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RES LaPalma User Manual

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Table of contents

1 . Introduction.....................................................................................................................................2
2 .
Overview............................................................................................................................2
3 .
Documentation....................................................................................................................2
3.1 .
4 .
LaPalma...................................................................................................................2
4.1 .
node...............................................................................................................................3
4.2 .
4.3 .
applications.............................................................................................................4
5 .
Systems....................................................................................................................................4
5.1 .
Filesystem.......................................................................................................................5
5.2 .
Filesystem.....................................................................................................................5
5.3 .
6 .
Jobs...................................................................................................................................6
6.1 .
(QOS)..........................................................................................................................6
6.2 .
6.2.1 .
6.2.2 .
directives....................................................................................................................7
6.2.3 . Examples...........................................................................................................................9
7 .
Environment..................................................................................................................10
7.1 . Modules..................................................................................................................................10
7.2 .
Compilers............................................................................................................................11
7.2.1 .
7.2.2 .
7.2.3 .
7.2.4 .
addressing.............................................................................................................12
7.2.5 . Optimization...................................................................................................................12
7.3 .
7.3.1 .
7.3.2 .
7.3.3 .
64 bit
Addressing............................................................................................................12
7.4 . Optimization..........................................................................................................................13
7.5 . Debuggers..............................................................................................................................13
7.6 .
8 .
help...................................................................................................................................13
9 . FAQ's............................................................................................................................................13
10 . Acknowledgements.....................................................................................................................14
APPENDIX..........................................................................................................................................16
A. SSH................................................................................................................................................16
LaPalma User's Guide
Copyright © 2018
files......................................................................................................................3
Drive.....................................................................................................................6
jobs........................................................................................................................7
commands..........................................................................................................7
Parallelism.....................................................................................11
Parallelism............................................................................................11
Parallelization................................................................................................12
Compilers...........................................................................................................12
Parallelism.....................................................................................12
Parallelism............................................................................................12
LaPalma...............................................................................................................13
Linux...................................................................................16
Linux...........................................................................................17
Windows......................................................................................21
Session.............................................................17
Session.............................................................................17
Windows.............................................................................17
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Summary of Contents for RES LaPalma

  • Page 1: Table Of Contents

    LaPalma User's Guide Copyright © 2018 Table of contents 1 . Introduction.............................2 System Overview..........................2 Online Documentation........................2 3.1 . pages..........................2 Connecting to LaPalma........................2 4.1 . Login node..........................3 4.2 . Transferring files........................3 4.3 . Graphical applications......................4 File Systems............................4 5.1 . Root Filesystem........................5 5.2 .

  • Page 2: Introduction

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

  • Page 3: Login Node

    The machine in which you will be logged in will be LaPalma (login1). This machine acts as front ends, and are used typically for editing, compiling, preparation/submission of batch executions and as a gateway for copying data inside or outside LaPalma.

  • Page 4: Graphical Applications

    'Tunneling' or 'Connection' menu of the client configuration window (see appendix A for further details). 5 . File Systems IMPORTANT: It is your responsibility as a user of the LaPalma system to backup all your critical data. NO backup of user data will be done in any of the filesystems of LaPalma.

  • Page 5: Root Filesystem

    Even though there is only one Lustre filesystem mounted on LaPalma, there are different locations for different purposes: /storage/home: This location has the home directories of all the users. When you log into LaPalma you start in your home directory by default. Every user will have their own home directory to store the executables, own developed sources and their personal data.

  • Page 6: Local Hard Drive

    /storage/apps so all users on LaPalma could make use of it. If the application needs some type of license and its use must be restricted, a private directory over /storage/apps will be created, so only the required users of LaPalma could make use of this application.

  • Page 7: Submitting Jobs

    class_b 1200 48 hours class_c 1200 24 housr debug 10 min interactive 1 hour The specific limits assigned to each user depends on the priority granted by the access committee. Users granted with "high priority hours" will have access to a maximum of 4032 CPUs and a maximum wall_clock_limit of 72 hours.

  • Page 8: Job Directives

    6.2.2 . Job directives A job must contain a series of directives to inform the batch system about the characteristics of the job. These directives appear as comments in the job script, with the following syntax: #SBATCH –-directive=<value> Some come directives have a shorter version, you can use both forms: #SBATCH -d <value>...

  • Page 9: Examples

    This will enable Array Jobs. Array jobs and task generation can be used to run applications over different inputs like you could also do with GREASY in past versions of LaPalma or MareNostrum. It will create as many jobs as you specify from ini to end and the step (step by default is 1). You can get the current task using $SLURM_ARRAY_TASK_ID.

  • Page 10: Software Environment

    % module switch gcc/4.8.5 7.2 .C Compilers In LaPalma you can find the next C/C++ compilers : gcc /g++ -> GNU Compilers for C/C++, versions 4.8.5 and 7.2.0 (by default). You can choose the compiler you want to use with modules.

  • Page 11: Distributed Memory Parallelism

    By default all compilers will use the 64 bit addressing 7.2.5 . Optimization The level optimization that we recommend for LaPalma (E5-2670 Sandy Bridge processors) is : -O3 -march=native Applications compiled with -march=native might be executed properly only on those machines where...

  • Page 12: Bit Addressing

     7.6 .Software in LaPalma There is a number of different software installed in LaPalma (compilers, applications, libraries, tools, etc.). Please, use modules to see all installed software. If you need a particular software or version that is not already installed, please, contact us.

  • Page 13: Getting Help

    9.9. Should I be careful wih the memory consumption of my jobs? Yes, you should. Each one of the LaPalma nodes has 32 Gb of RAM shared by 16 cores. Up to 90 % of this memory can be consumed for user jobs, while, at least, 10 % has to be available for the Operating System and daemons.

  • Page 14: Acknowledgements

    You should mention it in the acknowledgements of your papers or any other publications where you have used LaPalma: The author thankfully acknowledges the technical expertise and assistance provided by the Spanish Supercomputing Network (Red Española de Supercomputación), as well as the computer resources used: the LaPalma Supercomputer, located at the Instituto de Astrofísica de Canarias."...

  • Page 15: Appendix

    OpenSSH client that can be download from http://www.openssh.org, but any client compatible with SSH version 2 can be used. To accomplish a login in LaPalma with SSH you have to provide a public key. If you have not got already one you can generate a public/private key pair with the following instructions.

  • Page 16: Using The Ssh-Agent In Linux

    Once the public/private key pair is generated you have to send the public key file ~/.ssh/id_rsa.pub to res_support@iac.es A.1.1.Using the ssh-agent in Linux When doing lots of secure shell operations it is cumbersome to type the SSH passphrase for each such operation.
  • Page 17 Select RSA as Type of key and introduce 4096 in the field of “number of bits” and click on “Generate”:...
  • Page 18 The tool requires that you move the mouse randomly: Click on “Save public key” to store the public key and send it to res_support@iac.es Enter a passphrase consisting of 10 to 30 characters. The same rules as for creating safe passwords apply. It is strongly advised to refrain from specifying no passphrase.

  • Page 19: Using The Ssh-Agent In Windows

    Keep the private key file in a safe location and do not share with anyone. A.2.1.Using the ssh-agent in Windows As in the case of Linux, the package Putty provides a tool to avoid typing the SSH passphrase for each connection.
  • Page 20 Push “Add Key” and select the private key previously generated: Enter the passhphrase: The list is updated and you can click on “Close”:...
  • Page 21 Yes: IMPORTANT: If you see this warning another time and you haven't modified or reinstalled the ssh client, please, don't log in and contact with LaPalma support.
  • Page 22 Finally, a new window will appear asking for your username: To transfer files to or from LaPalma you need a secure ftp (sftp) o secure copy (scp) client. There are several different clients, but as previously mentioned, IAC recommends the use of putty clients for...

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