nyuuzyou/wikis huggingface dataset:
HPCC account requirements

center | 50px | Out-of-date page 
This page is out of date.
Please see the
HPC
page for information on accessing and using Blanca, the CSDMS HPCC.
= HPC Account Requirements =
To apply for an account on the CSDMS HPC, you will have to fill out each of the 2 forms below:
# Become a member of CSDMS. 
# Request a CSDMS HPC account.
Please use the CSDMS Help Desk if you encounter any problems setting up your account.
Email rc-help@colorado.edu if you have problems connecting, or working on the HPC.
HPCC ribbon-cutting ceremony 2009

=== HPCC ribbon-cutting ceremony 2009 ===
On February 4, 2009, CSDMS was proud to host a ribbon-cutting ceremony for its new supercomputer. The $750,000 cluster enables CSDMS to support a library of computational tools used by its community of scientists worldwide to model and predict natural and human-influenced environmental events. The new computer cluster, funded largely by CU-Boulder, the U.S. Geological Survey and Silicon Graphics of Sunnyvale, Calif., is now the single largest computing facility on campus.
Distinguished speakers included the University of Colorado at Boulder Vice-Chancellor for Research, Russell Moore, Executive Director of INSTAAR, Jim White, and Executive Director of CSDMS, James Syvitski plus the SGI VP of Sales, Rene Copeland, CSDMS Program Manager from the National Science Foundation, Richard Yuretich, and the CSDMS Steering Committee Chairman, Rudy Slingerland, who each spoke about the importance of HPCC access and abilities for the University and the growing CSDMS community.
The ceremony was attended by the CSDMS Steering Committee, CSDMS Integration Facility staff, key faculty from the University of Colorado at Boulder, and other distinguished guests. 
Please visit this link to read the full press release:
http://www.colorado.edu/news/r/a00df59e084bc3fae1e06e1a05ce2fb4.html
HPCCproject/modeling environmental change class

-->
__NOTOC__
=Utah State University Modeling Environmental Change Course=
==Project description==
This course is designed to be an introduction to the wide variety of approaches to mathematical modeling of environmental and ecosystem response to climate change. The goals are to a) identify key linkages at the interface of multiple disciplines, b) provide a conceptual overview of different modeling techniques, from ad hoc reduced complexity models to common off-the-shelf (and often highly parameterized) models, c) connect students with valuable tools and resources for obtaining data and finding/developing/coupling/calibrating/validating models, and d) give students hands-on experience with several models and data analysis tools. 
==Objectives==
Course objectives are the following: 
1. Understand fundamental mathematical modeling principles, generalizations, and theories through reading and lecture.
 
2. Apply modeling theory, analysis, and critical evaluation through hands-on modeling exercises to improve problem conceptualization, model coupling, problem solving, and decision making.
 
3. Develop the technical skills needed by watershed sciences / atmospheric sciences / mathematics professionals.
4. Communicate and collaborate with scientists, modelers, and mathematicians in related, but distinct disciplines.
Objectives specific to the course WMT project are to:
1. Introduce students to the concept of plug-and-play modeling
2. Provide students hands-on experience working in with WMT
3. Have students explore several simple hypotheses with regard to landscape evolution using the CHILD model
==Time-line==
September 1 - October 6, 2015
==Models in use==
CHILD
==Results==
The students used CSDMS CHILD lab exercises to develop parabolic hillslopes and explore the sensitivity of hillslope morphology to variations in parameter values. Secondly, students used CHILD to study landscape evolution of a simple block experiencing various rates of uplift and subsidence across a normal fault. Advanced students also studied the effects of different climatic forcing.
==Users==
Patrick Belmont 	Instructor
Simon Wang	Instructor
Sarah Null	Instructor
Luis Gordillo	Instructor
Eden Furtak	Grad student
Connor Penrod	Grad student
Bruce Call	Grad student
Mitchell Donovan	Grad student
Avik Mukherjee	Grad student
Sara Kelly 	Grad student
Colby Brungard	Grad student
Maggi Kraft	Grad student
Shannon Dixon	Grad student
Angus Vaughan	Grad student
Bimal Gyawali	Grad student
Todd Blythe	Grad student
Sammy Lyster	Grad student
Karthik Kumarasamy	Post doc
==Funding==
This was a class at Utah State University.
Category:Lecture project
HPCCproject:LakeTexomaRedRiverDelta

__NOTOC__
=Lake Texoma Project by Tyler Howe=
==Project description==
Fluvio-lacustrine systems are prone to experiencing significant flood events separated by longer low energy periods. During low flow, sediment is stored upstream of the lake as mid channel and side attached bars. During high-discharge events, water level rises above the topographically low delta front levees, the turbulent jet of the river is positioned upstream of the levee terminous where levees are less confining, and the previously stored sediment may be flushed from the channel into the lake basin. This project has mapped lithologic distribution of linear-deltas in both Lake Texoma and Lake Grapevine, TX, USA. Future modeling work will be focused on utilizing historical streamflow data gathered by the USGS to simulate sedimentation during intermittent high flow events to see if we can simulate the aerial distribution of lithofacies we found in the field.
==Objectives==
1. Use historical USGS flow guage data combined with bathymmetry surveys as inputs into hydrological models to simulate sedimentation into the Lake Texoma basin. 
2. Compare modeled sedimentation geometries with field mapping.
==Time-line==
November 2016 - May 2017
==Models in use==
No current models have been used. Currently entering the modeling phase of this project.
Models expected to use are flow models dealing with bed shear, flow velocity, channel depth and width, sediment grain size variability, and sediment partitioning.
==Results==
No model results to date. The field work results have defined a new fluvio-lacustrine facies that we are interested in validating with a dynamic surface model.
==Users==
List the CSDMS HPCC users of your project:
* Tyler Howe
==Funding==
This is a master's thesis project with no outside funding.
==Publications and presentations==
AAPG 2016
http://www.searchanddiscovery.com/abstracts/html/2016/90259ace/abstracts/2383441.html
AAPG 2017 (accepted, pending presentation)
==Links==
This would be the place to provide links that are related to your project.
Choose one of the two categories mentioned below, that your project suites the best
Category:Research project
HPCCproject:Modeling Stream Capture in Strike-Slip Settings

__NOTOC__
==
==Project description==
This project models a strike-slip fault system, a setting where stream capture occurs frequently, to investigate the role of stream size and sediment supply in stream capture behavior.
==Objectives==
This project aims to determine the role of stream size and sediment supply in the frequency and style of stream capture events.
==Time-line==
This work was started in spring 2014 and is ongoing.
==Models in use==
Channel-Hillslope Integrated Landscape Development model (CHILD)
==Results==
==Users==
* Sarah Harbert
==Funding==
==Publications and presentations==
==Links==
Category:Research project
Help template

==
The name should be the same as the name of the website
==Model Introduction==
~3lines that describe the module
==Extended model introduction==
Extended introduction to the module
==Model input parameters==
input variable1	variable description1	variable units1
variable2 	description2 	units2
==Model output parameters==
output variable1	variable description1	variable units1
variable2 	description2 	units2
==Coupling parameters==
===Uses ports===
This will be something that the CSDMS facility will add
===Provides ports===
This will be something that the CSDMS facility will add
==Main equations==
A list of the key equations. HTML format is supported; latex format will be supported in the future
===Numerical scheme===
output variable
==Notes==
Any notes, comments, you want to share with the user 
==Examples==
An example run with input parameters as well as a figure / movie of the output
Follow the next steps to include images / movies of simulations:
* Upload file: https://csdms.colorado.edu/wiki/Special:Upload
* Create link to the file on your page: [[Image:<file name>]].
See also: Help:Images or Help:Movies
==Developer(s)==
Name of the module developer(s)
==References==
Key papers
==External links==
Any link, eg. to the model questionnaire, the e-book that is on the CSDMS web, Gary Parkers website....
How To CSDMS Subversion

= Create a CSDMS subversion repository =
First of all, our subversion repository is located on river at: /data/svn. To add a new user:
> /usr/bin/htdigest /data/svn/conf/svn-auth-file Subversion <username>
This of course must be done as root. The username needn't be a mysticplum username (although it can be).
Create the new repository (again as root):
> svnadmin create /data/svn/newrepos
Create a project group that contains members that are allowed to view and commit changes to the project. In addition, allow anyone to be able to browse the contents of the repository. This is done by editing subversion/conf/svn-access-file. To create a new group, define it and its members under the [groups] section:
[groups]
newgroup = huttone
In this case, the group is called newgroup (it doesn't have to match a repository name) and the only member of the group is huttone. Now specify the access privileges of the repository:
[newgroup:/]
* = r
@newrepos = rw
The first line indicates the repository, the second allows viewing of the repository by anyone, and the third limits commits to only group members. Change ownership of the directory to be nobody:
> sudo chown -R nobody /data/svn/newrepos
The new repository can now be viewed with a browser at https://csdms.colorado.edu/svn/newrepos. Alternatively, repositories can be browsed at https://csdms.colorado.edu/viewvc.
==== The Initial Import ====
To get you unversioned files into the svn repository, use svn import. For example:
> svn import mydir https://csdms.colorado.edu/svn/newrepos -m "Inital import"
Adding newrepos/file1.f
Adding newrepos/file2.f
Committed revision 1.
This copied the contents of the directory mydir into newrepos.
> svn list https://csdms.colorado.edu/svn/newrepos
file1.f
file2.f
You can now use svn checkout to get a working copy of your files.
==== Repository Layout ====
Users are free to use whatever repository layout they wish however there we recommend that you store the main development line of your code in a trunk directory, branches in a branches directory, and tags in a tags directory. Thus:
> svn list https://csdms.colorado.edu/svn/newrepos
branches/
tags/
trunk/
> svn list https://csdms.colorado.edu/svn/newrepos/trunk
file1.f
file2.f
How To Install CCA Fedora

=== Fedora 8 ===
Unlike installing on Fedora 9, the CCA tools install process is fairly painless on Fedora 8. Before starting, make sure that you have the following programs installed on you machine,
gcc 	4.1.2
g++ 	4.1.2
python 	2.5.1
java 	1.7.0
gfortran	4.1.2
In addition, you should have a version of tclsh in your path.
=== Fedora 9 ===
Fedora 9 comes with gcc 4.3 which causes problems with the CCA build. In particular with the packages: spec_neo, spec_babel, and ccaffeine. With version 4.3, the GNU folks cleaned-up many of the include files, by removing unnecessary includes. For instance cstring is no longer included within string. This generates errors that look something like,
<geshi lang=bash>
error: 'strcmp' was not declared in this scope
</geshi>
There are two fixes:
# Use an older (but not too old) version of gcc. 4.1 is a good choice, but 3.4 is too old (the babel build uses options that are apparently not available in 3.4).
# Add the appropriate include directives to the offending files. Note that there is a long list of offending files. I will provide a fixed version of the packages, and an updated contractor that knows to download these packages.
For this build I used the following:
gcc 	4.3.0
g++ 	4.3.0
python 	2.5.1
java 	1.6.0
gfortran	4.3.0
If you don't have tclsh (I didn't), install it now. Finally, after unpacking the cca-tools-contractor.tar.gz, you will need to edit two files: packages/libxml2.py, and packages/ccafe_gui.py. The versions of these packages need to be updated, as neither of the indicated versions are available. The libxml2 version should be,
<geshi lang=python>
libxml2_version = "2.6.31"
</geshi>
If you already have libxml2 installed on your system, don't bother updating this as contractor should realize this and so won't try to build it. The ccafe_gui version should be set as:
<geshi lang=python>
ccafe_gui_default_version = "0.5.6"
</geshi>
Below is my install script for the Fedora build. This should be run from within the cca-tools-contractor at the same level as contract.py.
<geshi lang=bash>
#!/bin/sh
# Location to put the CCA tools
PREFIX=$HOME/cca
# Define the compilers
CC=/usr/bin/gcc
CXX=/usr/bin/g++
PYTHON=/usr/bin/python
JAVA=/usr/bin/java
F77=/usr/bin/gfortran
F90=/usr/bin/gfortran
# Configure contractor to build the CCA tools
./contract.py --configure \
 prefix=$PREFIX \
 cc=$CC \
 cxx=$CXX \
 java=$JAVA \
 f77=$F77 \
 f90=$F90
# Build the CCA toolchain
./contract.py
</geshi>
How To Install CCA Mac

=== Installing CCA Tools on Mac OS X ===
The CCA tools have been successfully built and installed on both OS X v10.4 (Tiger) and v10.5 (Leopard). Below we describe how to install CCA on Leopard. However, the installation on Tiger should be similar (and, in fact, probably easier).
Before starting, please read over the generic install instructions.
==== OS X v10.5.x ====
Some extra steps must be taken to install on Mac OS X:
* Ensure the correct Java version is being used. You can accomplish this be setting the environment variable JAVA_HOME to the location of the correct version of Java, and adding its bin directory to your path.
* Configure with babel version 1.2.1, and use the nightly builds.
* Use version 4.0.1 of the GNU compilers
The following script gives an example of how this is done.
<geshi lang=bash>
#!/bin/sh
PREFIX=/usr/local/cca
export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home
CC=/usr/bin/gcc-4.0
CXX=/usr/bin/g++-4.0
F77=/usr/bin/gfortran
F90=/usr/bin/gfortran
PYTHON=/usr/bin/python
JAVA=$JAVA_HOME/bin/java
./contract.py --configure \
 prefix=$PREFIX \
 cc=$CC \
 cxx=$CXX \
 f77=$F77 \
 f90=$F90 \
 python=$PYTHON \
 java=$JAVA babel_version=1.2.1 nightly=True
./contract.py
</geshi>
==== Troubleshooting ====
Fatal error when building babel.
The build process fails when building babel with errors that look like,
<geshi>
cc1: error: unrecognized command line option "-Wno-long-double"
</geshi>
Use an older version of gcc. Although this looks as though it is a problem with the c compiler, it is actually a problem with the Python distutils module. distutils adds its own set of compile flags and unfortunately, there is no way to override this. Setting CFLAGS, will only add flags, not replace them. The easiest solution is to use another version of gcc. If you are using version 4.2, try 4.0. You should use whatever version of gcc built the Python you are using. Notice that in my install script I specify /usr/bin/gcc-4.0.
How To Install CCA Problems

== Typical Problems installing CCA tools ==
=== Not using bash (version 3+) ===
From my experience, most CCA build problems arise from the assumption that `/bin/sh` is GNU bash (version 3 or greater). Make sure that this is the case for you by running the following command
<geshi lang=bash>
/bin/sh --version
</geshi>
This should print something like,
<geshi lang=bash>
GNU bash, version 3.2.17(1)-release (i386-apple-darwin9.0)
Copyright (C) 2005 Free Software Foundation, Inc.
</geshi>
If you get an error message, or a version lesser than 3, you'll probably have build problems. The easiest solution is to link `/bin/sh` to an up-to-date version of bash. If this is not possible, you can run a `sed` script to replace all occurrences of `/bin/sh` in the source files with the correct bash version. Although not the most elegant solution, it's worked for me.
=== libpython2.5 not found during babel make ===
libpython2.5 probably isn't in a usual place. On my machine it is found in `/usr/local/python/lib`. You can tell the compiler where to look by defining the environment variable LDFLAGS,
<geshi lang=bash>
export LDFLAGS="-L/path/to/python/library:$LDFLAGS"
</geshi>
=== tclsh not found during ccaffeine build ===
First, make sure tcl is installed on you machine. If not, install it. If it is, make sure that tclsh is in you path. On my machine it's located in `/usr/local/tcl-tk/bin`,
<geshi lang=bash>
export PATH=/usr/local/tcl-tk/bin:$PATH
</geshi>
=== babel build fails with "-Wno-long-double" on Mac ===
The build process fails when building babel with errors that look like,
<geshi>
cc1: error: unrecognized command line option "-Wno-long-double"
</geshi>
Use an older version of gcc. Although this looks as though it is a problem with the c compiler, it is actually a problem with the Python distutils module. distutils adds its own set of compile flags and unfortunately, there is no way to override this. Setting CFLAGS, will only add flags, not replace them. The easiest solution is to use another version of gcc. If you are using version 4.2, try 4.0. You should use whatever version of gcc built the Python you are using. Notice that in my install script I specify /usr/bin/gcc-4.0.
=== How do I check compiler versions? ===
You can determine the version of your GNU compilers with the following command:
<geshi lang=bash>
$ gcc --version | head -n 1
i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5488)
</geshi>
Your output may look slightly different but should be similar to the above. Similarly, to get your java and python versions type: 
<geshi lang=bash>
$ java -version | head -n 1
java version "1.5.0_16"
$ python --version
Python 2.5.1
</geshi>
Check if you have numpy installed,
<geshi lang=bash>
$ python -c "import numpy"
</geshi>
If nothing is printed to the screen, numpy is installed (replace numpy with Numeric if that is what you are using instead).
How To Install CCA Solaris

=== Solaris 5.8 ===
There is some extra work to install CCA on Solaris. The main problem is that the build system assumes `/bin/sh` is GNU bash > 3.0. If you are able to, the easiest fix is to link `/bin/sh` to the appropriate version of bash. On my machine,
<geshi lang=bash>
> sudo ln -s /usr/local/gnu/bin/bash /bin/sh
</geshi>
Careful with this! After installing CCA, you'll probably want to undo the link and return `/bin/sh` back to its normal self.
Now set the `LIBS` environment variable so that realtime library is linked to
<geshi lang=bash>
export LIBS="-lrt"
</geshi>
This library provides definitions of sem_destroy, sem_wait, sem_post, and sem_init. Without this, the build will fail during the make of ccaffeine.
Unfortunately, even after this the build will not succeed. The build should fail during the ccaffeine make complaining about `fcntl` not being declared. That's because `fcntl.h` is included. You'll need to edit `build/ccaffeine/cxx/dc/distributed/SocketConnectionManager.cxx`. Notice that `#include <fcntl.h>` is wrapped by a couple of `ifdef`s. Either get rid of the `ifdef`s or move the include statement outside of them. Now go back to the top-level build directory and run `contract.py` again. That should do it!
How To Install CCA Success

== Successful CCA Builds ==
CCA Tools Contractor Build version 0.2.2
{| border=1 cellspacing=0 cellpadding=5
! Operating System
! colspan=6 | Compiler (version)
|-
!
! c
! c++
! Python
! Java
! Fortran 77
! Fortran 90
|-
| OS X 10.5.x
| gcc (4.0.1)
| g++ (4.0.1)
| python (2.5.1)
| java (1.5)
| gfortran (4.1.2)
| gfortran (4.1.2)
|-
| OS X 10.5.x
| gcc (4.0.1)
| g++ (4.0.1)
| python (2.5.1)
| java (1.5)
| gfortran (4.2.1)
| gfortran (4.2.1)
|-
| Fedora 8
| gcc (4.1.2)
| g++ (4.1.2)
| python (2.5.1)
| java (1.6)
| gfortran (4.2.2)
| gfortran (4.2.2)
|-
| Ubuntu 7.10
| gcc (4.1.3)
| g++ (4.1.3)
| python (2.5.1)
| java (1.6)
| gfortran (4.1.3)
| gfortran (4.1.3)
|-
| Solaris 5.8
| gcc (4.1.2)
| g++ (4.1.2)
| python (2.5)
| java (1.6)
| gfortran (4.1.2)
| gfortran (4.1.2)
|-|}
How To Install CCA Ubuntu

=== Ubuntu 8 ===
The biggest problem with installing the CCA tool chain on Ubuntu is that /bin/sh was not bash. To fix this, I copied /bin/bash to /bin/sh. Note that setting the BASH environment variable to /bin/bash helped solve some problems but still was not enough for a successful build as some scripts use /bin/sh rather than $BASH.
<geshi lang=bash>
( cd /bin && tar cvf ~/sh.tar sh ) && sudo cp /bin/bash /bin/sh
</geshi>
To undo,
<geshi lang=bash>
sudo rm /bin/sh && ( cd /bin && sudo tar xvf ~/sh.tar )
</geshi>
The GNU java compiler doesn't seem to work with the CCA tools, so I installed the full sun version. You can find this with the package manager as sun-java6-jdk. You may also need to uninstall the GNU version (gij).
I needed to add the bin directory of the CCA install path to my PATH as well. Because I used an internal installation of libxml2, xml2-config, which is needed by the babel configuration, could not be found.
Finally, I had to edit the python files, packages/libxml2.py and packages/ccafe_gui.py to indicate different versions of these packages. libxml2 version 2.6.28, and ccafe_gui version 0.5.7 are no longer available for download. In libxml2.py:
<geshi lang=python>
libxml2_version = "2.6.32"
</geshi> 
In ccafe_gui.py:
<geshi lang=python>
ccafe_gui_default_version = "0.5.6"
</geshi>
With these changes, I used the following script to build and install the CCA tools.
<geshi lang=bash>
#!/bin/sh
# Do this to make /bin/sh be bash
# ( cd /bin && tar cvf ~/sh.tar sh ) && sudo cp /bin/bash /bin/sh
# Install the CCA tools here
PREFIX=$HOME/cca
# Use these compilers
PYTHON=/usr/bin/python
JAVA=/usr/bin/java
CC=/usr/bin/gcc
CXX=/usr/bin/g++
F77=/usr/bin/gfortran
F90=/usr/bin/gfortran
# Put the installation directory in your PATH so that
# libxml2-config can be found
export PATH=$PREFIX/bin:$PATH
# Configure the installation
./contract.py --configure \
 prefix=$PREFIX \
 python=$PYTHON \
 java=$JAVA \
 cc=$CC \
 cxx=$CXX \
 f77=$F77 \
 f90=$F90
# Run contractor
./contract.py
# Do this to return /bin/sh back to how it was
# sudo rm /bin/sh && ( cd /bin && sudo tar xvf ~/sh.tar )
</geshi>
How to publish your model

=How to publish your model=
CSDMS would like to see more papers on modeling, and if you want, you can publish just your code! To do so, consider the following steps:
* Make your source code available through any online repository or us the CSDMS repository if you like. Contact CSDMSsupport@colorado.edu and we'll set you up.
* Contribute a model description to the model repository.
* Apply for a DOI to a stable version of the source code
* And finally, consider one of the following journals to publish your code paper:
** JOSS
** Computers & Geosciences
** International Environmental Modelling and Software Society (iEMSs)
** Journal of Open Research Software
** SoftwareX
** Environmental Modelling & Software
** Geoscientific Model Development