA	2	80 MB QDR SDRAM	NUMAlink Shared Memory

Brutus runs SuSE Linux Enterprise Server 10 and uses Condor for resource and job management. Operating system patches are applied monthly or as security needs dictate.

FPGA algorithms may be serialized, placed, and routed (analogous to compilation) and then registered for use by Brutus jobs from the frontend node portia.rcac.purdue.edu, from which jobs may also be submitted. Mitrionics' Mitrion-C compiler for FPGA algorithm development is provided, as well as Xilinx VHDL tools. Pre-SPRed bitcode may also be used. Some algorithms such as BLAST are provided pre-installed by RCAC.

Obtaining an Account

Brutus is used primarily by researchers with allocations from the NorthWest Indiana Computational Grid (NWICG) and the TeraGrid. However, Purdue faculty, staff and students with the approval of their advisor may also request access using the online Research Computing Account Request Form.

Login / SSH

Direct login to Brutus is not allowed. Brutus has a dedicated front-end host, portia.rcac.purdue.edu, which all users may log in to and from which user may submit jobs to Brutus.

Connect to portia.rcac.purdue.edu via SSH.

SSH Client Software

All access to the RCAC systems must be through secure (encrypted) connections. Standard telnet and FTP are not supported. SSH, SCP, and SFTP may be used instead.

Secure Shell or SSH is a way of establishing a secure channel between a local and a remote computer. It uses public-key cryptography to authenticate the remote computer and (optionally) to allow the remote computer to authenticate the user. It is usually used to log in to a remote machine and execute commands similar to telnet, but it also supports tunneling and forwarding of X11 or arbitrary TCP connections. The associated SFTP and SCP protocols may be used to transfer files. There are many SSH clients available, depending on the operating system you use.

Linux / Solaris / AIX / HP-UX / Unix:

"ssh", "sftp", and "scp" are pre-installed. Log in using ssh myusername@servername.

Microsoft Windows:

PuTTY is an extremely small download and includes free SSH, SCP, and SFTP clients.
Secure CRT (SSH client) and Secure FX (SFTP client) are commercial clients which are available free to Purdue students, faculty, and staff with a Purdue career account.

Mac OS X:

"ssh", "sftp", and "scp" are pre-installed. You may start a local terminal window from "Applications->Utilities". Log in using ssh myusername@servername.
MacSSH and MacSFTP
NiftyTelnet 1.1 SSH

SSH Keys

SSH can be used in conjunction with many different means of authentication. One popular authentication method is called Public Key Authentication (PKA). PKA is a method of establishing your identity to a remote computer using related sets of encryption data called keys. PKA is a more secure alternative to traditional password-based authentication with which you are probably familiar.

To employ PKA via SSH, you manually generate a keypair (also called SSH keys) in the location from where you wish to initiate a connection to a remote machine. This keypair consists of two text files, one which is called a private key and one which is called a public key. You keep the private key file confidential on your local machine or local home directory (hence the name "private" key). You then login to a remote machine (if possible) and append the corresponding public key text to the end of a specific file, or have a system administrator do so on your behalf. In future login attempts, the public and private keys are compared to verify your identity, which then grants you access to the remote machine.

As a user, you can create, maintain, and employ as many keypairs as you wish. If you connect to a computational resource from your work laptop, your work desktop, and your home desktop, you can create and employ keypairs on each. You can also create multiple keypairs on a single local machine to serve different purposes, such as establishing access to different remote machines, or establishing different types of access to a single remote machine. In short, PKA via SSH offers a secure but flexible means of identifying yourself to all kinds computational resources.

Passphrases and SSH Keys

When a you create a keypair, you are prompted to provide a passphrase for the private key. This passphrase is different than a password in a number of ways. First, a passphrase is, as the name implies, a phrase. It can include most types of characters, including spaces, and has no limits on length. Second, this passphrase is not transmitted to the remote machine for verification. It is used only to allow the use of your local private key and is specific to a specific local private key.

Perhaps you are wondering why you would need a private key passphrase at all when using PKA. If the private key is kept secure, why the need for a passphrase just to use it? Indeed, if the location of your private keys were always completely secure, a passphrase might not be needed. In reality, a number of situations could arise in which someone may improperly gain access to your private key files. In these situations, a passphrase offers another level of security for you, the user who created the keypair.

Think of the private key/passphrase combination as being analogous to your ATM card/PIN combination. The ATM card itself is the object that grants access to your important accounts, and as such, should be kept secure at all times—just as a private key should. But if you ever lose your wallet or your ATM card is stolen, you are glad that your PIN exists to offer you another level of protection. The same is true for a private key passphrase.

When you create a keypair, you should always provide a corresponding private key passphrase. For security purposes, avoid using phrases that would be guessed by automated programs (e.g. phrases that consist solely of words in English-language dictionaries). This passphrase can never be recovered if forgotten, so make note of it. There are only limited situations when the use of a non-passphrase-protected private key is warranted—conducting automated file backups is one such situation. If you need to use a non-passphrase-protected private key to conduct automated backups to Fortress, see the No-Passphrase SSH Keys section.

SSH X11 Forwarding

SSH supports tunneling of X11 (X-Windows). If you have an X11 server running on your local machine, you may use X11 applications on remote systems and have their graphical displays appear on your local machine. These X11 connections are tunneled and encrypted automatically by your SSH client. You will need to have a local X11 server running, but free and commercial X11 servers are available for various operating systems.

Linux / Solaris / AIX / HP-UX / Unix:

An X11 server is at the core of all graphical sessions. If you are logged in to a graphical environment on these operating systems, you are already running an X11 server.

Microsoft Windows:

Xming is a free X11 server available for all versions of Windows, although it may occasionally hang and require a restart. Download the "Public Domain Xming" or donate to the development for the newest version.
Hummingbird eXceed is a commercial X11 server available for all versions of Windows.
Cygwin is another free X11 server available for all versions of Windows. Download setup.exe and make sure you select the following packages which are not included by default:
```
	Packages from the X11 group:
	
	X-startup-scripts
	XFree86-lib-compat
	xorg-*
	xterm
	xwinwm
	lib-glitz-glx1
	
	Under the Graphics group, also select opengl, if you want OpenGL 
	support. 
```
Then when the Cygwin X server is installed, start an xterm and type: XWin -multiwindow in it and then enter. You can now run your SSH client.

Mac OS X:

X11 is available as an optional install on the Mac OS X v10.3 Panther and x10.4 Tiger install disks. Run the installer, select the X11 option, and follow the instructions.

Enabling the forwarding

Once you are running an X11 server, you will need to enable X11 forwarding/tunneling in your SSH client:

"ssh": X11 tunneling should be enabled by default. To be certain it is enabled, you may use "ssh -X".
PuTTY: Prior to connection, in your connection's options, under "Tunnels", check "Enable X11 forwarding", and save your connection.
Secure CRT: Right-click a saved connection, and select "Properties". Expand the "Connection" settings, then go to "Port Forwarding" -> "Remote/X11". Check "Forward X11 packets" and click "OK".

Note that SSH will set the remote environment variable $DISPLAY to "localhost:XX.YY" when this is working correctly. If you had previously set your $DISPLAY environment variable to your local IP or hostname, you must remove any set/export/setenv of this variable from your login scripts. The environment variable $DISPLAY must be left as SSH sets it, which is to a random local port address. Setting $DISPLAY to an IP or hostname will not work.

Passwords

If you have received a default password as part of the process of obtaining your account, you should change it immediately when you log on for the first time. This can be done from any terminal/SSH session with the command "passwd". You will have the same password on all RCAC systems. If you change your password on any one RCAC system, it will change on all RCAC systems.

If you already have a Purdue career account, then you will initially be given the same userid and password as your career account. There is no need to change your career account password because you have received an account on RCAC systems.

There is not currently any requirement regarding how often you must change your password within RCAC, but for security reasons changing a password every six months, preferably every three months, is good practice.

All passwords should:

Be something you have never used as a password before, on this or any other system.
Be easy for you to remember and difficult for others to guess.
Be at least eight characters long.
Be a combination of upper and lowercase letters, numbers, and symbols.
TIP: Abbreviate a sentence or song lyric: "The dog Samson ate 4 new slippers!" = "TdSa4ns!"

Never share your password with another user or make your password known to anyone else. Systems staff will NEVER ask for your password, by email or otherwise.

Email

There is no local mail delivery available on Brutus. All email sent to Brutus will be forwarded to mail.rcac.purdue.edu for delivery.

Login Shell

When your account is activated, your default shell will probably be set to tcsh—an enhanced version of the Berkeley UNIX C shell (csh). The tcsh shell is completely compatible with the standard csh, and all csh commands and scripts work unedited with tcsh. For more details on tcsh, enter "man tcsh" while logged in.

The other popular shell is GNU Bourne-Again SHell (bash), which is completely compatible with the Bourne shell (sh). For more details on bash, enter "man bash" while logged in.

To change your shell temporarily or to try out another shell, just type the shell name as a command ("bash", "tcsh", "ksh"). This will run the new shell as a subshell. To return to your original shell, simple type exit.

To permanently change your login shell, use the command chsh:

$ chsh -s bash
     (or)
$ chsh -s tcsh

To see a list of all available shells:

$ chsh -l

The next time you log on, you will start in the new shell. However, you may switch back at any time.

Storage Options

File storage options on RCAC systems include home directories, scratch file systems, /tmp, and long-term or permanent storage. Each of these have different performance and intended uses, and some vary from system to system as well. Home directories and long-term storage are backed up nightly, but scratch and /tmp are not and may be occasionally purged without warning. Below is more detail about each of these storage options.

Home Directories

Your home directory is the default directory you are placed in when you log in.

You should use this space for storing files you want to keep long term such as source code, scripts, input data sets, etc. It should also be used for files you want to keep and which you use often. The home directory will physically reside on the BlueArc NFS Server. You can find the path to your home directory by logging in, and typing pwd:

$ pwd
/home/ba01/u103/myusername

The second component of the reply indicates the name of the host where your home directory physically resides. In this example, the home directory is on the RCAC home directory file server named "ba01" under area "u103". This will vary from person to person. Remember, you can always check where your home directory is located by doing a pwd command in your home directory.

Regardless of its physical location, your home directory and its contents are available on almost all the RCAC front-end hosts and their nodes via the Network File System (NFS). The only exception is Black.

Note that your home directory has a quota capping the size and/or number of files you may store within. For more information, refer to the Storage Quotas / Limits Section.

Lost Home Directory File Recovery

Only files which have been backed up overnight can be recovered. If you lose a file the same day you created it, it can NOT be recovered.

Files Lost Less than Seven Days Ago

For files lost less than seven days ago, RCAC has implemented self-service file recovery. Backups of all your files are made at midnight daily and you may access these directly.

To recover files lost after midnight today (same day as loss):

$ set BACKUP=`echo $HOME | sed "s,/u1,_snap/backup_snap/u1,;s,/home/,/autohome/,"`
$ cd $BACKUP

  (now locate the file or directory you wish to recover within here)

$ cp mylostfile $HOME
  (or)
$ cp -r mylostdir $HOME

To recover files lost prior to today, but in last week (2-7 day loss):

  (set this to the date you lost the files: 4-digit year, 2-digit month, 2-digit day)
$ set DATE=YYYYMMDD

$ set BACKUP=`echo $HOME | sed "s,/u1,_snap/backup_snap_$DATE*/u1,;s,/home/,/autohome/,"`
$ cd $BACKUP

  (now locate the file or directory you wish to recover within here)

$ cp mylostfile $HOME
  (or)
$ cp -r mylostdir $HOME

Files Lost More than Seven Days Ago

For files lost more than seven days ago, you will need to request RCAC recover your files from backup tapes. Please do so using the flost command from the front-end host of an RCAC resource:

$ flost

Scratch Directories

Scratch directories are provided by RCAC and are intended for short-term file storage only.

Backups are not performed on scratch directories. In the event of a disk crash or file purge, files in scratch directories can not be recovered. Please be sure to copy any important files to more permanent storage.

All files stored in RCAC scratch directories older than 90 days will be automatically removed (purged). Owners of these files will be notified one week before removal via email. For more information, please refer to our Scratch File Purging Policy.

RCAC scratch directories are provided by a central BlueArc server and are accessible from most RCAC systems. There are two primary scratch file systems: scratch95 and scratch96. A scratch directory already exists for all Brutus users. Your RCAC scratch directory is located under scratch95 or scratch96 within a subdirectory by the first letter of your username.

To find the path to your RCAC scratch directory, run myscratch:

	$ myscratch
	/scratch/scratch96/m/myusername

The variable $RCAC_SCRATCH is also set to your RCAC scratch directory path. Use this variable in any scripts. Your actual scratch directory path may change without warning, but this variable will remain current.

$ echo $RCAC_SCRATCH
/scratch/scratch96/m/myusername

To find the path to someone else's RCAC scratch directory, use the command findscratch:

$ findscratch someuser
/scratch/scratch95/s/someuser

Note that your RCAC scratch directory has a quota capping the size and/or number of files you may store within. For more information, refer to the Storage Quotas / Limits Section.

/tmp Directory

The /tmp directory is intended for temporary files that are used during the execution of a process or job or while you examine files created by your jobs. Used properly, /tmp may provide faster local storage to an active process than any other storage option. However, do not use it for longer-term storage or critical results.

Files stored in /tmp are not backed up and are removed whenever space is low or whenever the system is rebooted. In the event of a loss, files in /tmp can not be recovered, so use it only for files that can be recreated relatively easily.

Long-Term Storage

Long-term Storage or Permanent Storage is available to RCAC users on the DXUL/UniTree archival storage system, commonly referred to as "Fortress". DXUL (DiskXtender for Unix and Linux) and UniTree are a software package that manages a hierarchical storage system. Program files, data files and any other files which are not used often, but which must be saved, can be put in permanent storage. Fortress currently has a 1.2 PB capacity. However, since two copies are retained for every file, the usable capacity is only 600 TB.

Recently used files smaller than 0.5 MB have their primary copy stored on low-cost disks, but the second copy is on tape or optical disks. This provides a rapid restore time to the disk cache. However, the large latency to access a larger file (usually involving a copy from a tape cartridge) makes it unsuitable for use as active storage.

In addition to poor performance, these two uses can cause severe problems with the system itself:

DO NOT store any actively used files on Fortress.
DO NOT store large collections of small files on Fortress.

Do not use Fortress as a second home directory. Instead, use tar or some similar archive tool to combine all the smaller files you wish to store into a single large file first.

For active data storage you should use either local storage or a scratch file system. You may then copy any results you wish to archive to Fortress when computation is complete.

Fortress is directly accessible (via FTP, SSH, SCP, SFTP, and NFS) from all RCAC systems, as well as most systems in ECN and CS and from several other major servers on campus. To access Fortress in any way other than NFS, you must login to fortress.rcac.purdue.edu. RCAC has more information about Fortress, including how to obtain a Fortress account and how to access your files on Fortress.

Manual File Transfer to Long-Term Storage

There are a variety of ways to manually transfer files to your Fortress home directory for long-term storage.

SCP

You can use an SCP client to interactively transfer individual files and directories to Fortress. More information on SCP can be found in the File Transfer - SCP section of this guide.

SFTP

You can use an SFTP client to interactively transfer individual files and directories to Fortress. More information on SFTP can be found in the File Transfer - SFTP section of this guide.

Scripted File Transfer to Long-Term Storage

In the absence of NFS access to Fortress, you must login to fortress.rcac.purdue.edu to transfer files to long-term storage. There are limited situations where the use of a password or a passphrase-protected authentication keypair becomes impractical, and running scripted file backups to Fortress happens to be one of them. When you attempt to establish a connection to Fortress, you will literally be prompted to input a password or a local private key passphrase. Any time a script or automated process needs to establish the connection, it is unable to respond to such a request. To enable truly automated transfer of files to Fortress, you need to employ public key authentication via SSH with a non-passphrase-protected private key. For a conceptual overview of public key authentication, see the SSH Keys section of this guide.

Now, if your home directory is compromised and an attacker obtains your non-passphrase-protected private key, the attacker will be able to masquerade as you on machines that contain the corresponding public key. Luckily, certain usage restrictions can be customized for each keypair you employ. For example, you could create a non-passphrase-protected keypair and later specify that this public key shall only be used to run a file-backup script, and additionally, is only valid when connecting from a specific machine. Then, if the non-protected private key were to be compromised, the attacker would be saddened to realize that he could only run your file-backup script repeatedly.

It is very important to place a passphrase on all of your generated keypairs. Only use non-protected keypairs when absolutely necessary.

No-Passphrase SSH Keys

Here is how to set up a non-password-protected keypair for use with automated backup scripts to Fortress from Brutus.

Log on to Brutus
Create a non-passphrase-protected SSH keypair.

You should use this keypair for the sole purpose of automating backups on Fortress.

Specify your ~/.ssh/ directory and give the keypair a descriptive name (e.g. "bkup2fort_id_rsa") by using the "-f" flag:
```
$ ssh-keygen -t rsa -N "" -f ~/.ssh/mykeypairname
```
The ssh-keygen command should have created the following files:
```
$ ls ~/.ssh/mykey*
mykeypairname mykeypairname.pub
```
The first file is the private key. The second file is the public key counterpart.

Never distribute your private key or copy it to other machines.
Open the public key file with your favorite text editor and prepend the following text to restrict its use:
```
from="*.rcac.purdue.edu",no-port-forwarding,no-agent-forwarding,no-X11-forwarding,no-pty
```
This tells SSH to only allow connections from RCAC resources, to disable a number of forwarding functions, and to not allow interactive shell commands, respectively.

Copy your modified public key over to your Fortress home directory:

$ scp ~/.ssh/mykeypairname.pub myusername@fortress.rcac.purdue.edu:~/

Log into Fortress and cd to ~/.ssh. Create the ~/.ssh directory if neccessary:
```
$ ssh myusername@fortress.rcac.purdue.edu
$ cd ~/.ssh/
```
If a file named "authorized_keys" exists in the .ssh directory, set the proper permissions for it:
```
$ chmod 600 ~/.ssh/authorized_keys
```
If it does not exist, create it:
```
$ touch ~/.ssh/authorized_keys
$ chmod 600 ~/.ssh/authorized_keys
```
Append your modifed public key to the "authorized_keys" file in your Fortress ~/.ssh directory:
```
$ cat ~/mykeypairname.pub >> ~/.ssh/authorized_keys
```

View your "authorized_keys" file. The last entry should look similar to this:

$ cat ~/.ssh/authorized_keys

from="*.rcac.purdue.edu",no-port-forwarding,no-agent-forwarding,no-X11-forwarding,
no-pty ssh-rsa AABBB3NzaC1yc2EABBABIwAAAIEA3SXgmvos4jFLVFLRrh6YrN3s8FuBOUTCJ0NIsc+
FtFrSGD2bVV6yMCgpdgz9RZS7U5uTJOW2VBWsJSb6cjjnA2WJzDcS0bEU3lw+TJszv2sEfl/CwF6dyj2U2
k5VrXIpdosZVKyjoqzQXhFicIRv1/ykdO8xp+qcgc09NbcyGhs= myusername@resource.rcac.purdue.edu

Delete your public key file on Fortress (it's now stored in the "authorized_keys" file):
```
$ rm ~/mykeypairname.pub
```
Log out of Fortress:
```
$ exit
```

SCP

If you have followed the instructions in the No-Passphrase SSH Keys section to employ an unprotected SSH keypair between Brutus and Fortress, you can automate the backup process using backup scripts. Because of the restrictions you placed upon the public key, you cannot use this keypair to log on to an interactive SSH session on Fortress, but you can use it to send files from your Brutus home directory to Fortress via SCP, or to run local scripts that employ SCP.

Since you can have multiple private keys on Brutus (and a similarly, multiple public keys in any given "authorized_keys" file on Fortress), you always need to specify which keypair you intend to employ for a log-in attempt to Fortress. The most consistent way to do this is with SSH's "-o" flag. This passes options to configure SSH and can be used with all programs that use SSH for providing a secure connection (e.g. SCP, SFTP, and RSYNC).

To test automated SCP authentication from Brutus to Fortress, use the following command:

$ scp -o IdentityFile=~/.ssh/mykeypairname ./mylocalfile myusername@fortress.rcac.purdue.edu:~/myremotefile

If this works (i.e. you are not prompted for a passphrase or login password), you can move on to implementing a script using SCP commands like the one above.

While only you can ultimately decide the best approach for your automated backup process, the example scripts below show, in general, how to employ backup scripts on Brutus using SCP commands and public key authentication via SSH. The following bash script, named "fortress_backup_script_scp", uses SCP to recursively copy two directories on a user's Brutus home directory to the user's Fortress home directory:

#!/usr/local/bin/bash

# A script to use SCP to copy
# whole directories to Fortress

# Define some parameters

user=myusername
remotehost=fortress.rcac.purdue.edu
idfile=~/.ssh/mykeypairname

# Manually populate an array of directories on the 
# local machine we wish to back up on Fortress

localdir[0]=~/mydir2backup
localdir[1]=~/mydir2backup_also

# Get the number of directories to be backed up

numdirs=${#localdir[*]}
count=1

# Loop over every entry in the "localdir" array to
# copy each directory recursively to a folder of 
# the same name in our home directory on Fortress.

printf "\n>> Starting Secure Copy backup to Fortress\n"

for dir in "${localdir[@]}"
do
  printf ">> Copying directory $dir to Fortress ($count of $numdirs)\n"
  scp -r -o IdentityFile=$idfile $dir $user@$remotehost:~/
  let count++
done

printf ">> Done...\n\n"

The output for this script is as follows:

$ ./fortress_backup_script_scp
 
>> Starting Secure Copy backup to Fortress
>> Copying directory /home/ba01/u100/myusername/mydir2backup to Fortress (1 of 2)
bigfile2.tar.gz                                100%  121MB  30.3MB/s   00:04    
bigfile1.tar.gz                                100%  121MB  40.5MB/s   00:03    
>> Copying directory /home/ba01/u100/myusername/mydir2backup_also to Fortress (2 of 2)
bigfile4.tar.gz                                100%  121MB  40.5MB/s   00:03    
bigfile3.tar.gz                                100%  121MB  40.5MB/s   00:03  
>> Done...

By using these techniques, you can automate your file backups to Fortress safely and efficiently.

SFTP

Since you can have multiple private keys on Brutus (and similarly, multiple public keys in any given "authorized_keys" file on Fortress), you always need to specify which keypair you intend to employ for a log-in attempt to Fortress. The most consistent way to do this is with SSH's "-o" flag. This passes options to configure SSH and can be used with all programs that use SSH for providing a secure connection (e.g. SCP, SFTP, and RSYNC).

To test automated SFTP authentication from Brutus to Fortress, use the following command:

$ sftp -o IdentityFile=~/.ssh/mykeypairname myusername@fortress.rcac.purdue.edu
sftp> bye
$

If this works (i.e. you are not prompted for a passphrase or login password), you can move on to implementing a script using SFTP commands like the one above.

While only you can ultimately decide the best approach for your automated backup process, the example scripts below show, in general, how to employ backup scripts on Brutus using SFTP commands and public key authentication via SSH. The following bash script, named "fortress_backup_script_sftp", uses SFTP commands to navigate through Fortress directories, and pushes files from the user's Brutus home directory when needed.

#!/usr/local/bin/bash

# A script to use SFTP to push files to 
# Fortress for backup.

# Set up some parameters

user=myusername
remotehost=fortress.rcac.purdue.edu
idfile=~/.ssh/mykeypairname

printf "\n>> Starting Secure FTP backup session to Fortress\n"

# Invoke SFTP mode, specifying the correct private key, 
# and forcing batch file input from a "here-document"
# (i.e. the rest of this script).

sftp -o IdentityFile=$idfile -b - $user@$remotehost << EOF

cd ./mydir2backup
lcd ./mydir2backup

put -P ./bigfile1.tar.gz 
put -P ./bigfile2.tar.gz 

cd ../mydir2backup_also
lcd ../mydir2backup_also

put -P ./bigfile3.tar.gz 
put -P ./bigfile4.tar.gz 

bye
EOF

# Now we are back to the bash shell...

printf ">> Done...\n\n"

The output for this script is as follows:

$ ./fortress_backup_script_sftp

>> Starting Secure FTP backup session to Fortress
sftp> 
sftp> cd ./files2backup
sftp> lcd ./files2backup
sftp> 
sftp> put -P ./bigfile1.tar.gz 
Uploading ./bigfile1.tar.gz to /archive/fortress/home/myusername/mydir2backup/bigfile1.tar.gz
sftp> put -P ./bigfile2.tar.gz 
Uploading ./bigfile2.tar.gz to /archive/fortress/home/myusername/mydir2backup/bigfile2.tar.gz
sftp> 
sftp> cd ../files2backup_also
sftp> lcd ../files2backup_also
sftp> 
sftp> put -P ./bigfile3.tar.gz 
Uploading ./bigfile3.tar.gz to /archive/fortress/home/myusername/mydir2backup_also/bigfile3.tar.gz
sftp> put -P ./bigfile4.tar.gz 
Uploading ./bigfile4.tar.gz to /archive/fortress/home/myusername/mydir2backup_also/bigfile4.tar.gz
sftp> 
sftp> bye
>> Done...

$

By using these techniques, you can automate your file backups to Fortress safely and efficiently.

Environment Variables

There are many environment variables related to storage locations and paths which are automatically set for you upon log-in, or may be changed if necessary. In addition, many more environment variables are set for specific applications, such as compilers, when "modules" for these applications are loaded. (See the module command section for more information.)

Use environment variables instead of actual paths whenever possible to avoid problems if the specific paths to any of these change. Some of the environment variables you should have are:

$USER: your username
$HOME: path to your home directory
$PWD: path to your current directory
$RCAC_SCRATCH: path to scratch filesystem
$PATH: all directories searched for commands/applications
$HOSTNAME: name of the machine you are on
$SHELL: your current shell (bash, tcsh, csh, ksh)
$SSH_CLIENT: your local client's IP address
$TERM: type of terminal or terminal emulator being used
$OMP_NUM_THREADS: number of OpenMP threads

All environment variables begin with the dollar sign ($) and are all uppercase. They may be used on the command line or in any scripts in place of and in combination with hard-coded values:

$ ls $HOME
...

$ ls $RCAC_SCRATCH/myproject
...

$ ls $RCAC_SCRATCH/myproject/$HOSTNAME_data
...

You may find the value of any environment variable by using the echo command:

$ echo $RCAC_SCRATCH
/scratch/scratch95/m/myusername

$ echo $SHELL
/usr/local/bin/tcsh

You may list the values of all environment variables using the env command:

$ env
USER=myusername
HOME=/home/ba01/u101/myusername
RCAC_SCRATCH=/scratch/scratch95/m/myusername
SHELL=/usr/local/bin/tcsh
...

You may create or overwrite an environment variable using either export or setenv, depending on your shell:

  (for bash and sh)
$ export VARIABLE=value

  (for tcsh and csh)
% setenv VARIABLE value

Storage Quotas / Limits

Your disk usage is limited on RCAC systems. However, each filesystem (scratch, home directory, etc.) may have a different limit. If you exceed the soft limit or quota, you will see warnings whenever writing to the disk that you are over quota, but the write will still succeed. If you exceed the hard limit or limit, your write will fail until you either remove other files or your quota is increased. Generally, RCAC systems do not impose a soft limit—only a hard limit.

Checking Quota Usage

You may find out what your current quota is by using the quota command:

$ quota
Disk quotas for user myusername (uid 12345): 
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
     ba01:/u103 2346272       0 5000000           17508       0   65535

The columns are as follows:

Filesystem: This indicates the line is for the user's files on /u103/, which doing echo $HOME confirms is the user's home directory filesystem.
Blocks: This shows how many 1 KB blocks the user's files take up. In this case, 2346272 KB / 1024 = 2291 MB, or 2291 MB / 1024 = 2.24 GB.
Quota: This shows that soft limits are not being imposed (0).
Limit: This shows how many 1 KB blocks the user's hard limit is. In this case, (5000000 KB / 1024) / 1024 = 4.77 GB.
Grace: This would show the grace period (in days) for any soft limit (none in this case).
Files: This shows how many file pointers (inodes) the user is currently using. This is based more on the number of files and directories and not the size.
Quota: This shows that soft limits are not being imposed for file pointers (0).
Limit: This shows the user's file pointer hard limit. It is possible, though unlikely, to hit this and not the size limit if you create a large number of very small files.
Grace: This would show the grace period (in days) for any file pointer soft limit (none in this case).

You may also see the disk usage of any given directory by using du:

$ du -hs
1.1G    .

$ du -hs $HOME
138M    /home/ba01/u103/myusername

This can be very helpful in figuring out where your largest files or directories are, so that you may clean out unneeded large files and avoid hitting your quota.

Requesting Quota Increase

If you find you need additional disk space on an RCAC account, please first consider archiving and compressing old files and moving them to long-term storage. If this option does not resolve the issue, you may send an email to rcac-help@purdue.edu and request additional space.

Archive and Compression

There are several options for archiving and compressing groups of files or directories on RCAC systems. All of the following tools are provided:

zip (more information)
Simple compression and file packaging utility.
Examples:

  (compress file somefile.c)
$ zip somefile.zip somefile.c

  (extract contents of somefile.zip)
$ unzip somefile.zip

  (compress all files in a directory into one archive file)
$ zip -r somefile.zip somedirectory/

  (compress all ".c" files in current directory into one archive file)
$ zip -r somefile.zip . -i \*.c

tar (more information)
Saves many files together into a single archive file, and restores individual files from the archive. Includes automatic archive compression/decompression options and special features that allow tar to be used for incremental and full backups.
Examples:

  (archive file somefile.c)
$ tar cvf somefile.tar somefile.c

  (archive and compress file somefile.c)
$ tar czvf somefile.tar.gz somefile.c

  (list contents of archive somefile.tar)
$ tar tvf somefile.tar

  (extract contents of somefile.tar)
$ tar xvf somefile.tar

  (extract contents of gzipped archive somefile.tar.gz)
$ tar xzvf somefile.tar.gz

  (archive and compress all files in a directory into one archive file)
$ tar czvf somefile.tar.gz somedirectory/

  (archive and compress all ".c" files in current directory into one archive file)
$ tar czvf somefile.tar.gz *.c

gzip (more information)
Compression utility designed as a replacement for compress, with much better compression and no patented algorithms. The standard compression system for all GNU software.
Examples:
```
  (compress file somefile - also removes uncompressed file)
$ gzip somefile

  (uncompress file somefile.gz - also removes compressed file)
$ gunzip somefile.gz
```

bzip2 (more information)
Strong, lossless data compressor based on the Burrows-Wheeler transform. Also available as a library.
Examples:

  (compress file somefile - also removes uncompressed file)
$ bzip2 somefile

  (uncompress file somefile.bz2 - also removes compressed file)
$ bunzip2 somefile.bz2

compress (more information)
Adaptive Lempel-Ziv compressor. Not often used today.

Windows users can work with these same formats using some of the following software:

7-Zip
Free Windows software package that can handle all the above formats.
WinZip
Commercial Windows software package that can handle all the above formats.
WinRAR
Commercial Windows software package that can handle all the above formats.

File Transfer

There are a variety of ways to transfer data to and from RCAC systems. Which you should use depends on several factors, including the ease of use for you personally, connection speed and bandwidth, the size and number of files to be transferred.

FTP

FTP (File Transfer Protocol) is simple data transfer mechanism. FTP was not designed to provide secure communications, and so FTP is no longer supported on any RCAC systems. Most modern FTP clients support either SFTP or SCP however, which are similar, secure protocols for file transfer. Try using one of the other methods described here instead of FTP.

SCP

SCP (Secure CoPy) is a simple way of transferring files between two machines that use the SSH (Secure SHell) protocol. You may use SCP to connect to any system where you have SSH (log-in) access. SCP is available as a protocol choice in some graphical file transfer programs and also as a command line program on most Linux, Unix, and Mac OS X systems. SCP can copy single files, but will also recursively copy directory contents if given a directory name.

Command-line usage:

  (to a remote system from local)
$ scp sourcefilename myusername@hostname:somedirectory/destinationfilename

  (from a remote system to local)
$ scp myusername@hostname:somedirectory/sourcefilename destinationfilename

  (recursive directory copy to a remote system from local)
$ scp sourcedirectory/ myusername@hostname:somedirectory/

Linux / Solaris / AIX / HP-UX / Unix:

The "scp" command line program should already be installed.

Microsoft Windows:

WinSCP is a full-featured and free graphical SCP and SFTP client.
PuTTY also offers "pscp.exe", which is an extremely small program and a basic SCP client.
Secure FX is a commercial SCP and SFTP client which is available free to Purdue students, faculty, and staff with a Purdue career account.

Mac OS X:

The "scp" command line program should already be installed. You may start a local terminal window from "Applications->Utilities".

SFTP

SFTP (Secure File Transfer Protocol) is a reliable way of transferring files between two machines. You may use SFTP to connect to most RCAC systems. SFTP is available as a protocol choice in some graphical file transfer programs and also as a command-line program on most Linux, Unix, and Mac OS X systems. SFTP has more features than SCP and allows for other operations on remote files, remote directory listing, and resuming interrupted transfers. Command-line SFTP cannot recursively copy directory contents; to do so, try using SCP or graphical SFTP client.

Command-line usage:

$ sftp -B buffersize myusername@hostname

      (to a remote system from local)
sftp> put sourcefile somedir/destinationfile
sftp> put -P sourcefile somedir/

      (from a remote system to local)
sftp> get sourcefile somedir/destinationfile
sftp> get -P sourcefile somedir/

sftp> exit

-B: optional, specify buffer size for transfer; larger may increase speed, but costs memory
-P: optional, preserve file attributes and permissions

Linux / Solaris / AIX / HP-UX / Unix:

The "sftp" command line program should already be installed.

Microsoft Windows:

WinSCP is a full-featured and free graphical SFTP and SCP client.
PuTTY also offers "psftp.exe", which is an extremely small program and a basic SFTP client.
Secure FX is a commercial SFTP and SCP client which is available free to Purdue students, faculty, and staff with a Purdue career account.

Mac OS X:

The "sftp" command-line program should already be installed. You may start a local terminal window from "Applications->Utilities".
MacSFTP

LFTP

LFTP is a command-line file-transfer program for Linux and Unix systems. It supports SFTP, HTTP, and HTTPS file-transfers. LFTP has additional features not provided by SFTP such as bandwidth throttling, transfer queues, and parallel transfers. It may be used interactively or scripted.

LFTP with parallel transfers can be much faster than SCP or SFTP, so its use is encouraged when possible.

LFTP is provided only on some RCAC systems. However, it is simply a client, so it is not needed on the remote machine involved in a transfer (the remote system need only support SFTP).

Interactive usage:

$ lftp myusername@hostname

         (transfer all ".dat" files from remote system to local)
lftp :~> mget *.dat

         (transfer "filename.dat" file from local system to remote)
lftp :~> put filename.dat

         (transfer a directory and all contents from remote
          system to local, using 5 connections in parallel)
lftp :~> mirror --parallel=5 remotedirectory localdirectory/

         (transfer a directory and all contents from local
          system to remote, using 8 connections in parallel)
lftp :~> mirror -R --parallel=8 localdirectory remotedirectory/

Batch usage:

  (specify all actions on command line)
$ lftp myusername@hostname -e "mget *.dat"

  (specify all actions in the script file "mytransfer.lftp")
$ lftp myusername@hostname -f mytransfer.lftp

GridFTP

GridFTP is a fast method of transferring large files that uses Globus authentication credentials (x509 certificates). GridFTP is available on some RCAC resources, but only to users who are members of a Grid project, such as TeraGrid, NorthWest Indiana Computational Grid (NWICG), or Open Science Grid (OSG). Note that not all grids may access all RCAC resources.

For more information about how to use GridFTP, consult documentation for your participating grid.

Provided Applications

The third-party software on three commonly used RCAC systems is shown in the following table. Additional software may be available on other RCAC systems, and the software on a specific system can be seen by running the command "module avail" on that system. Please contact rcac-help@purdue.edu if you are interested in the availability of software not shown in this list.

	Radon	Steele	Julius/Caesar
R	✓	✓
AcGrace		✓
Amber	✓	✓
ANSYS	✓	✓
ATLAS	✓
BinUtils		✓
Boost	✓
ClustalX	✓
COMSOL	✓	✓	✓
CPLEX	✓	✓	✓
CUDA		✓
DX		✓
Ferret		✓
FFTW	✓	✓
FLUENT	✓	✓
GAMESS	✓	✓
GAMS	✓	✓
Gaussian	✓	✓	✓
GCC Compiler (C, C++, Fortran)	✓	✓	✓
GCC IA64 Cross-Compiler (xgcc-ia64)		✓
GMP	✓
GMT	✓	✓
GrADS		✓
GROMACS		✓
GhostScript		✓
GSL		✓	✓
HDF4 (Compiled for Intel, GNU, PGI)		✓
HDF5 (Compiled for Intel, GNU, PGI)		✓
ImageMagick		✓
IMSL	✓	✓	✓
Intel Compiler (C, C++, Fortran)	✓	✓	✓
Jasper	✓	✓
Java	✓	✓
LAM			✓
LAMMPS	✓	✓
LSTC			✓
Maple	✓	✓	✓
Mathematica	✓	✓	✓
MATLAB	✓	✓
Mitrionics FPGA Tools (mitrion)		✓
MPFR	✓	✓	✓
MPICH	✓	✓	✓
MPICH2		✓	✓
MPIExec		✓
MrBayes	✓
MUMPS		✓
MVAPICH (for Intel, PGI compilers)		✓
MVAPICH2 (for Intel, GNU, PGI compilers)		✓
MWRank	✓
NCBI	✓
NCL	✓	✓
NCO		✓
NetCDF (for Intel, GNU, PGI compilers)		✓
NTL	✓
NWChem	✓	✓
Octave		✓
PGI Compiler (C, C++, Fortran)	✓	✓
PKG-Config		✓
Python	✓	✓
RASC		✓	✓
SAS	✓
ScaLAPACK	✓	✓	✓
Stata			✓
Subversion	✓	✓	✓
Tau		✓
TecPlot		✓
TotalView	✓	✓	✓
UDUNITS		✓
VASP			✓
Vis5D		✓

Environment Management with the Module Command

RCAC uses the module command as the preferred method for a user to manage the processing environment. With this command, a user may load libraries and paths for using specific applications or compilers. These are organized into packages which may be loaded and unloaded as needed. Please use the module command and do not manually configure your environment, as RCAC staff will frequently make changes to the specifics of various packages. If you use the module command to manage your environment, these changes will not be noticeable.

Below follows a short introduction to the module command. You can see more in the man page for module. Typing module at the command line will give you a brief usage report.

List Available Modules

To see what modules are available on this system, use the "module avail" command:

$ module avail

------------------------ /apps/host/modules/versions -------------------------
3.1.6

-------------------- /apps/host/modules3.1.6/modulefiles ---------------------
dot         module-cvs  module-info modules     null        use.own

----------------------- /apps/host/modules/modulefiles -----------------------
R/2.6.2
R/2.7.0
amber/10
ansys/11.0
dx/4.4.4
fftw/2.1.5
fftw/3.1.2
fluent/6.3.26
gamess/24.MAR.2007.R3(default)
gaussian/D.01
gaussian/E.01(default)
gaussian03/D.01
gaussian03/E.01(default)
gcc/4.3.0
     ...

Load / Unload a Module

You should note that all modules consist of both a name and a version number. When loading a module, you may use only the name to load the default version, or specify which version you wish to load:

$ module load intel
  (load default Intel compiler)

$ module load intel/9.1.045
  (load version 9.1.045 of the Intel compiler)

Note that you will need to load any relevant modules within job submission scripts that use those applications. Loading the module before submitting your job is not sufficient. Also, if you use bash or ksh as your login shell, you will also need to add a line in any submission script to source /etc/profile before invoking "module". Users of csh and tcsh do not need to do this.

     ...
. /etc/profile
module load intel
     ...

To unload a module, use the “module unload” command. It will attempt to undo the changes to your environment, made by that module:

$ module unload intel
  (unload default Intel compiler)

$ module unload intel/9.1.045
  (unload version 9.1.045 of the Intel compiler)

List Currently Loaded Modules

To see what modules you have currently loaded, use "module list":

$ module list
Currently Loaded Modulefiles:
  1) intel/9.1.045

$ module unload intel
$ module list
No Modulefiles Currently Loaded.

Show Module Details

To learn more about what a module does to your environment, you may use the "module show module_name" command, where module_name is any name in the list from command "module avail". This can be either default name like "intel", "gcc", "pgi", and "matlab", or a specific version of amodule, such as "intel/9.1.045". Here is an example showing what loading the default Intel compiler does to the processing environment:

$ module show intel
-------------------------------------------------------------------
/opt/modules/modulefiles/intel/9.1.045:

module-whatis    invoke Intel 9.1 Compilers 
prepend-path     PATH /opt/intel/cce/9.1.045/bin 
prepend-path     PATH /opt/intel/fce/9.1.040/bin 
prepend-path     PATH /opt/intel/idbe/9.1.045/bin 
prepend-path     LD_LIBRARY_PATH /opt/intel/cce/9.1.045/lib 
prepend-path     LD_LIBRARY_PATH /opt/intel/fce/9.1.040/lib 
prepend-path     LD_LIBRARY_PATH /opt/intel/idbe/9.1.045/lib 
prepend-path     LD_LIBRARY_PATH /opt/intel/mkl/9.0/lib/em64t 
setenv           CC icc 
setenv           CXX icpc 
setenv           FC ifort 
setenv           F90 ifort 
setenv           LAPACK_INCLUDE -I/opt/intel/mkl/9.0/include 
setenv           LINK_LAPACK -L/opt/intel/mkl/9.0/lib/em64t \
-lmkl_lapack64 -lmkl_em64t -lmkl -lguide -lpthread 
setenv           LINK_LAPACK_STATIC -L/opt/intel/mkl/9.0/lib/em64t \ 
-lmkl_lapack -lmkl_em64t -lguide -lpthread 
-------------------------------------------------------------------

To show what loading a specific Intel compiler version does to the processing environment.

$ module show intel/9.1.045
-------------------------------------------------------------------
/apps/steele/modules/modulefiles/intel/9.1.045:

module-whatis    invoke Intel 9.1 Compilers 
prepend-path     PATH /opt/intel/cce/9.1.045/bin 
prepend-path     PATH /opt/intel/fce/9.1.040/bin 
prepend-path     PATH /opt/intel/idbe/9.1.045/bin 
prepend-path     LD_LIBRARY_PATH /opt/intel/cce/9.1.045/lib 
prepend-path     LD_LIBRARY_PATH /opt/intel/fce/9.1.040/lib 
prepend-path     LD_LIBRARY_PATH /opt/intel/idbe/9.1.045/lib 
prepend-path     LD_LIBRARY_PATH /opt/intel/mkl/9.1/lib/em64t 
setenv           CC icc 
setenv           CXX icpc 
setenv           FC ifort 
setenv           F90 ifort 
setenv           ICC_HOME /opt/intel/cce/9.1.045 
setenv           IFORT_HOME /opt/intel/fce/9.1.040 
setenv           MKL_HOME /opt/intel/mkl/9.1 
setenv           LAPACK_INCLUDE -I/opt/intel/mkl/9.1/include 
setenv           LINK_LAPACK -L/opt/intel/mkl/9.1/lib/em64t -lmkl_lapack -lmkl_em64t -lmkl -lguide -lpthread 
setenv           LINK_LAPACK_STATIC -L/opt/intel/mkl/9.1/lib/em64t -lmkl_lapack -lmkl_em64t -lguide -lpthread 
-------------------------------------------------------------------

Provided Compilers

Compilers are available on Brutus for Fortran 77, Fortran 90, Fortran 95, C, and C++. The compilers can produce general-purpose and architecture-specific optimizations to improve performance. These include loop-level optimizations, inter-procedural analysis and cache optimizations. The compilers support automatic and user-directed parallelization of Fortran, C, and C++ applications for multiprocessing execution. More detailed documentation on each compiler set available on Brutus follows.

Compiling OpenMP Programs

Compilers for C, C++, and versions of Fortran are available. To see a Fortran 77 program with OpenMP commands: omp_hello_f77.f. To see a C program with OpenMP commands: omp_hello.c. See the table below for how to compile your program. Any compiler flags accepted by ifort/icc compilers, can be used with OpenMP.

Language	Command example, Intel	Command example, GNU	Command example, PGI
C	icc -openmp program.c -o program	gcc -fopenmp program.c -o program	pgcc -mp program.c -o program
C++	icc -openmp program.cpp -o program	g++ -fopenmp program.cpp -o program	pgCC -mp program.cpp -o program
Fortran 77	ifort -openmp program.f -o program	-	pgf77 -mp
Fortran 90	ifort -openmp program.f90 -o program	gfortran -fopenmp program.f90 -o program	pgf90 -mp program.f90 -o program
Fortran 95	ifort -openmp program.f90 -o program	gfortran -fopenmp program.f90 -o program	pgf95 -mp program.f90 -o program

Compiling a Fortran 90 program gives the following output when successful (note that the compiler module is loaded first - in this example Intel):

	$ module load intel
	$ ifort -openmp omp_hello_90.f90 -o omp_hello
	omp_hello_90.f90(4): (col. 9) remark: OpenMP DEFINED REGION WAS PARALLELIZED.

A compilation of the example C program gives the following output when successful (also Intel):

	$ icc -openmp omp_hello.c -o omp_hello
	omp_hello.c(15): (col. 1) remark: OpenMP DEFINED REGION WAS PARALLELIZED.
	$

Note that in general, neither GNU nor PGI compilers will output anything for a successful compilation.

Compiling MPI Programs

Compilers for C, C++, and versions of Fortran are available. To see a Fortran 77 program with MPI commands: hello77.f. To see a C program with MPI commands: hello.c. See the table below for how to compile your program. Any compiler flags accepted by ifort/icc compilers, can be used with mpif77/mpicc.

Language	Command Example (Intel, GNU, PGI)
C	mpicc program.c -o program
C++	mpiCC program.C -o program
Fortran 77	mpif77 program.f -o program
Fortran 90	mpif90 program.f -o program

Compiling a Fortran 90 MPI program gives no output when successful:

	$ module load mpich2-intel
	$ mpif90 hello.f90 -o hello
	$

A compilation of a C MPI program gives no output when successful:

	$ mpicc hello.c -o hello
	$

Note that in general, neither Intel, GNU, or PGI compilers will output anything for a successful compilation.

Compiling Hybrid Programs

Compilers for C, C++, and versions of Fortran are available. To see a hybrid C++ program with OpenMP/MPI commands: hybrid.cpp. See the table below for how to compile your hybrid (OpenMP/MPI) program. Any compiler flags accepted by ifort/icc compilers, can be used with OpenMP.

Language	Command example, Intel	Command example, GNU	Command example, PGI
C	mpicc -openmp program.c -o program	mpicc -fopenmp program.c -o program	mpicc -mp program.c -o program
C++	mpiCC -openmp program.C -o program	mpiCC -fopenmp program.C -o program	mpiCC -mp program.C -o program
Fortran 77	mpif77 -openmp program.f -o program	-	mpif77 -mp program.f -o program
Fortran 90	mpif90 -openmp program.f -o program	mpif90 -fopenmp program.f -o program	mpif90 -mp program.f -o program

Example: (Compiling the C++ program mentioned above)

	$ module load mpich2-intel
	$ mpiCC -openmp hybrid.cpp -o hybrid
	hybrid.cpp(73): (col. 30) remark: OpenMP DEFINED LOOP WAS PARALLELIZED.
	hybrid.cpp(73): (col. 30) remark: OpenMP DEFINED REGION WAS PARALLELIZED.
	hybrid.cpp(34): (col. 3) remark: OpenMP DEFINED LOOP WAS PARALLELIZED.
	hybrid.cpp(25): (col. 1) remark: OpenMP DEFINED REGION WAS PARALLELIZED.
	$

Provided Libraries

Some libraries are preinstalled for use on Brutus. These may include parallel communications libraries as well as mathematical libraries. More detailed documentation on the libraries available on Brutus follows.

MPICH Library

MPICH2 (and MPICH) is available for some compiler combinations on Brutus. Refer to the compilers section for an overview of how to link in MPICH2 support. Here are some more documentation from other sources on the MPICH2 and MPICH libraries:

Intel Math Kernel Library (MKL)

Intel Math Kernel Library (MKL) contains ScaLAPACK, LAPACK, Sparse Solver, BLAS, Sparse BLAS, CBLAS, GMP, FFTs, DFTs, VSL, VML, and Interval Arithmetic routines. MKL can be found in the directory "/opt/intel/mkl/9.1" and it is divided into the following subdirectory structure:

lib/32 – Libraries for 32-bit Applications
- libmkl_ia32.a – Optimized Kernels (BLAS, CBLAS, Sparse BLAS, GMP, FFTs, DFTs, VML, VSL, Interval Arithmetic)
- libmkl_lapack.a – LAPACK Routines
- libmkl_lapack95.a – LAPACK95 Interface (libmkl_lapack.a also required)
- libmkl_solver.a – Sparse Solver Routines
- libguide.a – Threading Library for Static Linking
lib/em64t – Libraries for Intel EM64T Applications
- libmkl_em64t.a – Optimized Kernels (BLAS, CBLAS, Sparse BLAS, GMP, FFTs, DFTs, VML, VSL, Interval Arithmetic)
- libmkl_lapack.a – LAPACK Routines
- libmkl_lapack95.a – LAPACK95 Interface (libmkl_lapack.a also required)
- libmkl_solver.a – Sparse Solver Routines
- libguide.a – Threading Library for Static Linking
lib/64 – Libraries for Itanium 2 Applications
- libmkl_ipf.a – Optimized Kernels (BLAS, CBLAS, Sparse BLAS, GMP, FFTs, DFTs, VML, VSL, Interval Arithmetic)
- libmkl_lapack.a – LAPACK Routines
- libmkl_lapack95.a – LAPACK95 Interface (libmkl_lapack.a also required)
- libmkl_solver.a – Sparse Solver Routines
- libguide.a – Threading Library for Static Linking

Here are some example combinations of linking options:

  (static linking of LAPACK and Kernels)
$ <fortran_compiler> myprogram.f -L${MKLPATH} -lmkl_lapack -lmkl_ia32 -lguide -lpthread

  (static linking of Fortran-95 LAPACK Interface and Kernels)
$ <fortran_compiler> myprogram.f95 -L${MKLPATH} -lmkl_lapack95 -lmkl_lapack -lmkl_ia32 -lguide -lpthread

  (static linking of BLAS, Sparse BLAS, GMP, VML/VSL, Interval Arithmetic, and FFT/DFT)
$ <c_compiler> myprogram.c -L${MKLPATH} -lmkl_ia32 -lguide -lpthread -lm

  (dynamic linking of BLAS or FFTs)
$ <c_compiler> myprogram.c -L${MKLPATH} -lmkl -lguide -lpthread

It is recommended that you use dynamic linking of libguide. If so, ensure LD_LIBRARY_PATH is defined such that the correct version of libguide is found and used at run time. If you use static linking of libguide (discouraged), then:

If you use the Intel compilers, link in the libguide version that comes with the compiler (use the -openmp option).
If you do not use the Intel compilers, link in the libguide version that comes with the Intel MKL above.

Here are some more documentation from other sources on the Intel MKL:

Using cpp with Fortran

If the source file ends with .F, .fpp, or .FPP, it is automatically preprocessed by cpp before it is compiled. If you want to use the C preprocessor with source files that do not end with .F, use the following compiler option to specify the filename suffix:

GNU: -x f77-cpp-input

  Note that the preprocessing is not extended to the contents of 
  files included by the "INCLUDE" directive - the #include 
  preprocessor directive must be used instead.

For example, to preprocess source files that end with .f:

    gfortran -x f77-cpp-input program.f

Intel: -cpp

  To tell the compiler to link using C++ runtime libraries 
  included with gcc/icc, use -cxxlib -gcc/-cxxlib -icc.

For example, to preprocess source files that end with .f:

    ifort -cpp program.f

Generally, it is best to rename the file from <name>.f to <name>.F. The preprocessor will then be run automatically when the file is compiled.

A good page to look at for combining C/C++ and Fortran, is Using C/C++ and Fortran together.

Calling Fortran from C/C++

When calling your own Fortran routines from C/C++, you should not append an underscore (_) after the name.

A complete list of routines is in the XL Fortran Language Reference Manual.

Here are some links to pages that discuss how to use Fortran from C/C++:

Running Jobs on Brutus

There are a number of different compilers and programs installed on the RCAC systems. To access them, use module load <program>. To see the available modules, type module avail. To read more about the "module" command, look here.

The Brutus cluster is a part of BoilerGrid. To submit jobs to it, you may submit serial jobs to BoilerGrid and specifically request that the serial jobs be run on Brutus.

Running Jobs via Condor

Condor allows users to run jobs on systems which would otherwise be idle for however long as those systems are not needed by their primary users. Condor is one of several distributed computing systems RCAC makes available. Most RCAC resources, in addition to being available through normal means, are a part of BoilerGrid and can be used via Condor. If a primary user needs a machine, the Condor job is immediately either checkpointed and/or migrated and the resource made available. Thus, shorter jobs will have a better completion rate via Condor than longer jobs; however, even though jobs may have to be restarted elsewhere, BoilerGrid can offer a vast amount of computational resources to users. Not only are nearly all RCAC systems part of BoilerGrid, so also are large numbers of lab machines at the West Lafayette and other Purdue campuses. BoilerGrid is one of the largest Condor pools in the world. Some machines at other institutions are also a part of a larger Condor federation known as DiaGrid and can be used as well. For more information, refer to the BoilerGrid documentation.

Brutus Condor Tips

Example

This is an example of submitting a job that matches the specifics of the Brutus portion of BoilerGrid. The job submission file queues the program foo which has been compiled and linked for Brutus first. This job requires Condor to run the program only on systems like Brutus. A log file containing entries about when and where Condor runs, checkpoints, and migrates processes for the queued program will be written into file foo.log.

	# Basic parameters required for FPGA use:
	Universe = vanilla
	Requirements = Arch=="IA64" && ClusterName=="FPGA"
	#
	# ONLY if running through TeraGrid - uncomment the +TGProject = ... line 
	# Replace this with your TeraGrid allocation account number:
	# +TGProject = "TG-XXXXXXXXXX"
	#
	# Executable and arguments:
	Executable = foo
	#Arguments = if any, uncomment and replace here
	#
	# Stdout, stderr and Condor log:
	Output = foo.out
	Error = foo.err
	Log = foo.log
	#
	# Other Condor options:
	Getenv = true
	Transfer_executable = false
	Should_transfer_files = Never
	Notification = never
	#
	Queue

Brutus Frequently Asked Questions (FAQ)

There are currently no FAQs for Brutus.

Brutus Info