Tobyfit windows install

From Tobyfit

Contents 1 Tobyfit Windows install 1.1 Install with NGS grid access 1.1.1 Getting grid access 1.1.2 SRB access -- Deprecated June 2011 1.2 Installing MPICH2 1.3 Installing Tobyfit GUI 1.4 Installing Tobyfit server 2 Testing the Install

Tobyfit Windows install

It is possible to use Tobyfit without a certificate or a grid account, but the user will be limited to jobs that run on the local Windows machine. To do this, just follow the instructions from the section "Install MPICH" onwards.

If you have previously installed Tobyfit, possibly including enabling NGS access, you can just unpack the zip file and run setup.m, as explained in "Installing tobyfit GUI" below. However to get the updates which have been made to the supporting Gaptk library, which are quite minor for Windows users, you must first remove the existing Gaptk Installation before the install. On Windows this is usually in a location such as C:\Program Files\MATLAB\R200xxx\toolbox\GaptkComputeToolbox, and you should remove this before running setup.m.

Install with NGS grid access

Getting grid access

If you wish to use the grid enabled features of Tobyfit, i.e. the ability to use grid resources for high performance on large problems, you must get a grid certificate to identify yourself and then obtain permission to access grid resources.

The detailed steps needed to get an e-Science certificate and then apply for a NGS account are described on the NGS website How-to-join. The first step is the application for an e-Science certificate which may take a day or two. An email will inform you when your certificate is available and how to load it into your browser (note you must use the same browser that you used to request the certificate).

With a UK e-Science certificate you can apply for access to the hosts forming the National grid Service. Applications may take one to two weeks to be approved. Users of the NGS also have access to the NGS SRB (Storage Resource Broker), which is required to stage data transfers to grid resources.

The tool Certificate Wizard is a convenient way of converting a UK e-Science certificate into the form most often used for grid access and setting up your machine to recognise e-Science certificates. This should be run on the Windows machine that you requested your certificate from. It is best to first backup your certificate from the browser, as described in the How-to-join instructions above. You must use a short password (8 characters or less) for the certificate export, due to American export restrictions on the software, but you can (and should) use a better one later on - at the end of the wizard process there is the chance to reset the pass phrase to a longer value.

SRB access -- Deprecated June 2011

• • • Important updated

The NGS support of SRB has now been discontinued and you cannot get an NGS SRB account.

If you have access to an alternative SRB system, Tobyfit can continue to run in SRB mode, but support will be limited. A new version of Tobyfit is now available which uses gsiftp to transfer data instead of SRB. The version is available here.

Note that the server side code must also be updated to support this new mode of operation.

Installing MPICH2

To run the local version of the Tobyfit executable on a Windows system you must install the [MPICH2 package http://www.mcs.anl.gov/research/projects/mpich2/]. On 32 bit Windows select the latest version of the IA32 binary package and run the installer. Version 1.4 is the current release.

Older versions of this package can generate messages at the end of a job about socket errors. These are harmless, but it may be worth upgrading to the current version if you have an older release installed.

After installation goto the Start menu and under Programs select MPICH2->wmpiregister.exe. This will bring up a GUI where you should register your user ID and password for the Windows system. This is needed for Windows 7 and Vista to allow parallel jobs to be launched on the local machine. The password is stored in encrypted form.

On a 64 bit Windows system you should install both the 64bit and 32 bit versions of MPICH. The default install will use the 32 bit version to link executables.

Installing Tobyfit GUI

The latest zip of the GUI is available from here - in the zip file tf_gui_distv2.0.Rxxx.zip, where "xxx" is the SVN release number.

This version has been tested with Matlab R2007b and later versions. To compile local user models it requires the Intel Fortran compiler V9, V10, V11 or V12. While you can run simulations with the existing scattering models without the Intel compiler, it is not possible to build new scattering models without it. If you have access to remote grid service you can compile new scattering models on these hosts if they have the necessary compilers installed.

To install the Tobyfit package the zip file should be unpacked into a temporary directory, e.g. "c:\temp\" which will create the subdirectory "C:\temp\tf_gui_distv2.0". Then run Matlab, version 7.1 or later, and go to the "tf_gui_distv2.0" directory and run the script "setup". This will prompt the user for input in the command window. The script first checks if grid certificate files have been installed. A warning message will be given if no grid certificate is avaiabke but the installation can continue.

The script will ask for an installation path for the software, the default being "c:\", though on a shared system the home directory "C:\Users\<userid>\" may be preferred. Tobyfit Matlab files are unpacked into this location under the directory "e-science\Tobyfitproject", e.g. "c:\e-science\TobyFitProject". You will be asked if you want to add this directory, which contains the start-up command "tobyfit.m", to the default Matlab path. If you say "no" you will need to be in the given directory to start tobyfit, or update the Matlab path by hand when you need it.

The Matlab static Java class path needs to be updated to work with Tobyfit. The setup script can either edit the system file "classpath.txt" or create a copy of this file in the install directory. In the latter case Matlab must be started from the install directory or you will get error messages about missing Java jar files.

Installing Tobyfit server

Each grid resource that the user wants to have access must have a suitable version of the Tobyfit server code installed. Binary versions are available for the main NGS nodes, along with the RAL machines scarf and mordred. Details of how to do this are on the Tobyfit server installation page.

Testing the Install

Start Matlab and select the directory in which Tobyfit was installed and run the command "tobyfit". If all is OK this should then offer a Window asking for your grid certificate passphrase. You can ignore the Java warning messages that appear in the Matlab console window. A "proxy successfully created" window should then appear which you click OK on before the main GUI appears.

To run a simple test case, assuming that you have set up the localhost option:

• From the "File" menu, select "Load TFT"
• In the file browser that this gives, go into the "demo" directory and select "demo.tft".
• In the directory browser that is produced, just say "OK" to the highlighted "demo" directory.
• A text box will ask if you want to transfer data files for the remote job. Click "yes" to this on the first run. Note this will send data to all available resources (non-SRB mode).
• A final text box will ask if you want to load history information. Click "no" to this.
• At this point you should see some data appear in the GUI. These are the numerical values and file names read from the TFT file. You can step through the separate tabs to see all the values.
• To test running a local job on the Windows machine, select the "simulate" tab and click on "Do simulate".
• A new Job submission window will appear and you should select "manual", "local" resource, 1 or 2 processors and then click "OK".
• After a short pause an entry will appear in the job table of the main GUI with the Status "active".
• Press the "Query" button to update the status which should soon change to "completed".
• Select the results by clicking the "select" box on the new row. The details of the simulation should appear in the text area.
• The "plot" and "plot over" buttons can be used to compare the simulation with the original data.
• If you have set up access to the NGS nodes you can submit a job to one of the NGS nodes as well. The available nodes will be listed in the list given after "do simulate". Due to the overhead of grid batch queues, small jobs may take some time to run.