FAQs

How do I copy files between the RCE and FASSE?

We recommend using rsync to copy files between RCE and FASSE, although ssh, scp, and sftp will also work.

Examples:

Via rsync:

Note: This example uses the -v flag. The verbose option lists every file that is transferred and is probably not appropriate when copying large numbers of files or directories.

Note: If you have ssh keys for the RCE set up on your computer, you may not be prompted for your password when logging in to the RCE.

  1. SSH into FASSE.
  2. ...
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How do I copy files between RCE and Cannon (FAS RC)?

We recommend using rsync to copy files between RCE and FASRC, although ssh, scp, and sftp will also work.

Examples:

Via rsync:

Note: This example uses the -v flag. The verbose option shows every file that is transferred and is probably not appropriate when copying large numbers of files or directories.

Note: If you have ssh keys for the RCE set up on your computer, you may not be prompted for your password when logging in to the RCE.

SSH into FASRC.

ssh jharvard@...
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Use VPN for Filezilla, scp, and all file transfer software

Some users have reported difficulties transferring multiple files to the RCE.  This is because for security reasons, the RCE systems are set up to block users who log in too often from outside of Harvard.  File transfer programs log in each time a new set of files is sent, so they sometimes trigger this block.  This situation is easily remedied by logging into the Harvard VPN before transferring files.  This happens for all file transfer software, including Filezilla, Cyberduck, and CLI commands such as scp and sftp.  The one thing it does not apply to is mounting a... Read more about Use VPN for Filezilla, scp, and all file transfer software

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.