RCE FAQs

Geospatial packages in R such as rgdal and sf cannot be installed. Is there a work-around?

Support for geospatial R packages on the RCE is currently shaky at best. There are work-arounds, but they can be error-prone and are easy to break. You may wish to use another system for your geospatial work in R for the time being. Read on if you wish to try some work-arounds in order to install and run rgdal and other geospatial R packges on the RCE.

The basic issue The system GDAL library is too old, but cannot be updated beause other software depends on it. As a work-around we compiled GDAL 2.1.1 and made it available at

/nfs/tools/apps/gdal/2.1.1

To...

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Missing software packages in Anaconda Navigator

Launching Anaconda Navigator should present several pre-installed software packages, including Jupyter Notebook, Jupyter Lab, qtconsole, and Spyder.

If you do not see all of the expected applications on the Anaconda Navigator "Home" screen, you may need to update your package index, as follows:

  • Launch Anaconda Navigator.
  • Select "Environments" from the left menu.
  • Click the "Update Index..." button.
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How do I cite the RCE?

If you found the RCE useful in completing your published research, we would appreciate if you would mention us in a citation, using the following text:

"The computations for this paper were run on the Research Computing Environment supported by the Institute for Quantitative Social Science in the Faculty of Arts and Sciences at Harvard University."

How to remove a frozen RCE application

1) In nx, open a terminal from the Applications->System tools menu

2) Note the host your are on:  [cperry@rce6-5 ~]$ 

3) Run the command below and note the Schedd host and job ID. 

[cperry@rce6-5 ~]$ condor_q cperry

-- Schedd: HMDC.rce@rce6-1.hmdc.harvard.edu : <10.0.0.98:9619?sock=10410_9383_3>

 ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD               

...

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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....

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