Using Stata at 100% quota results in data loss

We uncovered a Stata bug where the application will overwrite output with zero byte content when you reach maximum quota. Please be aware of your quota status and expected output size before running a Stata job. HMDC has submitted a bug report to Stata and their developers are working on a fix.

How can I access the old CVS repository

HMDC houses a legacy CVS repository, we no longer create new CVS project repos, but old repos can be accessed using the following information:

First, find out which shell you work in, from a terminal prompt type the following:

echo $SHELL

If you see tcsh, type the following:

setenv CVS_RSH ssh

Otherwise type:

export CVS_RSH=ssh

Then type the following to checkout your repo to your current directory:

cvs -d <username>@cvs.hmdc.harvard.edu:/CVS/<project> checkout <project>

Replace <project> with the name of your project and <username> with your RCE username.  For example:

cvs -d kingcvs@cvs.hmdc.harvard.edu:/CVS/zelig checkout zelig

CVS clients

There are a number of CVS clients available for Windows and Mac, and they fall in and out of development on a regular basis.   Mac OSX does have a CVS command line client available using "Homebrew".  See the Homebrew website for more information.  There may also be a number of GUI based clients available, searching using your favorite search engine should provide the most up-to-date results.

Is phpMyAdmin available for database access?

Yes, but access is limited to within the RCE only. Create or log in to your NX session and navigate to phpmyadmin.hmdc.harvard.edu. Log in to phpMyAdmin using your database credentials. Make sure the proper host is selected in the drop down. If you don't know your host, check the email that was sent to you when you requested the database.

Why do I get the java error "Could not reserve enough space for object heap"?

When running an RCE Powered Application -- for example an RCE Shell -- you have the opportunity to reserve a requested amount of system memory. Unfortunately, the Java JRE is not aware of the resource limit you have set, and will try (and fail) to grab as much of the system memory as is free.

To correct this behavior, you can set the shell environment variables JAVA_OPTS and _JAVA_OPTIONS before launching your java application. These values must be set within the shell that launches your java application, so it may be helpful to set these values and run your java app from within a single interactive RCE Powered Shell, or to create a shell script that sets these values and then runs your java app.

For example, to restrict the Java JRE heap memory allocation to 1GB initially and a maximum size of 2GB, set the variables as follows:

in bash shell:

export JAVA_OPTS="-Xms1024m -Xmx2048m"
export _JAVA_OPTIONS="-Xms1024m -Xmx2048m"

in tcsh shell:

setenv JAVA_OPTS "-Xms1024m -Xmx2048m"
setenv _JAVA_OPTIONS "-Xms1024m -Xmx2048m"

How do I install software packages on the RCE?

As a RCE user, you are only allowed to install certain packages and modules to your own home directory. We have documentation for install popular packages on the follow pages:

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.

If you were redirected here from the RCE, you may have been trying to install a package using apt-get. This is a package manager for Debian-based systems, and isn't compatible with the RCE. If you need assistance with installing additional software that isn't available on the RCE, please contact us (or by phone: 617-495-4734) for support!

How to exit a job from a shell OR cannot start RCE job -- too many CPUs

The commands below will help you exit an RCE job from a terminal if the application window has disappeared, or you need to exit it and do not have access to your NX session. This can be accomplished by using an ssh client and connecting to rce.hmdc.harvard.edu, or opening a terminal window in the RCE. 

The same commands can be used If you are running into an error starting a new RCE job due to too many CPU's in use, you need to terminate your jobs that were tied to an old nx session. The commands that are highlighted below should enable you to remove these old jobs.

  1. Run this command to see your jobs:
    condor_q -pool cod6-head.priv your_username
    job_id  username  date_&_time   run_time   R  0   0.0  application_name

  2. Remove your job, using the job_id:
    condor_rm -pool cod6-head.priv -name HMDC.interactive@cod6-head.hmdc.harvard.edu job_id