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=== The CSDMS High Performance Computing Cluster ===
= The CSDMS High Performance Computing Cluster (Code name: Blanca) =


[[Image:Altix XE.jpg | 100px]]
The CSDMS High Performance Computing Cluster (HPCC) provides CSDMS researchers a state-of-the-art HPC cluster.


==== Hardware ====
Use of the CSDMS HPCC is available free of charge to the CSDMS community!  Follow [[HPCC_account_requirements|these guidelines]] to request a one year guest account on our machine.


== Attribution and Reporting of Results ==
When reporting results which were obtained on the CSDMS cluster, we request that the following language be used as an acknowledgement:


"We acknowledge computing time on the CU-CSDMS High-Performance Computing Cluster."


==== Software ====
Also, please notify us of any tech reports, conference papers, journal articles, theses, or dissertations which contain results which were obtained on blanca. Your assistance will help to ensure that our online bibliography of results is as complete as possible. Citations should be sent to [mailto:CSDMSsupport@colorado.edu us].


'''Web server node:''' (SSL certified)
== Hardware ==
# Mediawiki 1.12.1 (this is ''not'' the latest version)
[[File:sgi_logo_hires.jpg | right | 250px ]]
# Apache
 
# PHP version 5.1.x or later
The CSDMS High Performance Computing Cluster is an [http://www.sgi.com SGI] [http://www.sgi.com/products/servers/altix/xe Altix XE] 1300 that consists of 64 Altix XE320 compute nodes (for a total of 512 cores).  The compute nodes are configured with two quad-core 3.0GHz E5472 (Harpertown) processors.  54 of the 64 nodes have 2 GB of memory per core, while the remaining nodes have 4 GB of memory per core.  The cluster is controlled through an Altix XE250 head node.  Internode communication is accomplished through either gigabit ethernet or over a non-blocking [http://en.wikipedia.org/wiki/InfiniBand InfiniBand] fabric.
## With Perl Compatible regular expressions
 
## With Standard PHP Library
Each compute node has 250 GB of local temporary storage. However, all nodes are able to access 36TB of RAID storage through NFS.
# [http://www.viewvc.org ViewVC]
 
# [http://subversion.tigris.org Subversion]
The CSDMS system will be tied in to the larger 7000 core (>100 Tflop) '''Front Range Computing Consortium'''.  This supercomputer will consist of 10 Sun Blade 6048 Modular System racks, nine deployed to form a tightly integrated computational plant, and the remaining rack to serve as a GPU-based accelerated computing system.In addition, the Grid environment will provide access to NCAR’s mass storage system.
# [http://pear.php.net/package/VersionControl_SVN VersionControl_SVN 0.3.1 or newer] (with Dependencies:)
4.10
## PHP Version: PHP 4.0.0 or newer
 
## PEAR Package: PEAR 1.4.0b1 or newer
Some benchmarks that we've run on blanca:
## PEAR Package: PEAR 1.3.1 or newer
* The OSU [[ CSDMS_HPCC_OMB_benchmarks |micro-benchmarks]]
## PEAR Package: XML_Parser 1.0.1 or newer
 
# ArcGIS license server software
=== Hardware Summary ===
# [http://www.imagemagick.org ImageMagick]
{|
# [http://trac.edgewall.org/ Trac]
! align=left width=150 | Node
! align=left width=150 | Type
'''Database node:'''
! align=left width=200 | Processors
# MySQL 5.0.x
! align=left width=100 | Memory
! align=left width=150 | Internal Storage
'''Compute Nodes:'''
|-
: Free stuff:
| blanca.colorado.edu
# [http://www.pythonware.com/products/pil Python Imaging Library (PIL)]
| Head (Altix XE250)
# [http://www.unidata.ucar.edu/software/udunits Udunits]
| 2 Quad-Core Xeon<ref name=proc_specs>
# [http://www.unidata.ucar.edu/software/netcdf netcdf]
Processors are Quad-core Intel Xeon E5472 (Harpertown):
# [http://www.openmotif.org openmotif]
* Front Side Bus: 1600 MHz
# [http://www.eclipse.org) Eclipse]
* L2 Cache: 12MB
# [http://subclipse.tigris.org Subclipse]
</ref>
# [http://www.astro.caltech.edu/~tjp/pgplot Pgplot]
| 16GB<ref name=mem_specs>
# [http://www.hdfgroup.org/HDF5/release/index.html HDF5]
Memory is DDR2 800 MHz FBDIMM</ref>
# [http://www.mathworks.com Matlab]
| --
# [http://eucalyptus.cs.ucsb.edu/ Eucalyptus]
|-
# Languages:
| cl1n001 - cl1n056
## Python 2.6, 3000 (along with numpy and scipy where possible)
| Compute (Altix XE320)
## Java 1.6
| 2 Quad-Core Xeon <ref name=proc_specs/>
## GNU compilers > 4.0 (gcc, g++, gfortran)
| 16GB <ref name=mem_specs/>
: Not free stuff:
| 250GB SATA
# [http://www.esri.com/ Arc 8.0.2]
|-
# [http://www.esri.com/software/arcview/ ArcView 3.2]
| cl1n057 - cl1n064
# [http://www.rivix.com Rivertools]
| Compute (Altix XE320)
| 2 Quad-Core Xeon <ref name=proc_specs/>
| 32GB <ref name=mem_specs/>
| 250GB SATA
|}
 
<references />
 
== Software ==
[[Image:HPCC.png | 350px | right | The CSDMS HPCC]]
 
Below is a list of some of the software that we have installed on blanca.  If there is a particular software package that is not listed below and would like to use it, please feel free to send an email to [mailto:CSDMSsupport@colorado.edu us] outlining what it is you need.
 
=== Compilers ===
{|
! align=left width=100 |  Name
! align=left width=100 |  Version
! align=left width=100 | Module Name
! align=left | Location
|-
| [http://gcc.gnu.org/ gcc]
| 4.1
| gcc/4.1
| /usr
|-
| [http://gcc.gnu.org/ gcc]
| 4.3
| gcc/4.3
| /usr/local/gcc
|-
| [http://gcc.gnu.org/wiki/GFortran gfortran]
| 4.1
| gcc/4.1
| /usr
|-
| [http://gcc.gnu.org/wiki/GFortran gfortran]
| 4.3
| gcc/4.3
| /usr/local/gcc
|-
| icc
| 11.0
| intel
| /usr/local/intel
|-
| ifort
| 11.0
| intel
| /usr/local/intel
|-
| [http://www.mcs.anl.gov/research/projects/mpich2/ mpich2]
| 1.1
| mpich2/1.1
| /usr/local/mpich
|-
| [http://mvapich.cse.ohio-state.edu/ mvapich2]
| 1.2
| mvaich2/1.2
| /usr/local/mvapich
|-
| [http://www.open-mpi.org/ openmpi]
| 1.3
| openmpi/1.3
| /usr/local/openmpi
|}
 
=== Languages ===
{|
! align=left width=100 | Name
! align=left width=100 | Version
! align=left width=100 | Module Name
! align=left | Location
|-
| Python<ref>
Python 2.4 modules:
* [http://numpy.scipy.org/ numpy] 1.2.1
* [http://www.scipy.org/ scipy] 0.6.0
* [http://www.pythonware.com/products/pil Python Imaging Library (PIL)]
</ref>
| 2.4
| python/2.4
| /usr
|-
| Python<ref>
Python 2.6 modules:
* [http://numpy.scipy.org/ numpy] 1.3.0
* [http://www.scipy.org/ scipy] 0.7.1rc3
* [http://www.pyngl.ucar.edu/Nio.shtml PyNIO] 1.3.0b1
* [https://ipython.org/ iPython] 0.10
* [http://www.cython.org Cython] 0.11.3
</ref>
| 2.6
| python/2.6
| /usr/local/python
|-
| Java
| 1.5
| --
| --
|-
| Java
| 1.6
| --
| --
|-
| perl
| 5.8.8
| --
| /usr
|-
| [http://www.mathworks.com/ MATLAB]
| 2008b
| matlab
| /usr/local/matlab
|}
 
<references/>
 
=== Libraries ===
{|
! align=left width=100 |  Name
! align=left width=100 |  Version
! align=left width=100 | Module Name
! align=left | Location
|-
| [http://www.unidata.ucar.edu/software/udunits Udunits]
| 1.12.9
| udunits
| /usr/local/udunits
|-
| [http://www.unidata.ucar.edu/software/netcdf netcdf]
| 4.0.1
| netcdf
| /usr/local/netcdf
|-
| [http://www.hdfgroup.org/HDF5 hdf5]
| 1.8
| hdf5
| /usr/local/hdf5
|-
| [http://xmlsoft.org/index.html libxml2]
| 2.7.3
| libxml2
| /data/progs/lib/libxml2
|-
| [http://www.gtk.org/ glib-2.0]
| 2.18.3
| glib2
| /usr/local/glib
|-
| petsc
| 3.0.0p3
| petsc
| /usr/local/petsc
|-
| [http://www.mcs.anl.gov/research/projects/mct/ mct]
| 2.6.0
| mct
| /data/progs/mct/2.6.0-mpich2-intel
|}
 
=== Tools ===
{|
! align=left width=100 |  Name
! align=left width=100 |  Version
! align=left width=100 | Module Name
! align=left | Location
|-
| [http://www.cmake.org/ cmake]
| 2.6p2
| cmake
| /usr/local/cmake
|-
| [http://www.scons.org/ scons]
| 1.2.0
| scons
| /usr/local/scons
|-
| [http://subversion.tigris.org/ subversion]
| 1.6.2
| subversion
| /usr/local/subversion
|-
| [http://www.clusterresources.com/torquedocs21/ torque]
| 2.3.5
| torque
| /opt/torque
|-
| [http://modules.sourceforge.net/ Environment modules]
| 3.2.6
| --
| /usr/local/modules
|}

Latest revision as of 13:55, 15 October 2019

The CSDMS High Performance Computing Cluster (Code name: Blanca)

The CSDMS High Performance Computing Cluster (HPCC) provides CSDMS researchers a state-of-the-art HPC cluster.

Use of the CSDMS HPCC is available free of charge to the CSDMS community! Follow these guidelines to request a one year guest account on our machine.

Attribution and Reporting of Results

When reporting results which were obtained on the CSDMS cluster, we request that the following language be used as an acknowledgement:

"We acknowledge computing time on the CU-CSDMS High-Performance Computing Cluster."

Also, please notify us of any tech reports, conference papers, journal articles, theses, or dissertations which contain results which were obtained on blanca. Your assistance will help to ensure that our online bibliography of results is as complete as possible. Citations should be sent to us.

Hardware

The CSDMS High Performance Computing Cluster is an SGI Altix XE 1300 that consists of 64 Altix XE320 compute nodes (for a total of 512 cores). The compute nodes are configured with two quad-core 3.0GHz E5472 (Harpertown) processors. 54 of the 64 nodes have 2 GB of memory per core, while the remaining nodes have 4 GB of memory per core. The cluster is controlled through an Altix XE250 head node. Internode communication is accomplished through either gigabit ethernet or over a non-blocking InfiniBand fabric.

Each compute node has 250 GB of local temporary storage. However, all nodes are able to access 36TB of RAID storage through NFS.

The CSDMS system will be tied in to the larger 7000 core (>100 Tflop) Front Range Computing Consortium. This supercomputer will consist of 10 Sun Blade 6048 Modular System racks, nine deployed to form a tightly integrated computational plant, and the remaining rack to serve as a GPU-based accelerated computing system.In addition, the Grid environment will provide access to NCAR’s mass storage system. 4.10

Some benchmarks that we've run on blanca:

Hardware Summary

Node Type Processors Memory Internal Storage
blanca.colorado.edu Head (Altix XE250) 2 Quad-Core Xeon[1] 16GB[2] --
cl1n001 - cl1n056 Compute (Altix XE320) 2 Quad-Core Xeon [1] 16GB [2] 250GB SATA
cl1n057 - cl1n064 Compute (Altix XE320) 2 Quad-Core Xeon [1] 32GB [2] 250GB SATA
  1. ↑ 1.0 1.1 1.2 Processors are Quad-core Intel Xeon E5472 (Harpertown):
    • Front Side Bus: 1600 MHz
    • L2 Cache: 12MB
  2. ↑ 2.0 2.1 2.2 Memory is DDR2 800 MHz FBDIMM

Software

The CSDMS HPCC
The CSDMS HPCC

Below is a list of some of the software that we have installed on blanca. If there is a particular software package that is not listed below and would like to use it, please feel free to send an email to us outlining what it is you need.

Compilers

Name Version Module Name Location
gcc 4.1 gcc/4.1 /usr
gcc 4.3 gcc/4.3 /usr/local/gcc
gfortran 4.1 gcc/4.1 /usr
gfortran 4.3 gcc/4.3 /usr/local/gcc
icc 11.0 intel /usr/local/intel
ifort 11.0 intel /usr/local/intel
mpich2 1.1 mpich2/1.1 /usr/local/mpich
mvapich2 1.2 mvaich2/1.2 /usr/local/mvapich
openmpi 1.3 openmpi/1.3 /usr/local/openmpi

Languages

Name Version Module Name Location
Python[1] 2.4 python/2.4 /usr
Python[2] 2.6 python/2.6 /usr/local/python
Java 1.5 -- --
Java 1.6 -- --
perl 5.8.8 -- /usr
MATLAB 2008b matlab /usr/local/matlab
  1. ↑ Python 2.4 modules:
  2. ↑ Python 2.6 modules:

Libraries

Name Version Module Name Location
Udunits 1.12.9 udunits /usr/local/udunits
netcdf 4.0.1 netcdf /usr/local/netcdf
hdf5 1.8 hdf5 /usr/local/hdf5
libxml2 2.7.3 libxml2 /data/progs/lib/libxml2
glib-2.0 2.18.3 glib2 /usr/local/glib
petsc 3.0.0p3 petsc /usr/local/petsc
mct 2.6.0 mct /data/progs/mct/2.6.0-mpich2-intel

Tools

Name Version Module Name Location
cmake 2.6p2 cmake /usr/local/cmake
scons 1.2.0 scons /usr/local/scons
subversion 1.6.2 subversion /usr/local/subversion
torque 2.3.5 torque /opt/torque
Environment modules 3.2.6 -- /usr/local/modules
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