Harvard-MIT Data Center

We strive to make the RCE as useful to all users as possible. 

If you cannot find an application you need or require additional tools or resources, please contact us and we will be happy to assist you however we can.

You can access HMDC-managed systems from your desktop workstation, from workstations in the public labs, or from workstations outside the Harvard network, by means of our robust and secure remote access service.

One advantage of our remote access service is that user sessions can be suspended and resumed at will; this means that you can begin a session from an office workstation, suspend it, move to a lab workstation and resume the previous session, suspend it again, and then move to a home computer and resume the same session, all with no disruption of your environment. During this time the location and contents of windows remains consistent, processes and applications run without interruption, and any interface customizations remain in effect.

Our remote access service provides a familiar, consistent user experience to all HMDC affiliates. Since the RCE is built on open standards and does not require specialized or proprietary software, you can access the full Research Computing Environment from any modern workstation with a graphical user interface and a high-speed internet connection.

Remote access provides three categories of services:

• Research Environment (graphical desktop)
• Secure Shell (command-line tools)
• File Access (home directory)

Guide Overview

This guide describes how to access the Research Computing Environment (RCE) through a secure network connection. Refer to the guide Working in the RCE Summer 2009 for information about how to use the desktop applications, tools, and utilities after you connect. For information about how to exit from the RCE, see Exiting the RCE.

You use the NX Client application to connect to the RCE from a Windows, MacOS, or Linux workstation. The NX Client is available free of charge from NoMachine, a division of Medialogic S.p.A., at the following web site:

http://www.nomachine.com/download.php

Note: Before you connect to the RCE, read Setting Your Password.

Guide Overview

This guide provides information about basic features and functions that might be useful when you begin working within the RCE. The RCE supports the following applications, tools, and utilities described in this guide:

• Basics - Mouse conventions, workspaces, menus, directories, window sizing, terminal windows
• General office applications - Writer, Impress, Calc
• The emacs editor - Tutorial links, LaTeX documents and rendering
• Files - Transferring and printing
• Maintenance - Terminating, modifying ownership, changing passwords and shells, and more 

Before you can use any of the applications and tools available in the RCE, you must connect to the RCE successfully. Refer to the guide Connecting to the RCE Summer 2009 for detailed information.

Guide Overview

This is an historical guide that describes how to access the Research Computing Environment (RCE) through a legacy secure network connection. A newer version of this guide is available from this web site's Accessing the RCE menu option.

Refer to the guide Working in the RCE Summer 2009 for information about how to use the desktop applications, tools, and utilities after you connect.

You can use the Easy Connection script if you connect:

• From a system that operates on a minimum of Windows version 2000
• To any server running the RCE

You can connect manually to the RCE if you use a Mac OS or Linux workstation. Before you connect to the RCE, read Setting Your Password in the guide Connecting to the RCE Summer 2009.

Note: If you connect to the RCE from a public machine, read Security Issues for Public Machines.

The RCE offers tools for development of new R packages or other software development projects. Our tools include Concurrent Versioning System (CVS) tools designed specifically for use in the RCE, and automated tools that support R package builds.

Guide Overview

This guide helps you to use the Concurrent Versions System (CVS) version control system to record and track files and their changes in the RCE. (See CVS Basics for general information.) CVS enables you to collaborate on the use and management of source files among multiple users. Information included in this guide consists of:

• Setting up to use CVS
• Updating files from a repository
• Committing (saving) files to a repository
• Adding files to and removing files from a repository
• Working with CVS on the command line

Note: Before you can use CVS, you must connect successfully to the RCE. Refer to Connecting to the RCE Summer 2009 for detailed information about how to connect.

Guide Overview

We provide tools within the RCE that streamline common CVS commands and recommend that you use these tools from within your RCE session, particularly if you are unfamiliar with CVS. To learn more about our CVS workflow, please read Working with CVS in the RCE Summer 2009.

This guide is a reference for advanced users or for those who cannot make use of the RCE. It describes the following types of commands:

• Core CVS commands
• RCE-specific commands
• Specialized commands

Guide Overview

The program rbuild.pl propagates R package updates to a web site for public consumption. This guide describes rbuild in detail, including how it works and how to use the following features:

• Paths
• Configuration
• Notification
• Temporary files
• Lockfiles and errors
• Updates and forced rebuilds
• Bugfix builds
• Version numbers
• Options
• Text replacement

For questions, problems, or feature upgrades, contact us.

These topics introduce you to the statistical applications that are available in the RCE. For each of the following applications, this section describes how to launch and exit from the menus and from the command prompt, how to access help, and how to install new components:

• R
• GAUSS
• Mathematica
• MATLAB
• Octave
• SAS
• S-PLUS
• Stata and State/SE
• RCE Powered applications

The section Implementation Details provides general information about the implementation of statistical applications in the RCE, including where to find out more about these tools.

For information about how to access the RCE, refer to Connecting to the RCE Summer 2009.

Note: These topics define directory and path names that refer to the current version of applications installed in the RCE at the time of publishing. When applications are updated or modified, these names might change to reflect different version numbers.

This section describes basic activities that you perform in the R statistical application as it is implemented in the RCE. It includes information about how to perform the following:

• Launch and exit from the menus and from the command prompt
• Access help
• Install new components

See Implementation Details for general information about the implementation of R in the RCE, including where to find out more about the tool.

For information about how to access the RCE, refer to Connecting to the RCE Summer 2009.

This section describes basic activities that you perform in the GAUSS statistical application as it is implemented in the RCE. It includes information about how to perform the following:

• Launch and exit from the menus and from the command prompt
• Access help
• Install new components

See Implementation Details for general information about the implementation of GAUSS in the RCE, including where to find out more about the tool.

For information about how to access the RCE, refer to Connecting to the RCE Summer 2009.

This section describes basic activities that you perform in the Mathematica statistical application as it is implemented in the RCE. It includes information about how to perform the following:

• Launch and exit from the menus and from the command prompt
• Access help
• Install new components

See Implementation Details for general information about the implementation of Mathematica in the RCE, including where to find out more about the tool.

For information about how to access the RCE, refer to Connecting to the RCE Summer 2009.

This section describes basic activities that you perform in the MATLAB statistical application as it is implemented in the RCE. It includes information about how to perform the following:

• Launch and exit from the menus and from the command prompt
• Access help
• Install new components

See Implementation Details for general information about the implementation of MATLAB in the RCE, including where to find out more about the tool.

For information about how to access the RCE, refer to Connecting to the RCE Summer 2009.

This section describes basic activities that you perform in the Octave statistical application as it is implemented in the RCE. It includes information about how to perform the following:

• Launch and exit from the menus and from the command prompt
• Access help
• Install new components

See Implementation Details for general information about the implementation of Octave in the RCE, including where to find out more about the tool.

For information about how to access the RCE, refer to Connecting to the RCE Summer 2009.

This section describes basic activities that you perform in the SAS statistical application as it is implemented in the RCE. It includes information about how to perform the following:

• Launch and exit from the menus and from the command prompt
• Access help
• Install new components

See Implementation Details for general information about the implementation of SAS in the RCE, including where to find out more about the tool.

For information about how to access the RCE, refer to Connecting to the RCE Summer 2009.

Information provided in this section describes basic activities that you perform in the S-PLUS 7 statistical application as it is implemented in the RCE.

S-PLUS is an S language tool that is useful for the graphical and statistical analysis of data. The version of S-PLUS 7 installed in the RCE is the Enterprise Developer tool, which includes the S-PLUS Workbench and the Big Data library. The Big Data library provides objects, classes, and functions for use with large data sets.

In S-PLUS, a library is a directory that must contain a .Data directory and can contain other objects, commands, functions, scripts, and files.

This section describes basic activities that you perform in the S-PLUS statistical application as it is implemented in the RCE. It includes information about how to perform the following:

• Launch and exit from the menus and from the command prompt
• Access help
• Install new components

See Implementation Details for general information about the implementation of S-PLUS in the RCE, including where to find out more about the tool.

For information about how to access the RCE, refer to Connecting to the RCE Summer 2009.

This section describes basic activities that you perform in the Stata statistical applications as they are implemented in the RCE. It includes information about how to perform the following:

• Launch and exit from the menus and from the command prompt
• Access help
• Install new components

See Implementation Details for general information about the implementation of Stata in the RCE, including where to find out more about the tool.

For information about how to access the RCE, refer to Connecting to the RCE Summer 2009.

The Applications menu in the RCE includes the statistical applications on two submenus: Mathematics and RCE Powered Applications. The only difference between options on these menus is that the RCE Powered Applications version launches the tool on a batch server in the RCE. All other aspects of these applications are the same no matter how you launch them.

This section describes general information about the statistical applications available for use in the RCE, including the following:

• Description of statistical applications available
• Availability of application components
• Locating support documentation for applications
• Default working directory in the RCE

The Summer 09 update for the RCE provides new functionality, including a new access mechanism and updated documentation.  Please see Connecting to the RCE Summer 2009 for information about how to connect to the RCE using the NX protocol.

We are excited to offer a new tool and method for connecting to the RCE.  The NX protocol is an open protocol with client viewers that offer a consistent interface across the Mac, Windows, and Linux platforms.

Unlike the VNC protocol, there is no need to establish a secure tunneled connection. The NoMachine NX client (a free download from the NoMachine wesbite) handles all of this for you.  You simply have to enter your username and password to establish a secure connection to the RCE.

NX client comes with other benefits, including dynamic resizing of your session window, better handling of slower connections, and more.

Future RCE updates will deprecate the use of VNC and will support only NX client connections, and we encourage you to start using the NX client now. Please contact us if you encounter any issues.  For information on connecting to the RCE with NX client, refer to the guide Connecting to the RCE Summer 2009.

By popular demand, we have reviewed our cluster scheduler and have made numerous updates to ensure a more even and fair distribution of resources.

Users should now see faster service times even if the cluster is 100% utilized thanks to our new scheduler algorithms, which take into account historical usage and current runtime of jobs on the cluster.

Please see Getting Started with Batch Processing Summer 2009 for more information about how to use our batch cluster.

Several new options were added to the Applications menu, located in the upper-left corner of your RCE desktop. These items include the following:

• Documentation - Links to updated documentation available on this site.
• RCE Powered Applications - Scripts are included that enable our statistical applications to use the power of our cluster computing in an interactive, real-time mode. Select one of these options to run an interactive job that has sizeable requirements of memory, processing power, or storage.
• RCE Utilities - A graphical, user-friendly utility facilitates several common tasks, such as changing your shell, checking out CVS repositories, or checking for updates to the RCE.

For more information, see Connecting to the RCE Summer 2009 and Using Statistical Programs.

We updated our CVS utilities, and you now can access them via the contextual menu in the file system browser.

A Scripts submenu is available when you use the desktop background right-click menu. From the Scripts option, select CVS to locate utilities that automate common CVS tasks. For example, to add files to a CVS repository:

1. Navigate to the files that you choose to add to CVS by using your file browser.
2. Right-click your files, select Scripts, select CVS, and then choose Add Files.
   Your files are added to your CVS repository.

More information can be found in Working with CVS in the RCE Summer 2009.

New channels of communication were added that improve your ability to be made aware of scheduled downtimes or other interruptions in service.

For more information, see Outage Notification.

With the release of RCE Summer 2009, HMDC/IQSS held a workshop which covered:

1. Overview of RCE services/resources
2. Overview of batch submission
3. Updates avaiable in RCE Summer 2009

PDF versions of the slides used during the workshop are available via the following links:

• RCE_Workshop_-_RCE_Overview.pdf
• RCE_Workshop_-_Batch_Processing.pdf
• RCE_Workshop_-_Summer_2009.pdf

File(s): 

RCE_Workshop_-_Batch_Processing.pdf

RCE_Workshop_-_RCE_Overview.pdf

RCE_Workshop_-_Summer_2009.pdf

To configure your user account such that every time you connect to the RCE, some action is performed:

1. Write a script that performs the desired action. The scripting languages available in the RCE include the Bourne Again shell (/bin/bash) and Perl (/usr/bin/perl).
2. Copy this script to the directory ~/.rce/startup with the command cp <scriptname> ~/.rce/startup/.
   If the directory does not exist, create it with the command mkdir -p ~/.rce/startup.
3. Make sure the permissions on your script permit execution; to ensure that this is the case, run the command chmod +x ~/.rce/startup/<scriptname>.
   Your script is run every time you connect to the RCE.

Note: Be sure to test your script; a misbehaving script can prevent you from being able to connect to the RCE! In particular, your script must not require any keyboard input or other interaction with the user; it will not be able to communicate with you while it is running, and you will not be able to connect to the RCE while your script sits waiting for input.

When you first are assigned an RCE account, you receive an email that directs you to set your password. You must log in, set a password, and complete the account contact form before you can use any HMDC server function.

This section describes in detail how to set your password and account contact information for an HMDC RCE account, HMDC CGIS account, or HMDC email account.

1. If you have never set a password before and are activating a new RCE account, open the new RCE account email that was sent to you and click the link to set your password and activate your account.

2. If you are changing a password, go to the HMDC Account Self Service web site and log in with your username and current password.

   The HMDC Account Self Service web site is displayed. Any terms followed by a ^? can be defined by clicking the ^?.

   

   The Account Access field displays the RCE cluster hostname to which you have access, if any.

3. If you logged in to the HMDC Account Self Service web site with your HMDC RCE account username and password and your HMDC RCE account is not linked to an HMDC CGIS or Mail Account, then the Linkages section is displayed, allowing you to link accounts so that the contact information and password for the accounts are updated simultaneously.

   

4. You must complete the following contact information:

   • Contact Name - Make sure that your username is correct.

   • Office Location - Type an office room number in which you can be contacted.

   • Phone Number - Type a phone number at which you can be contacted.

   • Email Address - Make sure that your email address is correct.

     

5. You must set your password.

   In the Enter Password and Retype Password fields, enter a new password that complies with the following guidelines:

   • Is between 8 and 15 characters

   • Does not include a term found in a standard dictionary

   • Has at least two numbers

   • Has at least two special characters

6. Click Save Changes to enter your contact information and set your password.

   If you entered contact information and a new password that complies with the strong password guidelines, the message Modification successful: password changed. is displayed.

   

   If you do not enter a new password that complies with the guidelines, a Modification failed error message is displayed. You must enter a new password in both password fields, and then click Save Changes again.

   

7. After you successfully set your password, you will automatically be logged out of the HMDC Account Self Service web site.

   If you are setting a password for the first time, you will receive two emails after you complete the set password process. First, you receive an automated account manager reply acknowledging that your password entry was successful. Second, you receive a new RCE account email acknowledging that you activated your RCE account. This email specifies the server hostname to use when you log in to the RCE, corresponding to the Account Access information in HMDC Account Self Service. Be sure to log in to the RCE using your new password.

You can change your contact information and password at any time by using the HMDC Account Self Service web site. Go to the following location:

https://help.hmdc.harvard.edu/account_manager

The easiest way to check your RCE disk quotas is to connect to any server running the RCE and run the quotareport command.  An example of this command is shown below:

$ quotareport

User           Used Mb     Limit Mb  Used %   Volume Description            
juser           248.12       500.00     50%   home directory volume         

--------------------------------------------------------------------------

Group          Used Mb     Limit Mb  Used %   Volume Description            
admin          5319.77    102400.00      5%   research no-backups volume    
users             0.59      5120.00      0%   research no-backups volume    
drupal         2136.46      9500.00     22%   research project volume

The output above shows four disk quotas on three volumes. One is the user's personal home directory quota, and three are group quotas applied to project directory usage

Quotas are allocated as follows: Each project directory is designated a group, and each group has a quota on each volume. Each RCE user also has a separate home directory quota.

Please note that when you move files to your Trash, they count againt your home directory disk quota until you empty your Trash, regardless of where they were moved from

The default window behavior in the RCE uses the focus-follows-mouse model, in which the user selects windows by merely pointing at them, and the selected window jumps to the foreground. This model is familiar to users with a UNIX background; however, it can be confusing and frustrating to users with a Windows or Mac OS background.

Here's the procedure for changing the default window behavior:

1. Connect to the RCE.
   See Connecting to the RCE Summer 2009 for detailed information.
2. From the Applications menu, select Preferences and then choose Windows.
3. Remove the check from the Select windows when the mouse moves over them box.
4. Click Close.

The change takes effect immediately. Your windows now behave in a more Windows-like way; for example, you have to click something to select it.

R supports two primary ways of accessing compressed data. This allows you to keep your data files on disk compressed saving space, and often time (since the file I/O saved by compression is often more expensive than the cpu cycles it uses)

If you are storing your data in native format, simply use the compress option of save:

tst.df=as.data.frame(cbind(1:10,2:11)) # just some testing data
save(tst.df,file="test.Rbin", compress=T) # save a compressed R file

You can use load as normal, to read the compressed files:

load("test.Rbin")

To access any other kind of file with compression, simply use gzfile("") around the file name:

write.table(tst.df,gzfile("test.dat.gz")) # write a compressed file
read.table(gzfile("test.dat.gz"),row.names=1)# read it back in

Files compressed using the gzfile method can also be compressed and uncompressed using the UNIX gzip and gunzip commands (respectively).

We allocate storage to your RCE account in two different ways:

1. Home directory - By default, each RCE account is allotted a certain amount of storage in the home directory. This storage should be sufficient for general-purpose use (email, web browsing, document editing).

2. Project shares - If you require storage above and beyond the initial home directory allocation, or if you need to share your files with other RCE users, we create a project share and grant you access to it. Your project share is accessible via ~/shared_space/<share name>; while it may appear to be part of your home directory, it has its own quota, which will be significantly larger than your home directory's quota. Thus, if you have large files (data sets, job output, etc.) that are too big for your home directory, make sure that they are stored in the appropriate project share under ~/shared_space.

To check your storage utilization, please see "How do I check my RCE disk quota?"

When you copy and paste text between environments, you use the clipboard function.

If you have problems copying and pasting between environments, please try using the Restart Clipboard Sync utility, available from the RCE Utilities menu and then copy again before pasting.

The error Firefox is already running usually indicates that you must remove lock files before you can launch Firefox. For convenience, we offer tools to clean out these lock files from your RCE session.

To resolve this problem:

• If you are working inside the HMDC RCE click the Applications menu, select RCE Utilities, and then choose Clear Firefox Locks or Clear Thunderbird Locks. Then, try launching Firefox or Thunderbird again.
• If you are not working inside the HMDC RCE, type the following command on a command line to delete the Firefox lockfiles:
  

  rm -f ~/.mozilla/firefox/*.default/{lock,.parentlock}

For more information, please see http://kb.mozillazine.org/Profile_in_use or contact us.

To resolve this problem, try the following:

1. Right-click the gray bar at the bottom of your RCE window.
2. Select Add to Panel.
   A pop-up window appears.
3. Select Window List, and then click Add.

This problem is unlikely to occur under normal conditions.