Articles

Software management with GNU Guix

by Ludovic Courtes
Announcement, Documentation | No Comments

In addition to module, PlaFRIM users can manage software environments using GNU Guix, a general-purpose package manager. Why use Guix? Guix can be used in addition to and in parallel with module. There are several reasons why it might be useful to you: Guix provides more than 7,500 software packages including: utilities such as tmux, compiler toolchains (GCC, Clang), Python software (Scikit-Learn, NumPy, etc.), HPC libraries (Open MPI, MUMPS, PETSc, etc.). Pre-built binaries are usually available for packages you install, which makes installation fast. You get to choose when you upgrade or remove packages you've installed for yourself, and can roll…

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Post-processing/3D Visualization

by Philippe Depouilly
Documentation | No Comments

Using 3D visualization with VirtualGL and TurboVNC pre-requisite : - Install and setup on your desktop TurboVNC Viewer Connect to plafrim : module load slurm visu/srun srun-visu The first time, TurboVNC will ask you for a password to secure the X11 session Wait for a result like : Waiting for a slot on a visualization serverUsing 3D visualization with VirtualGL and TurboVNC Desktop 'TurboVNC: visu01:1 (login)' started on display visu01:1 Starting applications specified in /home/login/.vnc/xstartup.turbovnc Log file is /home/login/.vnc/visu01:1.log Launched vncserver: visu01:1 Now, in another terminal, open a new SSH session to plafrim like this: "ssh plafrim -N -L 5901:visu01:5901…

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Preemption queue “testpreempt”

by Nathalie Furmento
Documentation | No Comments

The queue "testpreempt" The queue "testpreempt" allows to run jobs outside the usual limits on unused computing resources (during the day but mostly at night and on weekends) without blocking the access to the resources for jobs running on the other queues. This means the jobs can be stopped ("preempted") suddenly at every moment if a regular job needs the ressources. The job will be restarted when the resources become available. The code must regularly backup its state ("checkpoint") and make sure the backup is safe (the job could be stopped while backing up) and be able to restart on…

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iRODS Storage Resource

by Nathalie Furmento
Documentation | No Comments

Introduction An iRODS Storage Resource is available at the MCIA (mésocentre Aquitain). It allows to backup your research data. Information IMPORTANT : Encryption is not available (without authentification). Data are unencrypted both on the disks and on the network. If necessary, you need to encrypt data by yourself. Data are scattered over 7 sites (Bordeaux and Pau). IRODS keeps 3 copies of every file: one nearby the storage resource the data was first copied on, one at the MCIA (near Avakas), one in another storage resource. Default quota : 500Gb. Help : https://redmine.mcia.univ.bordeaux.fr/projects/irods How to use the system One needs…

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KNL Cluster

by François Rue
Documentation, Scientific animation | No Comments

A KNL based cluster (Knights Landing (KNL) ) has been installed in February 2017. The cluster consists of 4 KNL interconnected by OmniPath. Knights Landing (7230) is a highly configurable architecture. Memory bandwidth is one of the common bottlenecks for performance in computational applications. KNL offers a solution to this problem. To do so, the 2nd generation of Intel Xeon Phi (KNL) has on-package high-bandwidth memory (HBM) based on the multi-channel dynamic random access memory (MCDRAM). This memory is capable of delivering up to 5x performance (≥400 GB/s) compared to DDR4 memory on the same platform (≥90 GB/s). The on-package…

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Module policy

by Nathalie Furmento
Announcement, Documentation | No Comments

In order to increase and to ease the use of the modules on the platform, modules are grouped within categories. Each module belongs to a specific category, which can be for example trace or statistics. The module naming policy is as follows: <category>/<module>/<option>/<version> the number of options being between 0 and as many as you want. Everyone in the group plafrim-dev is allowed to create new modules in the directory /cm/shared/dev. Modules files must be placed in the subdirectory modulefiles and follow the naming policy. Thus a module named fxt in the category trace with the version 0.3.1 and without…

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Workload manager: SLURM

by redouane bouchouirbat
Announcement, Documentation | No Comments

SLURM (Simple Linux Utility for Ressource Management) is a scalable open-source scheduler used on a number of world class clusters. This is a brief description page to give some hints and guidance to users to allow them to launch a job on the platform. Once connected to the platform, you have to load the slurm module $ module load slurm There is two ways to launch a job. 1. Interactive jobs Method 1: You need to allocate some ressources. $ salloc  -N2 -t 00:30:00 salloc: Granted job allocation 7397 squeue is used to have a look on the job state:…

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