High Performance Computing Service – Part 3: Transfer your files

At this stage, all the files are ready.

Now, let’s organize the stores adding subdirectories then transfer the files from my desktop computer to the HPC server.

1. ON THE HPC: I have organized the stores in this way:

 mkdir $HOME/R #for custom library 
 mkdir $HOME/scripts 
 mkdir $HOME/R/scripts/r #for my R scripts  
 mkdir $WORK/inputs 
 mkdir $WORK/outputs 
 mkdir $WORK/outputs/Rdata 
 mkdir $WORK/outputs/Rout

2. FROM MY DESKTOP: transfer the files created in Part 2 to the HPC server.

 scp topmodel.tar.gz login.cx1.hpc.ic.ac.uk:$HOME/R         #to install R packages (e.g. fuse) move the tarball to HPC
 scp batch.sh login.cx1.hpc.ic.ac.uk:$HOME/                 #script to set up the runs
 scp fuse_1.0.tar.gz login.cx1.hpc.ic.ac.uk:$HOME/scripts   #to install R packages (e.g. fuse) move the tarball to HPC

3. INSTALL PACKAGES AND ANY OTHER APPLICATION IT MAY BE NEEDED

 module load R/2.15 intel-suite/2012     
 R CMD INSTALL $HOME/R/fuse_1.0.tar.gz                       #install the package (alternatively, you can download it from cran)

4. ON THE HPC: RUN THE BATCH FILE

 qsub batch.sh

For examples of the above mentioned files, see PART 2.

For information on using the HPC service see http://www.hpc.ic.ac.uk

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s