Software to connect to the remote server:

Software to enable graphics (X-Forwarding):

SFTP Clients for File Transfer:

Connecting to the SCC

Use scc1, scc2, or scc4 login node to connect to the Shared Computing Cluster:
ssh username@scc4.bu.edu

An example for user ktrn:

[local prompt] > ssh    ktrn@scc4.bu.edu  # Windows
[local prompt] > ssh -Y ktrn@scc4.bu.edu  # Mac
[local prompt] > ssh -X ktrn@scc4.bu.edu  # Linux



Check if graphics works (X-forwarding is enabled):

[scc2 ~] > xclock &

You should see a pop-up window with clock in it:


If you do not see clock:
Windows: make sure Xserver icon on the op-left side of MobaXterm is green.
Apple OS X: make sure you logout of your computer after you installed xQuartz, start xQuartx (you should see xQuartz icon on the bottom of your screen) and that you use -Y with your ssh command when you login to the SCC

File Transfer

There are a number of ways you can transfer files to the SCC from a local computer and back. See directions on our website:
http://www.bu.edu/tech/support/research/system-usage/getting-started/get-started-file-transfer/

Example of scp command (from a local terminal window). Transfer a file to the home directory on the SCC:

[local prompt] date > date.txt
[local prompt] scp date.txt username@scc2.bu.edu:.


To download a file from a website, use wget command, i.e.:

[scc2 ~] wget http://rcs.bu.edu/classes/cbs/helloWorld.R


Home Directories

On the SCC, each user has a 10 GB home directory which is backed up nightly and protected by Snapshots. Additional quota is not available for home directories. To check the home directory quota, use the quota -s command:

[scc2 ~] quota -s
Home Directory Usage and Quota:
Name           GB    quota    limit in_doubt    grace |    files    quota    limit in_doubt    grace
ktrn      5.71915     10.0     11.0      0.0     none |   117443   200000   200000        0     none

Home directories are private to the user. The permissions are set that only the owner has permissions to view, modify or execute the files in the home directory. Home directories should NOT be used for the production work. Once quota is reached, your jobs will fail and many programs will not run (or even start).

Project Directories

You can view wich projects you belong to executing command groups. You might belong to one or more SCC projects. The first project on your list is your default project.

[scc2 ~] groups
cbs

Each SCC project has its project space. Use pquota command to see the directories associated with the project and their sizes:

pquota cbs
                                      quota    quota       usage     usage
project space                          (GB)   (files)       (GB)   (files)
-----------------------------------  ------  --------  ---------  --------
/projectnb/cbs                         4000  33554432    2939.36   9624805

projectnb partition is used for this project:

cd /projectnb/cbs    # change directory to the project directory
ls -l                  # check the content of the directory

Each memomber of cbs project has his/her own subdirectory in this folder

mkdir koleinik     # create subdirectory with a name koleinik
ls -l              # check what folders are there

cd koleinik        # change current directory to be the one you just created
pwd                # view the current directory path



SCC Text editors

SCC has all standard Linux editors like emacs, vi (vim, gvim) and nano. There is also a note-pad like editor gedit

Software on the SCC

The module package is available on the Shared Computing Cluster, allowing users to access non-standard tools or alternate versions of standard packages. This is also an alternative way to configure your environment as required by certain packages. You can read more about module command usage on our webpage:
http://www.bu.edu/tech/support/research/software-and-programming/software-and-applications/modules/

To view all available modules:

module avail

To list all available version for a particular package:

module avail R

------------------------------ /share/module/gis -------------------------------
R_earth/2.14.0 R_earth/2.15.3 R_earth/3.1.0

---------------------------- /share/module/imaging -----------------------------
RHSEG/1.47

-------------------------- /share/module/programming ---------------------------
R/3.0.0              R/3.3.2_intel-2016   R/R-2.13.0
R/3.1.1              R/3.4.0              R/R-2.15.1_gnu-4.4.6
R/3.2.0              R/3.4.2              R/R-2.15.3_gnu-4.4.6
R/3.2.3(default)     R/3.4.2_intel-2016   R/R-3.0.0_gnu-4.4.6
R/3.3.0              R/3.4.3              R/R-3.1.1
R/3.3.2              R/3.5.0



module avail sas

--------------------------- /share/module/statistics ---------------------------
sas/9.3          sas/9.4(default) sas/9.4M2



Work with R

To select a particular version of python:

module load R/3.2.3

To view which modules are loaded:

module list

Currently Loaded Modulefiles:
  1) R/3.2.3     2) gcc/7.2.0

To start Rstudio:

rstudio &

SCC Batch System


Running an interactive job

Login nodes are most suitable for code development and debugging. Non-interactive batch processing is an environment for running jobs that take more than a few minutes and which require no interactions between the user and the application software. There are occasions where longer duration jobs that require user interaction may arise or additional resources (like high memory nodes) are needed. Use qrsh command with appropriate options to start an interactive job.

An example workflow for the interactive job is below:

qrsh -P cbs


cd /projectnb/cbs/koleinik    # change working directory
module load R/3.2.3          # load R module
rstudio &

Once you finish with running your interactive job, execute exit or logout to free up the resources.

Running a batch job

In any text editor create a file which will submit your code to the batch system. A simple example of a file that submits an R job may look like this:

#!/bin/bash -l

#Specify project
#$ -P cbs

#Request appropriate time ( default 12 hours )
#$ -l h_rt=12:00:00

#Send an email when the job is done or aborted (by default no email is sent)
#$ -m e

# Give job a name
#$ -N hello

#$ Join output and error streams into one file
#$ -j y


#load appropriate envornment
module load R/3.2.3


#execute the program
Rscript myscript.R



SAS

module avail sas

--------------------------- /share/module/statistics ---------------------------
sas/9.3          sas/9.4(default) sas/9.4M2
To submit a SAS job your submition script might look like: 
#!/bin/bash -l

#Specify project
#$ -P cbs

#Request appropriate time (default 12 hours; gpu jobs time limit - 2 days (48 hours), cpu jobs - 30 days (720 hours) )
#$ -l h_rt=12:00:00

#Send an email when the job is done or aborted (by default no email is sent)
#$ -m e

# Give job a name
#$ -N hello

#$ Join output and error streams into one file
#$ -j y



#load appropriate envornment
module load sas/9.4

#execute the program
sas -noterminal helloWorld.sas



Track SCC job

qstat -u username

You can read more about checking the status of submitted jobs on our website:
http://www.bu.edu/tech/support/research/system-usage/running-jobs/tracking-jobs/

Getting help

Email us at help@scc.bu.edu.
Please include the following information in your email: Your user name, your working directory and detailed description of the problem: what script you are running, what error you are getting etc. There is no need to attach your script to your email.

Additional Resources

Our website: http://www.bu.edu/tech/support/research/
Getting started: http://www.bu.edu/tech/support/research/system-usage/getting-started/
SCC Cheat Sheet (pdf): http://scv.bu.edu/documents/SCC_CheatSheet.pdf
Running jobs: http://www.bu.edu/tech/support/research/system-usage/running-jobs/