• Logging in
• HPC Filestore
• Some Notes on Panasas
• Copying files to the HPC
• Copying files from the HPC to the IUS

Once you are given an account on the HPC you may access it by logging in to the "frontend" machine by typing the following in a session on the Interactive Unix Service (IUS):

ssh corona.hpc.lancs.ac.uk

From a local PC, the head node can be accessed using any ssh (secure shell) capable application using the same name.

When logging in for the first time you may get the following message:

Host key not found from the list of known hosts.
Are you sure you want to continue connecting (yes/no)? 

Reply yes to the question and you will then be prompted for your password. This will be the same as your IUS password.

When you next log in you will only be prompted for your password.

You will have an allocation of home filestore on the HPC's Panasas fileserver. This is separate from your allocation on IUS or any other service. The default quota allocation for home directories is 200 megabytes, which can be increased on request if necessary.

The full path to your home directory on the HPC fileserver is of the form:

/home/hpc/NN/username

where NN is the same 2 digit number which appears in the path to your IUS filestore.

There are also two other user filestore spaces available; storage and scratch. The paths to these directories can be determined by taking the path to your home directory (above) and replacing `/home' with `/storage' or `/scratch' respectively. For convenience, users can refer to their own storage and scratch spaces using the labels $global_storage and $global_scratch. Please Note: These labels cannot be used within qsub scripts. For example you cannot add the line "#$ -o $global_storage/myprogram.stdout" to redirect output from qsub to a file called myprogram.stdout in your storage space - instead, you must specify the full pathname.

Users' storage space is - like the home directory - subject to a quota, with an initial allocation of 2 gigabytes. Unlike the home dirctory, files placed in storage space are not backed up; users should store vital files in their home directory.

Scratch space is not subject to quota - users may use as much space as is available on the volume (200 gigabytes). Scratch space is not backed up, and files stored there are subject to deletion after 14 days.

You may view your quota details at any time using the command panquota.

On the Panasas filesystem, each file incurs an overhead which is taken from a user's quota. In the case of small files, this overhead is relatively high - some 128 Kb per file, even if it contains only a few bytes. Generating a large number of very small files can thus very quickly exhaust a user's file quota.

Best practice is to avoid generating large numbers of small files wherever possible. Where not possible, project directories and their contents should be archived using a tool such as tar as soon as project work is finished.

Files may be copied from the IUS into your HPC filestore by using the command scp on the IUS.

First, log in to the HPC and create a directory to receive the files. Suppose you call this directory project_files.

Then on the IUS change to the directory which contains the files you want to copy and then type, for example:

scp  *  corona.hpc:project_files

This will copy every file in the current directory on the IUS to the directory project_files on the HPC.

The first time you use scp it may prompt you with the following:

Host key not found from the list of known hosts.
Are you sure you want to continue connecting (yes/no)? yes

Reply with yes and you will then receive a prompt for your password. Thereafter you will only have to give your password.

To copy any subdirectories and their contents, use the -r option to the scp command:

scp  -r  *  corona.hpc:project_files

Copying files from the HPC to the IUS is most easily done by running scp ON THE HPC

To copy all the files in the current directory on the HPC to a directory project_files on the IUS type in your HPC login session:

scp  *  cent1:project_files

Transferring files between the HPC and a local desktop PC requires your PC to run a client application capable of the secure file transfer protocol. There are several applications available, and PC Managed Builds come with PuTTY and WinSCP pre-installed. For those without a Managed Build, the application installer can be found at \\central_soft\free\software\misc\winscp

Note: Take care to ensure that text files are transferred in text mode in order to avoid problems casued by format differences between Unix and Windows text files.

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