RCE FAQs

Copy/Paste to the RCE desktop isn't working!

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 ApplicationsRCE UtilitiesRestart Clipboard Sync.

Can I install my own software packages?

Many common statistical applications are already available, pre-installed in the RCE. If you need additional software for your work in the RCE, you are free to download, build, and install software within the space that has been allocated for your RCE home directory and project space.

When you run your configure script, give it an argument of --prefix=$HOME.

If the software you need is available from a trusted repository, we may also be able to add your software to the list of default applications in the RCE. Please contact us with your request.

I'm unable to log in -- what can I do?

There are several troubleshooting steps to take if you cannot log in to the RCE desktop:

  1. Verify that your credentials are correct by logging into the HMDC Account Self Service page. If you cannot log in, then the problem lies with your RCE credentials, and you will not be able to progress any further.  Please reset your password by visiting the Account Self Service page and clicking the "Forgot your password?" link, then try again.  If, after resetting your password, you are still unable to log into the Account Self Service page, please stop troubleshooting and contact us.
  2. Verify that you are logging into the correct RCE host.  Once you have logged into the Account Self Service page, make sure that you see a column labeled "HMDC RCE (Server) Account Information".  Check the "Account Access" section to find out the name of the RCE host to which you have access.  If you cannot determine the name of the RCE host to which you have access, check the email you received when your RCE account was originally created.  If you cannot find that email, please stop troubleshooting and contact us.
  3. Verify that you can connect to the RCE via SSH.  See Secure Shell under Accessing the RCE for instructions.  If you cannot connect to the RCE via SSH, then you will be unable to establish a NX connection.  Please stop troubleshooting and contact us. In your response, please include the name of the RCE host to which you tried to connect, the username that you used (but not the password!), and your IP address (visit http://www.whatismyip.com for this ); also, please include the full text of any error messages you saw.
  4. Verify that you have not exceeded your home directory's quota.  Once you have connected to the RCE via SSH, please check your disk quota usage.  Instructions for doing so are here: "How do I check RCE disk quota?".  If you have exceeded your home directory's disk quota, you will need to resolve this issue before you'll be able to continue.  Your options are as follows:
    1. Make sure that your Trash is empty.    When connecting via SSH, you can use the 'emptytrash' command to empty your Trash.  You should not see any output from this command; if you do, please stop troubleshooting and contact us
    2. Move large files to a project share or delete them.  If you have access to one or more project shares, they will appear in the output of the 'quotareport' command.  The "How do I check my RCE disk quota?" page contains some examples of using the command line to identify large files and move them to a project share; if you'd like assistance with this task, please let us know.  You can move and delete files using the command-line tools, or you can connect to the RCE via SFTP to organize your files graphically. After you have moved or deleted large files, run the 'quotareport' command again to recheck your disk usage.  Once you have resolved any quota issues affecting your home directory, you'll still need to terminate any existing NX session and reestablish it; please see the next troubleshooting step for further instructions.  If you cannot resolve your quota issues, please stop troubleshooting and contact us.
  5. Verify that you can establish a brand new NX session.  Once you have connected to the RCE via SSH, please terminate any existing NX sessions.  Instructions for doing so are here:  "How do I terminate my NX session?" . If you have multiple NX sessions, you'll need to terminate all of them before starting a new one.  Keep running the 'nxcleanup' command until it tells you that you have no NX sessions, then establish a new session. If you are unable to establish a new NX session after successfully completing all of these troubleshooting steps, please contact us.

How do I check RCE disk quota?

What is Quota?

Your "quota" is a limit on your data storage space.

Types of Quotas

  • User Quotas: Each RCE user has a separate home directory quota of 500MB. Please note that when you move files to your Trash, they still count against your home directory disk quota until you empty your Trash, regardless of where they were moved from.
  • Group Quotas: Each research project in the RCE is designated a "group" and each group is given a "project space" with a separate quota. You may also have a personal group with only yourself as a member and a project space for your personal social science research projects. This is where we recommend you store large files, secure confidential data, and build custom software.

Checking Quota

To check your quota, first open a terminal window on an RCE server...

  • From outside an existing NX session, open a ssh connection (see Secure Shell under Accessing the RCE for instructions).
  • From within the RCE desktop, select ApplicationsAccessoriesTerminal.

Then type:

quotareport

Additionally, you can use "list" and "disk usage" to track file size:

  • ls -lah (format as a list, show hidden files including .Trash, make file sizes human readable)
  • du -hs /path/to/directory/ (make sizes human readable, summary)
  • du -ach --max-depth=1 /path/to/directory/ (list size of files, show a grand total, make sizes human readable; get folder size, but don't include sub-folders)
  • du -sh ./* | grep '[0-9]M' | sort -nr | head (find all file sizes, show only the largest ones that are at least a megabyte, sort descending, show only the top 10)

Making Space

Use the File Browser in the RCE to find and delete unneeded files, or use the terminal commands below...

  • Deleting files: rm file_name
  • Deleting entire directories: rm -rf directory_name
  • Empty the trash when done: rm -rf ~/.Trash/*

How do I terminate my NX session?

  1. Open a terminal window in the RCE
    • If you can access your current RCE desktop session, click ApplicationsAccessories → Terminal.
    • From outside an existing NX session, open a ssh connection (refer to Secure Shell under Accessing the RCE for instructions).
  2. Type the following command: nxcleanup
  3. If you have multiple NX sessions running, you will be prompted to select from a list of sessions. Select the desired session and press Return.
  4. If your session is on another server, you will be prompted to confirm the connection.

Can I run multi-threaded jobs?

If you would like to use multiple CPU cores simultaneously, please be sure to create the appropriate resource reservations so that your jobs do not compete with other jobs for a CPU, and are allocated resources for your exclusive use.

Many applications and programming libraries can make use of multiple CPU cores simultaneously by running multiple active threads or processes.

We do not currently place any technological limitations on CPU core usage in cluster computing, and instead ask that you observe the rule of "one CPU core per job instance" unless specifically reserving additional cores for your jobs. In both batch and interactive cluster computing, available cluster resources may be lower during periods of intense utilization.

  • Batch cluster jobs are allocated one CPU core (and 4GB memory) per instance, although you can queue an unlimited number of job instances for high-throughput parallel computing.
  • For RCE Powered (interactive) jobs, you can request an allocation of up to 24 CPU cores (and up to 250GB RAM), but each job submission queues only one instance.
    • Stata/MP will reserve 8 cores per job by default
    • To request a different number of CPU cores, use condorInteractiveSubmit.pl -c num_cpu -x command

Some applications and libraries require additional options to set the number of CPU cores used.

  • To set the number of CPU cores used by the R Goto linear algebra library: Sys.setenv(GOTO_NUM_THREADS=1)
  • To run Matlab on a single CPU core: matlab -singleCompThread

For assistance with setting CPU core usage for other applications, please contact HMDC Support.

How can I make my batch submission track iteration number?

To track iteration number for batch submissions, use one of the following:

  • Add --args '$(Process)' to the Arguments line of your Condor submit file. This passes to the R process the process number of the R run, which progresses from 0 to one less than the number of runs.
  • Capture the argument in a variable in your R code by entering the following line: run <- commandArgs(TRUE). The R object run contains the run number. You then can use this object to construct appropriate output file names for your job.

How do I use files in my home directory from my batch job?

When you submit a batch job, the R script is copied to a staging area and then executed by a cluster node. This means that you must set paths explicitly in your R scripts. To set paths, add the following code to the beginning of all your R scripts. This tells R to find the absolute path to your home directory, then set the working directory to that path:

setwd(path.expand("~<username>"))

Use this code to address such problems as the following:

Loading required package: MASS Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file '<filename>', reason 'No such file or directory' Execution halted 

Note: If you use a subdirectory, include the path to the subdirectory in the setwd command referenced previously.