User Guide new config : Différence entre versions
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(→ Softwares) |
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pastix/5.2.2.20-nompi | pastix/5.2.2.20-nompi | ||
qwt/6.1.2-qt5 | qwt/6.1.2-qt5 | ||
+ | trilinos/trilinos-12.2.1 | ||
vtk/6.2.0-qt5 | vtk/6.2.0-qt5 | ||
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* blas, atlas | * blas, atlas | ||
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* openblas | * openblas | ||
* gmsh 2.8.5 | * gmsh 2.8.5 | ||
* Python (including scipy, numpy, pycuda) | * Python (including scipy, numpy, pycuda) | ||
− | * | + | * R 3.2.1 |
− | |||
* Erlang | * Erlang | ||
* GDB & DDD | * GDB & DDD |
Version du 3 septembre 2015 à 14:01
nef new configuration is currently a BETA VERSION with no warranty concerning jobs and data : service may be interrupted, configuration modified and data spaces may be cleared
Front-end
The cluster is based on several front-end servers and a lot of compute nodes.
2 servers are available:
- nef-frontal.inria.fr alias nef.inria.fr : main front-end, ssh and submission front-end
- nef-devel2.inria.fr : compilation, ssh and submission front-end
Currently, the only way to use the cluster is to connect to one of the front-end with ssh. Then you can have access to the computing resources available by using the Oar job manager.
The nef cluster is not part of the internal (production) network of Inria; therefore Inria (iLDAP) accounts/passwords are not used.
First steps
- First you need to apply for an account on the nef cluster. You must give your ssh public key to have an account.
- Then connect to one of the main front-end nef.inria.fr or nef-devel2.inria.fr using ssh
- Then you can import your data / sources files using rsync,scp on the nef front-end and compile your programs on nef-devel2.inria.fr
- Use the job manager to start your tasks
- You can view the current running jobs using the Monika web interface. You can also see jobs in gantt format DrawGantt .
Disk space management
All data stored on the cluster ARE NOT backed up ! They are LOST and NOT RECOVERABLE in the case of accidental deletion or server hardware failure.
Each user has a dedicated directory in the /home storage.
- A quota system is activated on the shared storage server:
- The soft limit is 40GB
- The hard limit 350GB
- The delay is 4 weeks
- You can use 40GB of data without restrictions; as soon as the soft limit is reached, you have 4 weeks in which to delete files and go back under the soft limit. You can never use more than the hard limit.
- A warning message will be sent by mail every Sunday when a limit is reached.
- You can check you current disk occupation with the
quota -s
command
A distributed scalable file system is available under /data for several usages :
- long term storage : 1TB quota per team shared among the team members ; teams may buy additional quota please contact the cluster administrators
- scratch storage (for transient / short term storage) : variable total size, no quota is currently applied per user or per team, but data may be periodically purged by administrators
- data is tagged as long term storage or scratch storage based on Unix group of files :
- use
chgrp my_team_unix_group my_file
to tag my_file as long term storage - use
chgrp scratch my_file
to tag my_file as scratch storage
- use
- check your quota with
sudo beegfs-ctl --getquota --uid my_logname
or your team quota withsudo beegfs-ctl --getquota --gid my_team_unix_group
More (legacy) storage is available for the ABS, ASCLEPIOS, MORPHEME, NEUROMATHCOMP and TROPICS team members in /epi/<teamname>/<username>.
There is also temporary disk space available on each node, in the /tmp directory
Softwares
All nodes are installed using a Linux Centos 7 64bit distribution
Main softwares available on the cluster:
- 3.10.0 linux x86_64 kernel
- PGI 14.10 compilers
- GCC 4.8.3 (C,C++, Fortran77, Fortran95 compilers)
- OpenMPI 1.8.8 / 1.6.4
- Paraview 4.2.0
- Mvapich2 1.9a2
- Java 1.8 + java3D 1.5.2
- Matlab 2015a (
/mist/opt/matlab2015a/bin/matlab
) - Intel Parallel Studio 2015 (
/misc/opt/intel2015/
) - CUDA 7.0 (/usr/local/cuda) + CUDA SDK (/usr/local/cuda/samples)
- DDT debugger (
/opt/allinea/ddt
, see Documentation) - Environment Modules: type
module avail
to list all available modules:
boost/1.58.0 likwid/4.0.1 mpi/intel64-5.0.3.048 mpi/openmpi-1.8.8-gcc mpi/openmpi-x86_64 mpi/mvapich2-x86_64 mpi/openmpi-1.8.8-pgi petsc/3.4.5 scotch/6.0.4 hypre/2.9.1a metis/5.1.0 pastix/5.2.2.20-nompi qwt/6.1.2-qt5 trilinos/trilinos-12.2.1 vtk/6.2.0-qt5
Other tools/libraries available:
- blas, atlas
- openblas
- gmsh 2.8.5
- Python (including scipy, numpy, pycuda)
- R 3.2.1
- Erlang
- GDB & DDD
- Valgrind
- GSL & GLPK
- boost 1.53.0 and 1.58.0