To terminate your NX session from outside an existing NX session:

1. Open a ssh connection to your RCE server (this might be rce.hmdc.harvard.edu, kennedy.fas.harvard.edu, or some other hostname; you received this information when your RCE account was created). See How do I connect to the RCE using SSH? for instructions.

2. Once connected, type the following command: nxcleanup

3. If you have multiple NX sessions running, you will be prompted to select from a list of sessions:

    WARNING: You appear to have more than one NX session running. Please select a session to terminate: Server Session Started 0) rce-2.hmdc.harvard.edu 2010-08-17 13:08:16 1) rce-6.hmdc.harvard.edu 2010-09-29 15:49:17 Choose (0-1): 
   

   Select the desired session and press Return.

4. If your session is on another server, confirm the connection:
   

   Your NX session is not running on this node (rce-5), but on the affiliated node rce-2
   
   Would you like to connect to the node rce-2 to terminate your session there?
   (Enter y or n) [yes]: yes
   
   The authenticity of host 'rce-2.hmdc.harvard.edu (140.247.115.106)' can't be established.
   RSA key fingerprint is ae:6a:fa:31:e2:f1:7d:c6:a0:f8:47:78:7b:d0:bf:cc.
   Are you sure you want to continue connecting (yes/no)? yes

To terminate your NX session from within an existing NX session

1. From the RCE desktop, select Applications–>Accessories–>Terminal.

2. Once your Terminal has opened, type the following command: nxcleanup

3. If you have multiple NX sessions running, you will be prompted to select from a list of sessions:

    WARNING: You appear to have more than one NX session running. Please select a session to terminate: Server Session Started 0) rce-2.hmdc.harvard.edu 2010-08-17 13:08:16 1) rce-6.hmdc.harvard.edu 2010-09-29 15:49:17 Choose (0-1): 
   

   Select the desired session and press Return.

4. If your session is on another server, confirm the connection:
   

   Your NX session is not running on this node (rce-5), but on the affiliated node rce-2
   
   Would you like to connect to the node rce-2 to terminate your session there?
   (Enter y or n) [yes]: yes
   
   The authenticity of host 'rce-2.hmdc.harvard.edu (140.247.115.106)' can't be established.
   RSA key fingerprint is ae:6a:fa:31:e2:f1:7d:c6:a0:f8:47:78:7b:d0:bf:cc.
   Are you sure you want to continue connecting (yes/no)? yes

To reset your RCE password, please visit the HMDC Account Self Service web site and click "Forgot your password?"

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.

   HMDC Account Self Service will only change passwords for accounts that are authenticated. If you log in with your RCE account credentials, your RCE account password will be changed. If you log in with your CGIS account credentials, your CGIS account password will be changed. If you log in with your Mail account credentials, your Mail account password will be changed.

   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 Linkagessection is displayed. This allows you to "link" accounts by providing authentication information for a second account after authenticating your RCE account. When you create account linkages, a password change or contact information change will update all linked accounts 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.

Additional commands to help with quota:

#find all directory sizes, and grep for large ones in M(egabytes) 

rce-4:cperry [~]$ cd ~; du -sh ./* | grep '[0-9]M' | sort -nr | head 3
70M ./Data.dta 
35M ./Data1.dta 
30M ./Data2.dta 
... 

#find all files over 10M 
rce-4:cperry [~]$ find -size +10000 

#mv file to your shared space 
rce-4:cperry [~]$ mv Data1.dta ~/shared_space/<your project share>/ 

#set group ownership to the appropriate group 
rce-4:cperry [~]$ chgrp <your project share> ~/shared_space/<your project share>/Data1.dta 

1. Set up a project space:

   The simplest way to share files with collaborators in the RCE is to use a "project space" which you all have access to.  You can send a support request asking for a "shared project space." Be sure to include the names of your collaborators.

   Once you have a "project space" it will be linked from your RCE home directory under ~/shared_space/ by the name of the project. You may request more than one project space, but limitations on storage allocation apply.

2. Grant your collaborators access to the files you create in the project space:

   By default, when you create files in the RCE, only you can modify them. However, if you are working in a project group, you may want to also grant your collaborators access to modify files you have created. To do so, run the fixGroupPerm.sh script, per the linked instructions for Making files group writeable in your project space.

   You will need to run this script after each time you create files in your shared project space. If you are running a script to create the files (e.g. R code, or a Stata .do file), it may be simplest to add a call to the fixGroupPerms.sh script at the end of your code.

3. Change your default file creation mode (optional):

   If most or all of your work in the RCE is done in collaborative project spaces, you may want to change the default file creation mode (i.e. the file access permissions) for your RCE account so that all files you create can be modified by members of the group which owns them.

   If you decide to pursue this option, two important caveats apply:

   1. This change only affects the default access mode assigned to newly-created files. The application creating the file can override the default to set a more restrictive access mode on the files.

   2. The access mode on the files/directories you create apply to whichever group owns the file/directory, which may or may not be your collaborative group.

   You can run the command ls -l on a file to view its ownership. Group ownership will be displayed in the fourth column.

   If you are creating files under ~/shared_space, then they should automatically be created with ownership by your collaborative group.

   If you create files in your home directory, however, they will be owned by the "users" group and the access permissions (e.g. allow read/write/access by the group) will apply to all RCE users.

   Restricting access to your home directory itself can help limit the impact of such an exposure.

   If you understand and accept these caveats, you can proceed to change your default file creation mode for your RCE account by doing the following:

   1. Open an RCE session.

   2. Run the File Sharing Config Helper by clicking Applications > RCE Utilities > File Sharing Config Helper

   3. Terminate your RCE session and start a new RCE session

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 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.

If the gray bar at the bottom of the RCE window does not respond when clicked, open a terminal window and type the following command:

pkill -HUP gnome-panel

This problem is unlikely to occur under normal conditions.

When running a Stata .do file on the batch cluster via condor_submit_util, you have to add some additional arguments in order to get your job to stop when Stata encounters an unrecoverable error (which is probably the behavior you want).

The command line below runs Stata with the file my_dofile.do:

@condor_submit_util --executable /usr/local/bin/stata-se --arguments '-b <path to your home directory>/my_dofile.do' --noinput

HMDC is not yet officially supporting the use of MacOS 10.7 Lion for connecting to the RCE. Although we hope to add official support in the near future, the latest current release 3.x of the third-party NX remote desktop viewer software used in the RCE does not yet support MacOS 10.7 Lion.

The latest beta prerelease version 4.x of the NX remote desktop viewer software also does not work on Lion with the existing RCE infrastructure.  The work-around is to use OpenNX which can be downloaded from here:  http://opennx.net/. 

* If OpenNX does not work, you will be able to connect if you "ssh -X username@rce.hmdc.harvard.edu" from a Terminal window.   Then launch NX with the command "nxclient".

Please note that some users have reported problems even with OpenNX.  If you have difficulty, please do a software update on your Mac and try again.

At this time, the recommendation from HMDC support is to refrain from upgrading to MacOS 10.7 Lion until we can offer official RCE support.

Please contact HMDC support at support@help.hmdc.harvard.edu for further questions or concerns.

Your RCE account includes a command-line shell which you can access through SSH, in addition to the standard graphical RCE desktop accessible through NX. Refer to Accessing the RCE for instructions on graphical desktop access.

To make an SSH connection to the RCE, follow the instructions below for your operating system (Windows, MacOS, or Linux).

For Windows:

1. Install a secure shell (SSH) client application.

   An SSH client application enables you to set up an SSH tunnel to an RCE server and to use your session securely on that server. HMDC supports use of the SecureCRT application, which is available at the FAS software URL (if you are an FAS affiliate):

   http://downloads.fas.harvard.edu/download

       If you don't have access to fas downloads, you can download and install putty.exe from http://www.chiark.greenend.org.uk/~sgtatham/putty/

1. To configure a new connection to the RCE server, launch the SSH client you installed.

   If you launch SecureCRT, the Connect window is displayed (Figure 1).

   Figure 1. New SecureCRT Connect Window

    

   Note: The first time you launch a program like SecureCRT you might receive a Windows Security Alert, such as the example shown in Figure 2. Click the Unblock button to enable SecureCRT to function as required.

   Figure 2. Windows Security Alert Message

2. Click the New Session button.

   The New Session Wizard appears (Figure 13).

   Figure 3. New Session Wizard

3. Use the Protocol pull-down menu to select the SSH2 protocol, and then click Next.

   The wizard prompts you to enter the RCE server hostname to which you choose to connect (Figure 4).

   Figure 4. New Session Wizard - RCE Server Hostname

4. Enter the RCE server hostname to which you choose to connect, and then click Next.

   When your RCE account was first created, you received email from HMDC with this server hostname. This is the machine name to which you are granted access. Usually, you connect to one of the rce.hmdc.harvard.edu servers.

   The New Session Wizard prompts you to name the session (Figure 5). The session name defaults to the server hostname that you just entered.

   Figure 5. New Session Wizard - Session Name

5. Accept the default session name, and click Finish.

   The Connect window is displayed, and your RCE server connection appears in the list of options (Figure 6).

   Figure 6. SecureCRT Connect Window with New Entry

6. Select the RCE server connection, and then click the Connect button.

   The system prompts you with a New Host Key warning (Figure 7).

   Figure 7. New Host Key Warning Message

7. Click the Accept & Save button to save the host key in your local system cache.

   Note: If you click the Accept Once button, the system prompts you to accept this key again the next time log in to this server.

   The Enter SSH Username window is displayed (Figure 8).

   Figure 8. Enter SSH Username Window

8. Type your RCE account username, then click OK.

   The Enter Secure Shell Password window is displayed (Figure 9).

   Figure 9. Enter Secure Shell Password Window

9. Type your RCE account password, then click OK.

   The connection window contains an active connection, as shown in Figure 10. You now are logged in to the RCE server through SSH.

   Figure 10. Active SSH Connection in Connect Window

For Mac or Linux:

1. Open a terminal window and use the SSH client built into the MacOS/Linux to connect to the VNC server. Type the following:

   ssh username@hostname

   Replace username with your RCE account username, and replace hostname with the name of the RCE server you want to connect to. When your RCE account was first created, you received email from HMDC with this server hostname. This is the machine name to which you are granted access. Usually, you connect to one of the rce.hmdc.harvard.edu servers.

   The first time that you connect to the RCE server, your system prompts you with a warning message about the host.

   The authenticity of host 'hostname (address)' can't be established. 
   RSA key fingerprint is fingerprint.
   Are you sure that you want to continue connecting (yes/no)? 

2. Type yes, and then press Enter to continue.

3. The system notifies you that you added the host permanently to the list of known servers on this machine, and then prompts you to enter your login account password.

   Warning: Permanently added 'hostname (address)' (RSA) to the list of know hosts.
   username@hostname's password:

4. Type your RCE account password and press Enter to continue.

   A welcome message is displayed, followed by the system prompt.

   *******************************************************************************
   *                   Welcome to rce-2.hmdc.harvard.edu                         *
   *                                                                             *
   *  For information about this and other HMDC servers:                         *
   *      http://support.hmdc.harvard.edu/kb-983/research_support_overview       *
   *                                                                             *
   *  Please note that you are governed by the IT standard uses and practices    *
   *  of Harvard University while using this machine. See the following URL for  *
   *  more information:                                                          *
   *      http://support.hmdc.harvard.edu/kb-930/hmdc_policies                   *
   *                                                                             *
   *******************************************************************************

   <hostname:username> [~]>

5. You now are logged in to the RCE server through SSH.

Instructions for installing your own ado-files in Stata can be found in the Stata 11 documentation. To find the appropriate section of the manual, do the following:

1. Launch an instance of RCE Powered Stata.

2. Select Help–>PDF Documentation. Adobe Reader will open, displaying the combined subject table of contents.

3. From the navigation bar on the left, expand “User’s Guide”, then click “Table of contents”.

4. Select chapter 17, “Ado-files”. In particular, section 17.7, “How do I add my own ado-files?”, will be relevant. Section 17.7 shows the result of running the ‘sysdir’ command from within a Stata session. While the documentation shows this command being run on a Windows system, you will see different results in the RCE. Copy your ado-files to the PERSONAL directory, as shown in the output of the sysdir command.

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.