Using the Wisconsin Undergraduate Research Cluster(WURC)

From UW-Math Wiki
Revision as of 18:04, 3 February 2020 by Jheim (talk | contribs)
Jump to navigation Jump to search

Wisconsin Undergraduate Research Cluster

The Wisconsin Undergraduate Research Cluster is a high-performance parallel computing cluster for use by undergraduates for research. It consists of a cluster of computers on a local area network with identical software allowing processing to be shared among them. This is known as a beowulf cluster.

Operating System

The operating system on the WURC is currently Ubuntu 19.10, Eoan Ermine.

Available Software

The following is a list of some of the major commercial and open-source software packages and tools available on the WURC. This list is necessarily incomplete as the WURC has hundreds of Ubuntu packages installed. When in doubt, the user is encouraged to simply try a command to see if it is already installed. To request additional software, please contact your instructor.

Compilers and Interpreters

  • Intel C++
  • Intel Fortran
  • g++
  • gfortran
  • python (2.7 and 3)
  • perl

Mathematical Packages

  • Bertini2
  • Gap
  • Macaulay2
  • Magma
  • Maple
  • Mathematica
  • Matlab
  • Octave
  • Sage

Connecting

To connect to the WURC, a user must have the following:

  1. A valid University Of Wisconsin-Madison netid and password
  2. A network connection on a University Of Wisconsin-Madison network (including Eduroam and WiscVPN)

Connecting With ssh

Secure Shell (ssh) is a cryptographic network protocol for secure remote login and command execution. Implementations of clients for ssh are available in Windows, Macintosh OSX, and Linux.

  • Windows

Windows 10 has a built-in, optional ssh client. To install it, do the following:

  1. Click Settings or press Windows+i to open the Settings app.
  2. Click 'Apps'
  3. Select 'Manage optional features'
  4. Click the 'Add a Feature' button.
  5. From the list of features, select 'Openssh Client' and click the Install button.

Note that the Openssh Client will not appear on the list if it is already installed. Once the openssh client is installed, you can open a command window and simply type, "ssh <netid>@wurc.math.wisc.edu". The first time you connect, you will be asked to accept the server key. Type yes to accept the key. This message will not appear the next time you connect from the same computer. If it does, consult your instructor. You will then be prompted to enter your netid password.

The University of Wisconsin-Madison provides no-charge software through our Campus Software Library. Among the offerings are SecureCRT, a secure login client, and SecureFX, a secure file transfer client. These programs provide a more feature-rich environment than the built-in Windows client. To use SecureCRT and SecureFX, log into the Campus Software Library with your netid and password and follow the instructions for installing SecureCRT and SecureFX. Questions on installing SecureCRT and SecureFX should be directed to the DoIT Help Desk.

Once you have SecureCRT installed, you can connect to the WURC by clicking on quick connect and entering wurc.math.wisc.edu as the host name and your netid as the user name. Change the authentication to password. Do not change any other settings. Enter your netid password when prompted.

  • Macintosh OSX:

Macintosh OSX has built-in ssh and sftp clients. To use these tools, do the following:

  1. Switch to a Finder window and open the Utilities folder. The shortcut key to open the Utilities folder is Command+Shift+u.
  2. Click on the Terminal app.
  3. In the terminal window, type "ssh <netid>@wurc.math.wisc.edu".
  4. The first time you connect, you will be prompted to accept the server key. Type "yes" to accept the key.
  5. You will be prompted to enter a password. Enter your netid password.

The University of Wisconsin-Madison Campus Software Library has versions of SecureCRT and SecureFX for Mac OSX Questions on installing SecureCRT and SecureFX should be directed to the DoIT Help Desk.

Once you have SecureCRT installed, you can connect to the WURC by clicking on quick connect and entering wurc.math.wisc.edu as the host name and your netid as the user name. Change the authentication to password. Do not change any other settings. Enter your netid password when prompted.

  • Linux:

Linux has built-in ssh and sftp clients. Most linux distrabutions will install the openssh client by default. If ssh and sftp are not installed on your Linux system, you can install them by doing the following:

  • Red Hat: sudo yum -y install openssh-client
  • Debian and Ubuntu: sudo apt-get -y install openssh-client

To connect to the WURC from a Linux computer using ssh, do the following:

  1. Open a terminal window by pressing Alt+Super+t
  2. Type, "ssh &ltnetid&lt>@wurc.math.wisc.edu"
  3. The first time you connect, you will be prompted to accept the server key. Type "yes" to accept the key.
  4. You will then be prompted for a password. Enter your UW netid password.

Using ssh keys

Public key authentication is a way of logging into an ssh server using a cryptographic key pair instead of a password. Besides being convenient, using an ssh key pair makes it impossible for someone to steal your password by looking over your shoulder or by using a key logger. If you frequently use a public computer, in a library for example, you should consider using an ssh key pair for authentication to the WURC. Even if you never use a public computer, you may consider using an ssh key pair just for the convenience.

To begin using an ssh key pair, do the following:

  1. Log onto the WURC as usual with your netid and paswsword.
  2. Type "ssh-keygen". We recommend that you accept the defaults for the type of key and the location. You may add a passphrase to the ssh key although that will make it less convenient to use.If you accepted the defaults, a public/private key pair will be generated in the .ssh folder.
  3. Change to the .ssh folder, "cd .ssh".
  4. Create a file called authorized_keys by copying the file id_rsa.pub to it, "cp id_rsa.pub authorized_keys".
  5. Log out of the WURC by typing, "exit".
  6. Copy the key pair you just generated back into the .ssh folder on your local machine. The next few steps should be the same for Windows, Mac OSX, and Linux.
  7. Change to the .ssh subfolder, "cd .ssh".
  8. Connect to the WURC via sftp, "sftp <netid>@wurc.math.wisc.edu". You will still have to enter your netid password at this point.
  9. Copy the key pair back to your local machine, "get .ssh/id_rsa*".
  10. Exit sftp by typing exit. You should now be able to connect to the WURC via either ssh or sftp without retyping your password.

Using sftp

Sshfs allows you to mount your home folder on the WURC as a network drive on your local machine. This, in turn, allows you to use an IDE (integrated development environment) or text editor on your local machine to develop your code. The alternative is to use a text editor like emacs or vi on the WURC to edit your code or to edit the code on your local machine and copy it to the WURC after each change. Using sshfs and an IDE is much more efficient and will greatly increase your productivity.

Sshfs clients are available for all three major operating systems, Windows, Mac OSX, and Linux.

  • Windows
  1. Install winfsp.
  2. Install sshfs-win.
  3. In Windows Explorer select "This PC" then select "Map Network Drive". Enter the preferred drive letter and path, "\\sshfs\<netid>@wurc.math.wisc.edu".
  4. Alternately, in the Windows command shell, you can use the "net use" command to map the drive. Open a command window and type, "net use W: \\sshfs\<netid>@wurc.math.wisc.edu".


  • Macintosh OSX
  • Linux
  1. Install sshfs from the package repository for your Linux distro.
    1. Red Hat: "yum install sshfs"
    2. Debian/Ubuntu: "apt-get install sshfs"
  2. Create a mount point for the network drive, "mkdir wurc".
  3. Mount the network drive, "sshfs <netid>@wurc.math.wisc.edu ./wurc".

Wisconsin Undergraduate Research Cluster

The Wisconsin Undergraduate Research Cluster is a high-performance parallel computing cluster for use by undergraduates for research. It consists of a cluster of computers on a local area network with identical software allowing processing to be shared among them. This is known as a beowulf cluster.

Operating System

The operating system on the WURC is currently Ubuntu 19.10, Eoan Ermine.

Available Software

The following is a list of some of the major commercial and open-source software packages and tools available on the WURC. This list is necessarily incomplete as the WURC has hundreds of Ubuntu packages installed. When in doubt, the user is encouraged to simply try a command to see if it is already installed. To request additional software, please contact your instructor.

Compilers and Interpreters

  • Intel C++
  • Intel Fortran
  • g++
  • gfortran
  • python (2.7 and 3)
  • perl

Mathematical Packages

  • Bertini2
  • Gap
  • Macaulay2
  • Magma
  • Maple
  • Mathematica
  • Matlab
  • Octave
  • Sage

Connecting

To connect to the WURC, a user must have the following:

  1. A valid University Of Wisconsin-Madison netid and password
  2. A network connection on a University Of Wisconsin-Madison network (including Eduroam and WiscVPN)

Connecting With ssh

Secure Shell (ssh) is a cryptographic network protocol for secure remote login and command execution. Implementations of clients for ssh are available in Windows, Macintosh OSX, and Linux.

  • Windows

Windows 10 has a built-in, optional ssh client. To install it, do the following:

  1. Click Settings or press Windows+i to open the Settings app.
  2. Click 'Apps'
  3. Select 'Manage optional features'
  4. Click the 'Add a Feature' button.
  5. From the list of features, select 'Openssh Client' and click the Install button.

Note that the Openssh Client will not appear on the list if it is already installed. Once the openssh client is installed, you can open a command window and simply type, "ssh <netid>@wurc.math.wisc.edu". The first time you connect, you will be asked to accept the server key. Type yes to accept the key. This message will not appear the next time you connect from the same computer. If it does, consult your instructor. You will then be prompted to enter your netid password.

The University of Wisconsin-Madison provides no-charge software through our Campus Software Library. Among the offerings are SecureCRT, a secure login client, and SecureFX, a secure file transfer client. These programs provide a more feature-rich environment than the built-in Windows client. To use SecureCRT and SecureFX, log into the Campus Software Library with your netid and password and follow the instructions for installing SecureCRT and SecureFX. Questions on installing SecureCRT and SecureFX should be directed to the DoIT Help Desk.

Once you have SecureCRT installed, you can connect to the WURC by clicking on quick connect and entering wurc.math.wisc.edu as the host name and your netid as the user name. Change the authentication to password. Do not change any other settings. Enter your netid password when prompted.

  • Macintosh OSX:

Macintosh OSX has built-in ssh and sftp clients. To use these tools, do the following:

  1. Switch to a Finder window and open the Utilities folder. The shortcut key to open the Utilities folder is Command+Shift+u.
  2. Click on the Terminal app.
  3. In the terminal window, type "ssh <netid>@wurc.math.wisc.edu".
  4. The first time you connect, you will be prompted to accept the server key. Type "yes" to accept the key.
  5. You will be prompted to enter a password. Enter your netid password.

The University of Wisconsin-Madison Campus Software Library has versions of SecureCRT and SecureFX for Mac OSX Questions on installing SecureCRT and SecureFX should be directed to the DoIT Help Desk.

Once you have SecureCRT installed, you can connect to the WURC by clicking on quick connect and entering wurc.math.wisc.edu as the host name and your netid as the user name. Change the authentication to password. Do not change any other settings. Enter your netid password when prompted.

  • Linux:

Linux has built-in ssh and sftp clients. Most linux distrabutions will install the openssh client by default. If ssh and sftp are not installed on your Linux system, you can install them by doing the following:

  • Red Hat: sudo yum -y install openssh-client
  • Debian and Ubuntu: sudo apt-get -y install openssh-client

To connect to the WURC from a Linux computer using ssh, do the following:

  1. Open a terminal window by pressing Alt+Super+t
  2. Type, "ssh &ltnetid&lt>@wurc.math.wisc.edu"
  3. The first time you connect, you will be prompted to accept the server key. Type "yes" to accept the key.
  4. You will then be prompted for a password. Enter your UW netid password.

Using ssh keys

Public key authentication is a way of logging into an ssh server using a cryptographic key pair instead of a password. Besides being convenient, using an ssh key pair makes it impossible for someone to steal your password by looking over your shoulder or by using a key logger. If you frequently use a public computer, in a library for example, you should consider using an ssh key pair for authentication to the WURC. Even if you never use a public computer, you may consider using an ssh key pair just for the convenience.

To begin using an ssh key pair, do the following:

  1. Log onto the WURC as usual with your netid and paswsword.
  2. Type "ssh-keygen". We recommend that you accept the defaults for the type of key and the location. You may add a passphrase to the ssh key although that will make it less convenient to use.If you accepted the defaults, a public/private key pair will be generated in the .ssh folder.
  3. Change to the .ssh folder, "cd .ssh".
  4. Create a file called authorized_keys by copying the file id_rsa.pub to it, "cp id_rsa.pub authorized_keys".
  5. Log out of the WURC by typing, "exit".
  6. Copy the key pair you just generated back into the .ssh folder on your local machine. The next few steps should be the same for Windows, Mac OSX, and Linux.
  7. Change to the .ssh subfolder, "cd .ssh".
  8. Connect to the WURC via sftp, "sftp <netid>@wurc.math.wisc.edu". You will still have to enter your netid password at this point.
  9. Copy the key pair back to your local machine, "get .ssh/id_rsa*".
  10. Exit sftp by typing exit. You should now be able to connect to the WURC via either ssh or sftp without retyping your password.

Using sftp

Sshfs allows you to mount your home folder on the WURC as a network drive on your local machine. This, in turn, allows you to use an IDE (integrated development environment) or text editor on your local machine to develop your code. The alternative is to use a text editor like emacs or vi on the WURC to edit your code or to edit the code on your local machine and copy it to the WURC after each change. Using sshfs and an IDE is much more efficient and will greatly increase your productivity.

Sshfs clients are available for all three major operating systems, Windows, Mac OSX, and Linux.

  • Windows
  1. Install winfsp.
  2. Install sshfs-win.
  3. In Windows Explorer select "This PC" then select "Map Network Drive". Enter the preferred drive letter and path, "\\sshfs\<lt;netid&gt>@wurc.math.wisc.edu".
  4. Alternately, in the Windows command shell, you can use the "net use" command to map the drive. Open a command window and type, "net use W: \\sshfs\<lt;netid>@wurc.math.wisc.edu".
Retrieved from "https://wiki.math.wisc.edu/index.php?title=Using_the_Wisconsin_Undergraduate_Research_Cluster(WURC)&oldid=18876"