Computational resources

DSASD

 Electronic Numerical Integrator and Computer (ENIAC), 1946 Developed by the US Army during World War II to calculate missile trajectories,the now “ancient” ENIAC weighed more than 30 tons and occupied 1,800 sq. ft. of space. No one would have imagined that within 50 years its computing power would be surpassed by something as tiny as a laptop computer.

This document aims to provide some important and useful information on the computational resources available to CM Sector members. These resources are:

  • personal workstations (usually Linux PCs)
  • computational servers (“number-crunching” machines)
  • specific software packages (e.g. compilers, math libraries, etc.)

and are set up and maintained by people of the sector and by SIS, the SISSA computer staff. Information about this kind of resources is organized in the following sections:

Other kind of computer resources (file/account server, printers, web server, mail server, local network, etc.) are provided and maintained directly by SIS. For questions and problems concerning this kind of resources, please refer to the SIS webpage (which contains manuals, instructions, an index of services and a FAQ section) or contact directly the SIS Helpdesk, preferably by e-mail (helpdesk@sissa.it) or by phone (ext. 822). The Helpdesk office is open from Monday to Friday 9.30-11.30 and during the afternoon from Monday to Thursday 15.00-16.00 (the afternoon service is not guaranteed in case of reduced staff). Assistance by e-mail is available from Monday to Thursday 8.30-17.30 and on Friday 8.30-14.00.

If you use your laptop at SISSA, in order to have full access to the network resources of SISSA you first have to register your notebook through a simple procedure described at this link.

The Condensed Matter cluster

Each member of the CM Sector is entitled to get a user account on the workstations belonging to the Sector (which, as a whole, will be referred to as “Condensed Matter cluster” or “CM cluster”). If you need such an account or a renewal of your existing account (before it has expired!) please contact Stefano de Gironcoli or Andrea Dal Corso and follow the instructions described at the following link.

These accounts allow CM users to access any of the machines belonging to the CM cluster, though each new user will be usually provided with one personal workstation within his/her office. Moreover, with the same username and password one can have access to other services, such as:

  • an e-mail account with address username@sissa.it (or alias name.surname@sissa.it), also accessible via webmail
  • remote login to the SISSA ssh gateway (shannon.sissa.it)
  • login to the Linux and Windows workstations at the entrance of the SISSA main building.

Anyone using the CM cluster should know some important points about it:

  • Cluster type is NFS/LDAP. NFS (Network File System) means that all the files contained in your home directory (/u/cm/username) reside physically on a remote machine (calledfilesrv-cm), which is connected to all the machines of the cluster through the network. Therefore you can see the same home directory from any of the CM cluster machines and have access to all the files you’ve stored in that directory. LDAP is a centralized authentication system which brings the information about the user accounts to every PC of the cluster and so allows each CM user to login on any of them with the same username and password .
  • You can store data in your home directory up to a maximum amount of bytes (your “quota”, which is about 1 GB); in order to check your quota and the space left for your data on filesrv-cm, type the command quota -v . You can still write your data on local disks, by creating a subdirectory in the /scratch/ directory (each of the CM cluster machines should have one), for istance by issuing
    mkdir /scratch/username from a Linux shell. Some PCs have also a /data/directory, which you can use to store your data as well. Notice that these local directories will be never backed-up.
  • All the workstations belonging to the CM cluster are interconnected through a LAN (Local Area Network) and are accessible one from another via SSH, the Secure SHell utility (e.g. if you are logged on a CM cluster machine called “qui”, you can login on a machine called “quo” using the command ssh quo ). In this way it is possible to be logged on different machines at the same time.
  • On the other hand you should avoid to start more than one graphical session simultaneously (e.g. you should not use KDE or Gnome simultaneously on different PCs), or use the graphical session on different PCs (which may have different software versions). For the graphical session always use your workstation. The above mentioned wrong usage of the graphical session may cause: overwriting of desktop configuration files in your home directory, hang-ups of the machine or file inconsistencies.
  • Data in your home directory is also accessible from outside SISSA by connecting to shannon (full hostname: shannon.sissa.it) with SSH, since this machine mounts the same home directory as the CM cluster (i.e. the files in /u/cm/username you see when working on shannon are the same as those seen from any of the CM cluster machines). If you need to have a lot of data temporarily available on line and its size does not fit in your quota, you can copy that data to the /scratch/ directory of shannon (which can also be seen from outside SISSA). For example, if you have a big archive called huge.tar.gz on the local scratch of qui, you can copy it on shannon by issuing:
    scp /scratch/username/huge.tar.gz shannon:/scratch/username while being logged on qui (the directory /scratch/username may not exist on shannon; in this case you must first create it on shannon). In order to copy the content of an entire directory tree (i.e. all subdirectories and files) you can use the scp command with the options -Crp , as in the following example:
    scp -Crp ./mytree shannon:/scratch/username . Notice that the scratch directory of shannon is periodically cleaned up by automatically removing those files which are older than 15 days, so do not keep there the originals of your data.
  • For serious security matters most of the PCs of the CM cluster are not accessible from outside the cluster itself (e.g. you are not allowed to login on them with SSH from outside SISSA), so you will not be able to acces their local disks from the outside. For more information about this, you can ask to Giacomo Mazza or Helpdesk.
  • Installation and setup of all the machines is under the responsibility of SIS staff. Please do not move or disconnect from the LAN your workstation or any other PC in your room. If you have particular needings or requests regarding the usage of PCs or laptops in SISSA, please contact Giacomo Mazza or the Helpdesk staff. Do not switch off or unplug the machines without properly shutting down the operating system, because this operation could damage the filesystem and cause loss of data.
  • All PC belonging to the CM cluster have Linux operating system and are provided with the most widely used scientific application software, both open source and licensed. A list of the software currently available under license is mantained by SIS. If you want to use one of the programs listed there and you can’t find it on your PC, or if you need some additional open source program for your research activity, please contact Giacomo Mazza or the Helpdesk directly.
  • By default every PC should be connected to the printers; at the network printers webpage you can find a list of the available network printers, as well as some links to useful printing utilities (installation wizards, printer queue monitor, etc.). You can monitor and manage your print jobs through the printer spooler webpage (http://spooler.printers.sissa.it).
  • In order to change your passwordthere are two ways. The first way is to follow these two steps:
    1. login into shannon (ssh username@shannon.sissa.it or simply ssh shannon if your already logged in to the CM cluster)
    2. issue the command sissa-passwd and follow the instructions.

    The other possibility is to select “Change your password” on the webmail page. Since the password is shared among all SISSA informatic services, this procedure will change it not only on the CM cluster, but also on all other machines connected to the LDAP system. This means that you will have to access to all the machines or services listed above (shannon, e-mail account, webmail, etc.) using the new password. The obsolete commands passwd and yppasswd must not be used.

  • For small computational needings, each CM user should preferably utilize his/her own personal workstation in the cluster. Nevertheless, some of the machines may be free in some periods or unused during some part of the day (e.g. by night) and therefore can be used for computations by users other than the owner. This must be done in the strict respect of the policy described in the “Usage policy of the CM cluster machines for computations” section. If your applications have larger computational requirements, you can ask for an account on the parallel machines hosted at SISSA or at CINECA (see the High Performance Computing section below for further details).

In the case you will need more information about the CM cluster and the services related to it, you can contact Giacomo Mazza or the Helpdesk.

[top]

Usage policy of the CM cluster machines for computations

There isn’t any queue system in the CM cluster, so it is fundamental to behave correctly in order to avoid misunderstandings. Here are some very general rules; fair-play and flexibility are basic requirements.

  1. Resources are to be used, nevertheless personal PC belonging to the cluster should not generally used for computations by other users but the owner.
  2. Some fast PCs (see the list of machines to identify them) in the cluster can however be used to run some computations. If a PC is the personal workstation of another user, you should ask for permission to him/her before running your computations on it. You should not run more than one production job at a time on them and always run your executable at the lowest priority using the command nice -19 ./executable .
  3. Do not run jobs on the SISSA ssh gateway (shannon), since that machine is not devoted to computations, but only to manage your email (e.g. with pine or mutt) or access from the outside the files in your home directory.
  4. For I/O intensive applications (i.e. huge data on input/output files), you are strongly suggested to use the local disk of the machine where your executable is running and not your home directory. Since the latter is accessed by the machine through the network, the reading and writing procedure could slow down terribly and make the performance of your application worse.

[top]

High Performance Computing

For large computational requirements there are some parallel platforms at disposal. Some of them are hosted locally at SISSA, while the most powerful are hosted at CINECA (Consorzio Interuniversitario del Nord Est per il Calcolo Automatico).

CINECA is one of the main High Performance Computing facility in Italy and it provides machines for parallel and high performance calculations. If you need to access some of these facilities, you must contact your supervisor. Rules and computer time are allocated through INFM grant (see infm.cineca.it and contact Carlo Cavazzoni for further details) or through the SISSA-CINECA partnership.

Some clusters are installed at the SISSA/Democritos site and are available for serial and parallel computations. Detailed information about these machines (system features, usage policies, user documentation, howto’s, etc.) can be found at the Democritos Cluster-Wiki page. In order to get an account, please first contact your responsible at SISSA (who should belong to the permanent scientific staff) and then write to helpdesk-hpc@sissa.it. Some additional information about SISSA/Democritos HPC machines can be found at the Documentation page of the Democritos website.

[top]

Useful information and links

[top]