[Openmmworkshop-day1and2] Software for OpenMM workshop -- please install soon!

[Joy P. Ku]

Dear Day 1 Workshop participants,

 

In order to hit the ground running, please download and install the
following files before coming to the workshop.  

 

Let us know of your success or problems as soon as possible, so we can
help you.  This is especially important with the GPU drivers since
successful installation appears to be very machine-dependent. 

 

Links for all files are available via http://simtk.org/home/openmm with
detailed instructions below.

  

REQUIRED:

1)      OpenMM binaries

2)      OpenMM source code

3)      Modified source code files for OpenMM-accelerated GROMACS

4)      If you have a supported NVIDIA or ATI GPU (on certain machines -
see details below), download and install the latest drivers.  These will
replace your current drivers.  However, you will not get acceleration on
your GPUs without these updated drivers.

5)      Make sure you have the source code for the MD code that you intend
to work on on the laptop that you're bringing

 

OPTIONAL:

1)      Download (easy) and compile (harder) GROMACS 4 with the modified
files for OpenMM acceleration.  Running a test simulation with GROMACS is
one way to verify that OpenMM is set up correctly on your laptop.

 

 

If you are also attending Day 2, install Zephyr (Windows only) from
http://simtk.org/home/zephyr and try it out.  

 

We very much look forward to seeing next week.

 

Best,

Joy

 

 

OpenMM Workshop Detailed Download (and Install) Instructions

 

1.       Go to http://simtk.org/home/openmm

 

2.       Click on Downloads in the left-hand column

 

3.       Download the binary files for the OpenMM libraries for your
platform (e.g., OpenMMPreview2-Windows.zip).  Save and unzip the file.

 

4.       Click on OpenMMPreview2-Source.zip.  Save and unzip this file.

 

5.       Linux and Mac users:  download GromacsOpenMMPreview2 for your
platform (under the OpenMM-Accelerated GROMACS header).  Unzip the file.

 

Windows users:  click on link to "GromacsOpenMM-Windows Source"  under the
OpenMM-Accelerated GROMACS header.  From the new webpage that opens,
download the file Gromacs4.3pre_for_OpenMMZephyr0.2_Source.tar.gz (under
the header "Additional GPL source code").  Unzip the file.

 

6.        GPU Drivers, only required if you have a supported NVIDIA or ATI
GPU on certain machines - 

 

SUPPORTED NVIDIA GPUs:
http://www.nvidia.com/object/cuda_learn_products.html  

              

 

SUPPORTED ATI GPUs:
http://ati.amd.com/technology/streamcomputing/requirements.html

                NOTE:  ATI GPU driver currently supported on Windows XP,
Windows Vista, Red Hat Enterprise Linux for laptops/desktops

 

a.       DRIVER FOR NVIDIA GPU:   download and install CUDA version 2.0 or
later (see link under OpenMM header).  Download the driver and toolkit.  

 

Testing installation:  To verify that you've installed things correctly,
you should also download the SDK code samples and run a sample program
(e.g., deviceQuery or nbody, default location is C:\Documents and
Settings\All Users\Application Data\NVIDIA Corporation\NVIDIA CUDA
SDK\bin\win32\Release on Windows XP, 32-bit).  Executables are only
provided on Windows;  you will need to compile source code to run the
examples if you are running on Linux.

 


b.      DRIVER FOR ATI GPU:  download and install Catalyst Software Suite
9.1 (see link under OpenMM header).  Catalyst Software Suite 8.12 will
also work.  

 

Checking version:  On Windows, you can check what version you have by
going to Start -> All Programs -> Catalyst Control Center -> Catalyst
Control Center.  In the Catalyst Control Center, click Information Center
-> Graphics Software -> Catalyst Version.  If you don't see a listing for
Catalyst Version, you don't have the driver at all and need to download
it.

 

Windows software needed for installing:  Update Windows if needed (SP3 is
needed for XP and SP1 is needed for Vista).  You will also need Microsoft
.NET Framework 2.0
(http://ati.supportcenteronline.com/ics/support/default.asp?deptID=894
<http://ati.supportcenteronline.com/ics/support/default.asp?deptID=894&tas
k=knowledge&questionID=20870> &task=knowledge&questionID=20870).  Check to
see if you have .NET Framework 2.0 by going to Start -> Control Panel ->
Add or Remove Programs.  Look to see if Microsoft .NET Framework 2.0 is
listed.  If not, you need to download and install it.

 

Testing installation:  To verify that you've installed things correctly,
you should download SDK v1.3-beta
(http://ati.amd.com/technology/streamcomputing/sdkdwnld.html).  Look in
the bin folder (default location on Windows XP is C:\Program Files\AMD\AMD
Cal 1.3.0_beta).  Run 'basic.exe' which will perform a simple test that
runs code on the GPU. 

 

  

7.        [Optional]  Download and compile GROMACS 4 according to the
README file that comes with the download. 

  

 

________________________________________________

 

Joy P. Ku

Director of Dissemination

Simbios, Stanford University

 

(W) 650.736.8434 

(F) 650.723.7461

Email:  joyku at stanford.edu

Website:  http://simbios.stanford.edu

 

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