it center der rwth aachen university lab system environment paul kapinos 2014.10.07
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IT Center der RWTH Aachen University
Lab System Environment
Paul Kapinos
2014.10.07
aiXcelerate 2014 – Lab System EnvironmentPaul Kapinos | IT Center der RWTH Aachen University
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Lab nodes: integrated to HPC Cluster
OS:
Scientific Linux 6.5 (RHEL6.5 compatible)
Batch system:
LSF 9.1
not for this lab
Storage:
NetApp filer ($HOME / $WORK) no backup on $WORK
Lustre ($HPCWORK) not available
aiXcelerate 2014 – Lab System EnvironmentPaul Kapinos | IT Center der RWTH Aachen University
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Software Environment
Compiler:
Intel 15.0 (and older)
GCC 4.9 (and older)
Oracle Studio, PGI
MPI:
Open MPI, Intel MPI
No InfiniBand! 1GE only
Warnings and 1/20 of usual performance
Default:
intel/14.0 + openmpi/1.6.5
aiXcelerate 2014 – Lab System EnvironmentPaul Kapinos | IT Center der RWTH Aachen University
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How to login
Frontends
login / SCP File transfer:
$ ssh [-Y] [email protected]
$ scp [[user@]host1:]file1 [...] [[user@]host2:]file2
then jump to the assigned lab node
$ ssh lab5[.rz.rwth-aachen.de]
cluster.rz.RWTH-Aachen.DE cluster2.rz.RWTH-Aachen.DE
cluster-x.rz.RWTH-Aachen.DE GUI cluster-x2.rz.RWTH-Aachen.DE GUI
cluster-linux.rz.RWTH-Aachen.DE cluster-linux-nehalem.rz.RWTH-Aachen.DE
cluster-linux-xeon.rz.RWTH-Aachen.DE cluster-linux-tuning.rz.RWTH-Aachen.DE
cluster-copy.rz.RWTH-Aachen.DE ‘scp’ cluster-copy2.rz.RWTH-Aachen.DE ‘scp’
aiXcelerate 2014 – Lab System EnvironmentPaul Kapinos | IT Center der RWTH Aachen University
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Lab Node Assignment
Please use your’s allocated node only
or agree in advance with the node owner
aiXcelerate 2014 – Lab System EnvironmentPaul Kapinos | IT Center der RWTH Aachen University
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Lab nodes
Intel(R) Xeon(R) CPU E5-2699 v3 @ 2.30GHz
Packages(sockets) / Cores per package / Threads per core : 2/18/2
Cores / Processors(CPUs) : 36 / 72
AVX2: 256bit register
2x Fused Multiply Add (FMA) >> double peak performance cf. previous chips
64GB RAM
Stream: >100Gb/s (Triad)
No InfiniBand connection
MPI via 1GE network still possible
Warnings and 1/20 of usual performance
aiXcelerate 2014 – Lab System EnvironmentPaul Kapinos | IT Center der RWTH Aachen University
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Module System
Many compilers, MPIs and ISV software The module system helps to manage all the packages
List loaded modules / available modules$ module list$ module avail
Load / unload a software$ module load <modulename>$ module unload <modulename>
Exchange a module (Some modules depend on each other)$ module switch <oldmodule> <newmodule>
$ module switch intel intel/15.0 Reload all modules (May fix your environment)
$ module reload Find out in which category a module is:
$ module apropos <modulename>
aiXcelerate 2014 – Lab System EnvironmentPaul Kapinos | IT Center der RWTH Aachen University
9
MPI
No InfiniBand connection
MPI via 1GE network, >> warnings and 1/20 of usual performance Default: Open MPI 1.6.5
e.g. switch to Intel MPI:
$ module switch openmpi intelmpi
Wrapper in $MPIEXEC redirects the processes to ‘back end nodes’
by default your processes run on (random) non-Haswell node
use the ‘-H’ option to start the processes on favoured node
$ $MPIEXEC -H lab5,lab6 -np 12 MPI_FastTest.exe other options of the interactive wrapper
$ $MPIEXEC -help | less
aiXcelerate 2014 – Lab System EnvironmentPaul Kapinos | IT Center der RWTH Aachen University
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Documentation
RWTH Compute Cluster Environment
HPC Users‘s Guide (a bit outdated):
http://www.rz.rwth-aachen.de/hpc/primer
Online documentation (including example scripts):
https://doc.itc.rwth-aachen.de/
Man-Pages for all commands available
In case of errors / problems let us know:
aiXcelerate 2014 – Lab System EnvironmentPaul Kapinos | IT Center der RWTH Aachen University
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Lab
We provide laptops
Log in to the laptops with the local „hpclab“ account (your own PC pool
accounts might also work)
Use X-Win32 to log in
to the cluster (use “hpclab0Z”
or your own account)
Log in to the labZ node (use
“hpclab0Z” account)
Feel free to ask questions Source: D. Both, Bull GmbH