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Altamira User's Guide

Contents

  1. Altamira User's Guide
    1. Introduction
    2. System Overview
    3. Connecting to Altamira
      1. Login Node
      2. Transferring Files
    4. File Systems
      1. Root Filesystem
      2. GPFS Filesystems
      3. Local Hard Drive
    5. Running Jobs
    6. Software
    7. Acknowledgment in publications
    8. Getting Help
    9. Appendices
      1. A. SSH

Introduction

This user's guide for the Altamira supercomputer is intended to provide the minimum amount of information needed by a new user of this system. As such, it assumes that the user is familiar with many of the standard aspects of supercomputing as the Unix operating system.

We hope you can find most of the information you need to use our computing resources: from applications and libraries to technical documentation about Altamira. Please read carefully this document and if any doubt arises don't hesitate to contact our support group at <res_support@ifca.unican.es>.

System Overview

Altamira comprises 156 compute nodes, 5 GPU compute nodes, a login server and several service servers. Every compute node has two processors at 2.6 GHz running Scientific Linux 6.2 system with 64 GB of memory RAM and 400 GB local disk storage. All the servers provide a total of 132 TB of disk storage accessible from every compute node through GPFS (Global Parallel File System).

The networks that interconnect the Altamira are:

Connecting to Altamira

Once you have a login and its associated password you can get into Altamira system, connecting to the login node altamira1.ifca.es.

You must use Secure Shell (ssh) tools to login into or transfer file into Altamira. We do not accept incoming connections from protocols as telnet, ftp, rlogin, rcp, or rsh commands. Once you are logged into Altamira you cannot make outgoing connections for security reasons.

To get more information about the secure shell version supported and how to get ssh for your system (including windows systems) see Appendix A.

Here you have an example of logging into Altamira from a UNIX environment: 

user@localsystem:~$ ssh -l usertest altamira1.ifca.es
usertest@altamira1.ifca.es's password: 

/--------------------------------------------------------------\
|                      Welcome to Altamira                     |
|                                                              |
|  - Applications are located at /gpfs/res_apps                |
|  - For futher information read User's Guide at               |
|      http://grid.ifca.es/wiki/Ojancano/Userguide             |
|                                                              |
|   Please contact res_support@ifca.unican.es for questions    |
|                                                              |
\--------------------------------------------------------------/

[usertest@login1 ~]$

The first time that you connect to the Altamira system secure shell needs to interchange some initial information to establish the communication. This information consists of the acceptance of the RSA key of the remote host, you must answer 'yes' or 'no' to confirm the acceptance of this key.

Please change your initial password after you login the first time into the machine. Also use a strong password (do not use a word or phrase from a dictionary and do not use a word that can be obviously tied to your person). Finally, please make a habit of changing your password on a regular basis.

If you cannot get access to the system after following this procedure, first consult Appendix A for an extended information about Secure Shell, or you can contact us, (see Getting Help to know how to contact with us).

Login Node

Once inside the machine you will be presented with a UNIX shell prompt and you'll normally be in your home ($HOME) directory. If you are new to UNIX, you'll have to learn the basics before you could do anything useful.

The machine in which you will be logged in will be the login node of Altamira (login1). This machine act as front end, and it is used typically for editing, compiling, preparation/submition of batch executions and as a gateway for copying data inside or outside Altamira.

It is not permitted the execution of cpu-bound programs on this node, if some compilation needs much more cputime than the permitted, this needs to be done through the batch queue system. It is not possible to connect directly to the compute nodes from the login node, all resource allocation is done by the batch queue system.

Transferring Files

As it have been said before no connections are allowed from inside Altamira to the outside world, so all scp and sftp commands have to be executed from your local machines and not inside Altamira.

Here there are some examples of each of this tools transferring files to Altamira: 

localsystem$ scp localfile usertest@altamira1.ifca.es:
usertest@altamira1.ifca.es's password:

localsystem$ sftp usertest@altamira1.ifca.es
usertest@altamira1.ifca.es's password:
sftp> put localfile
sftp> exit

These are the ways to retrieve files from Altamira to your local machine: 

localsystem$ scp usertest@altamira1.ifca.es:remotefile localdir
usertest@altamira1.ifca.es's password:

localsystem$ sftp usertest@mn1.bsc.es
usertest@altamira1.ifca.es's password:
sftp> get remotefile
sftp> exit

On a Windows system, most of the secure shell clients comes with a tool to make secure copies or secure ftp's. There are several tools that accomplishes the requirements, please refer to the Appendix A, where you will find the most common ones and examples of use.

File Systems

IMPORTANT It is your responsibility as a user of the Altamira system to backup all your critical data.

Each user has several areas of disk space for storing files. These areas may have size or time limits, please read carefully all this section to know about the policy of usage of each of these filesystems. There are 3 different types of storage available inside a node:

Root Filesystem

GPFS Filesystems

Local Hard Drive

Running Jobs

Software

Acknowledgment in publications

Getting Help

IFCA provides to users consulting assistance. User support consultants are available during normal business hours, Monday to Friday, 09 a.m. to 18 p.m. (CEST time).

User questions and support are handled at: <res_support@ifca.unican.es> If you need assistance, please supply us with the nature of the problem, the date and time that the problem occurred, and the location of any other relevant information, such as output

Appendices

A. SSH

SSH is a program that enables secure logins over an insecure network. It encrypts all the data passing both ways, so that if it is intercepted it cannot be read. It also replaces the old an insecure tools like telnet, rlogin, rcp, ftp,etc. SSH is a client-server software. Both machines must have ssh installed for it to work.

We have already installed a ssh server in our machines. You must have installed an ssh client in your local machine. SSH is available without charge for almost all versions of Unix. We recommend the use of OpenSSH client that can be download from http://www.openssh.org, but any client compatible with SSH version 2 can be used.

In windows systems we recommend the use of putty. It is a free SSH client that you can download from http://www.putty.nl/. But you can also, any client compatible with SSH version 2 can be used.

To transfer files to or from Altamira you need a secure ftp (sftp) o secure copy (scp) client. There are several different clients, but as previously mentioned, we recommend the use of putty clients for transferring files: psftp and pscp. You can find it at the same web page as putty ( http://www.putty.nl/ ).

Some other possible tools for users requiring graphical file transfers could be:

For using psftp you need to pass it the machine name (altamira1.ifca.es), and then the username and passwd. Once you are connected, it's like a Unix command line. With command help you will obtain a list of all possible commands. But the most useful are:

get file_name
To transfer from Altamira to your local machine.
put file_name
To transfer a file from your local machine to Altamira.
cd directory
To change remote working directory.
dir
To list contents of a remote directory.
lcd directory
To change local working directory.
!dir
To list contents of a local directory.