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FAQ

d. Software

Where is ftp?

Modern secure transfer protocols like SFTP and SCP secure data during transit and should be used when moving files from one place to another. However you may still need to use plain, un-secured FTP to download data sets or other files from remote locations while logged into Odyssey.

While we do not offer the largely outmoded 'ftp' program on the cluster, we do offer the feature-rich and largely command compatible 'lftp'. From any login or compute node type 'man lftp' to see its usage and options.

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How do I load a module or software on Odyssey?

Step 1: Login to Odyssey through your Terminal window. Please see here for login instructions.

Step 2: Load a module/software by typing: module load MODULENAME. Replace MODULENAME with the specific software you want to use. A complete listing of modules can be found on the module list page. Only the modules that begin with centos6/ are supported on the current cluster.

To see what modules you have loaded type: module list

To unload a module type: module unload MODULENAME

Details can be found in the modules section of the Running Jobs page.

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FileZilla: I have to enter my OpenAuth code every 30 seconds

If you are using Filezilla to transfer files to Odyssey, and you are prompted frequently (like every 30 seconds!) to enter your RCUsername and/or OpenAuth token code, then most likely you did not configure FileZilla according to our instructions.

Please see this document on how to avoid the OpenAuth challenge frustration while transferring files to and from Odyssey.

Last updated: February 25, 2016 at 12:33 pm

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Git/Github: 403 Forbidden while accessing https://github.com…

If you issue a git push to a cloned repository, you might receive the following error:

error: The requested URL returned error: 403 Forbidden while accessing https://github.com/yourusername/planets.git/info/refs
fatal: HTTP request failed

Authorization to Github repositories on Odyssey is can be a little tricky. Please follow our instructions at https://rc.fas.harvard.edu/resources/documentation/software/git-and-github-on-odyssey/

Last updated: February 25, 2016 at 12:33 pm

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Unable to locate a modulefile…

If you are trying to execute a module load and see the error

ModuleCmd_Load.c(200):ERROR:105: Unable to locate a modulefile...

Well, have you opted-in and sourced the new module system?

A little while back we switched how modules were handles but didn't require users to make the switch and disrupt their workflow. All the modules you see in the portal and via module-query are on the newer module system, which can be accessed by running

source new-modules.sh

at login, as a part of your ~/.bashrc file, or part of your SLURM script.

Please take a few brief moments and review our information on the new Lmod system at https://rc.fas.harvard.edu/resources/documentation/software-on-odyssey/intro/.
 
 
Last updated: February 25, 2016 at 12:33 pm

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How do I run a Matlab script on Odyssey?

To run a Matlab script (with no graphical interface component) on the Odyssey cluster, login using your preferred terminal application then activate the application by loading the module (Note: There are several versions available).

example: module load matlab/R2016b-fasrc01

Then, assuming your script is named calc.m, either run it through an interactive session

srun --pty --mem 1000 -p interact matlab -nojvm -nodisplay -nosplash < calc.m

or use the matlab command in a batch script

#!/bin/bash
#SBATCH -o calc.out
#SBATCH -o calc.err
#SBATCH -p serial_requeue
#SBATCH -n 1
#SBATCH --mem 1000
#SBATCH -t 1000

matlab -nojvm -nodisplay -nosplash < calc.m

Make sure that `calc.m` finishes with an `exit` command. Otherwise, the process will hang waiting for further input.

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Perl modules: Can’t locate XX.pm in @INC

Perl modules have been developed over the past 15 to 20 years, and the installation method has changed significantly. Unfortunately, you might run into a program that needs to install a really old Perl module, and its installation is just not behaving properly under the new installation methods. You might see something like the following:

[bfreeman@rclogin12 PfamScan]$ ./pfam_scan.pl --help
Can't locate Data/Printer.pm in @INC (@INC contains: /n/sw/fasrcsw/apps/Core/perl-modules.....

The remedy can be rather simple:
1. Follow our new lmod - Perl instructions here on setting up your home directory for installing Perl modules 'locally'.

Note that the export PERL5LIB command must include both $LOCALPERL and $LOCALPERL/lib/perl5 (it's subdirectory) as some installation routines honor one; some the other.

2. Sometimes, you might need to install the module manually. Try both the Makefile.PL build and the Build.PL build if one or the other doesn't work.

3. In CPAN, you can do this manual install method without the hassle of the download process:

cpan
look Data::Printer

This latter command will download the module and unpack it for you, and leave you at the shell, where you can try either the Makefile.PL or Build.PL build process.
 
 
Last updated: February 25, 2016 at 12:33 pm

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CC BY-NC 4.0 This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. Permissions beyond the scope of this license may be available at Attribution.