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


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.
[[Image:Altix XE.jpg | 100px | right ]]
 
Our '''CSDMS HPCC System''' is an SGI Altix XE 1300 with integrated 512 x 3.0GHz/12M/1600MHz/80W E5472 processors, using non-blocking Infiniband Interconnect with 1.152TB of memory, with one head node, 28 compute nodes, 4 compute nodes with heavy memory, associated infrastructure, 72TB/7200RPM/SATA Raid storage, web server 4 x 2.33GHz/8GB RAM E5420 processor.<br>
== Attribution and Reporting of Results ==
The CSDMS-HPCC (≈ 6Tflops) is configured with two HPC approaches:
When reporting results which were obtained on the CSDMS cluster, we request that the following language be used as an acknowledgement:
# massive shared memory among fewer processors,
 
# the more typical parallel configuration each running Linux Red Hat with Fortran, C and C++ compilers.
"We acknowledge computing time on the CU-CSDMS High-Performance Computing Cluster."
This system offers to potential CSDMS researchers a state of the art HPC, once their code can be scaled up to take advantage of the capaboilities of these systems.
 
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].
 
== Hardware ==
[[File:sgi_logo_hires.jpg | right | 250px ]]
 
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.
 
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.
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
4.10


Some benchmarks that we've run on blanca:
* The OSU [[ CSDMS_HPCC_OMB_benchmarks |micro-benchmarks]]


==== Software ====
=== Hardware Summary ===
{|
'''Compute Nodes:'''
! align=left width=150 | Node
: Free stuff:
! align=left width=150 | Type
# [http://www.pythonware.com/products/pil Python Imaging Library (PIL)]
! align=left width=200 | Processors
# [http://www.unidata.ucar.edu/software/udunits Udunits]
! align=left width=100 | Memory
# [http://www.unidata.ucar.edu/software/netcdf netcdf]
! align=left width=150 | Internal Storage
# [http://www.openmotif.org openmotif]
|-
# [http://www.eclipse.org) Eclipse]
| blanca.colorado.edu
# [http://subclipse.tigris.org Subclipse]
| Head (Altix XE250)
# [http://www.astro.caltech.edu/~tjp/pgplot Pgplot]
| 2 Quad-Core Xeon<ref name=proc_specs>
# [http://www.hdfgroup.org/HDF5/release/index.html HDF5]
Processors are Quad-core Intel Xeon E5472 (Harpertown):
# [http://www.mathworks.com Matlab]
* Front Side Bus: 1600 MHz
# [http://eucalyptus.cs.ucsb.edu/ Eucalyptus]
* L2 Cache: 12MB
# Languages:
</ref>
## Python 2.6, 3000 (along with numpy and scipy where possible)
| 16GB<ref name=mem_specs>
## Java 1.6
Memory is DDR2 800 MHz FBDIMM</ref>
## GNU compilers > 4.0 (gcc, g++, gfortran)
| --
|-
| cl1n001 - cl1n056
| Compute (Altix XE320)
| 2 Quad-Core Xeon <ref name=proc_specs/>
| 16GB <ref name=mem_specs/>
| 250GB SATA
|-
| cl1n057 - cl1n064
| Compute (Altix XE320)
| 2 Quad-Core Xeon <ref name=proc_specs/>
| 32GB <ref name=mem_specs/>
| 250GB SATA
|}


==== Request an HPCC account ====
<references />
The HPCC is for members who participate in one of the three ways outlined below.


# They have submitted code into the CSDMS Repository, to either run their models in advance of science, or to advance their developing modeling efforts that will ultimately become part of the Repository.  Provide the community beforehand with [[Models questionnaire|metadata of the model]] you want to run on the HPCC
== Software ==
# The HPCC is also for members who wish to apply compliant CSDMS models developed by others within the CSDMS framework, to help them advance their science.   
[[Image:HPCC.png | 350px | right | The CSDMS HPCC]]
# The HPCC is for members who wish to experiment with new data systems in support CSDMS models, or to develop visualizations of the model runs.


Once you meet the above requirements you can request an [[HPCC account request | '''CSDMS HPCC account''']].
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.
   
Your HPCC guest account will be valid for ''one year''. You will receive an email as soon as your account expires. Your data (model, source code, simulations, etc) will be removed from the HPCC if you don't extend your account (by email to [mailto:csdms@colorado.edu CSDMS@colorado.edu]). Unfortunately, we have to charge a fee if data needs to be recovered after an account expires.


==== HPCC Access ====
=== Compilers ===
Once you have an account you can access the CSDMS HPCC with any secure-shell (SSH)  application (primarily ssh, scp, sftp) from workstations located in the CU Internet domain (*.colorado.edu) or from workstations connected to the colorado.edu domain through a virtual private network (VPN) connection. A VPN account will automatically be created for users outside the colorado.edu domain.
{|
! 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
|}


[http://www.colorado.edu/its/vpn/clients.html Download VPN software] if you do not have installed it already on your machine. Choose your operating platform and simply follow the installation procedure. You need your ''IdentiKey username'' and ''password'' (both provided to you when you applied for a HPCC account).  
=== 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
|}


Displaying of the graphical desktop of the HPCC master-control node to your personal workstation is possible through SSH Tunneling X Windows software. This might require prior installation and configuration of software on your workstation. See information below on how to operate the graphical desktop for [[#SSH Tunneling X Windows for Mac OSX | Mac]] and for [[#SSH Tunneling X Windows for Windows|Windows]] operating systems.
<references/>


===== SSH Tunneling X Windows for Mac OSX =====
=== Libraries ===
You will need X11 to tunnel X Windows to a Mac. Fortunately, Mac OSX comes with X11. If you're using an older version of OSX, [http://http://www.apple.com/downloads/macosx/apple/macosx_updates/x11formacosx.html download X11 from the apple site].<br>
{|
Open X11, select '''Applications''' and then '''Terminal'''.
! align=left width=100 |  Name
In the terminal type:
! align=left width=100 |  Version
ssh -Y beach.colorado.edu -l <your_username>
! align=left width=100 | Module Name
Type <password> and that's it. Now you can test the Tunneling by for example typing <matlab>.
! 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
|}


===== SSH Tunneling X Windows for Windows =====
=== Tools ===
Install [http://www.straightrunning.com/XmingNotes/ Xming] on your windows machine.  
{|
''Needs more info''
! 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

Sgi logo hires.jpg

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

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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