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FTrees – installation
FTrees Installation Guide
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1. Download and unpack
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Linux/Unix:
After downloading and unpacking (tar xvf <file>) the FTrees software
package, you have the following files and directories:
- config_ft.dat FTrees default configuration file
- doc/ Directory containing help documents: you
can find the full user guide here:
doc/ftrees_ug.pdf
- example/bat Contains example FTrees batch scripts
- example/mol Contains an example molecule input file
- example/fdf Contains an example feature tree file
- example/gdf Contains example FlexV input files
- ftrees link to the FTrees executable
- ftrees-2.4.3-<osystem> FTrees executable
- flexv FlexV executable
- install.readme Readme file containing information about the
installation process
- predict/ Default output directory for results
- static_data/ Contains the static data required by FTrees
- tmp/ Place holder for temporary files generated
at runtime by FTrees and destroyed at end
- tutorial Tutorial directory
On Unix-like systems, ftrees-2.4.3-<osystem> is the main executable. If it
does not have the 'x'-flag, set it with "chmod +x ftrees-2.4.3-<osystem>".
Windows:
Start the exe that was downloaded and follow the steps in the installation
wizard - set up a desktop icon for easy access.
One extra file whose existence should be highlighted at this stage if
you missed it already is: "doc/ftrees_ug.pdf"!
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2. License Keys
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Our software is license key protected. Please be aware that you cannot run
FTrees under any circumstances without a valid license. If you do not already
have a license, please use the form at:
http://www.biosolveit.de/license/
to request a license for our software or to request further information about
the licensing procedure. Alternatively you may mail us at:
license@biosolveit.de
To obtain a valid license you must determine the processor or system ID of your
computer. To do this you can use the small ID generation tool 'FlexIDgen'.
You can download this from:
http://www.biosolveit.de/download
Linux/Unix: If this executable does not have the 'x' flag, set it with
chmod +x flexidgen.
Alternatively, you may complete the installation of FTrees and
try to start it without a license. FTrees will in this case fail
to start and print the ID information on the screen. For Linux/Unix
you may also start the tool with the -i flag:
ftrees -i
to see the ID information.
After you receive your license keys from us, you are ready to proceed
with the next stage of the installation.
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3.1 BioSolveIT license scheme for Linux/Windows/IRIX platforms
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For the Linux, Windows and IRIX versions of FTrees we use the FlexLM license
management system which allows flexible administration of your licenses.
License format: Each line of a license file includes the name of the licensed
tool or module, and -- among other information -- the version number and the
expiration date of the license.
Example:
INCREMENT FTrees BIOSOLVE 2.0 28-feb-2006 uncounted
HOSTID=COMPOSITE=4320AF0900A SIGN="00A5 1FD4 AB95 92C9 EE24
53F5 9850 2E00 4932 F19F F559 A04E 21E4 D7DA 9031"
INCREMENT FTrees_ffs BIOSOLVE 2.0 28-feb-2006 uncounted
HOSTID=COMPOSITE=4320AF0900A SIGN="003D BD5D EE5D 77F7 24DA
660F 45FE 5600 E8CF 6914 E470 E6D6 E5E4 02F4 BC35"
This license information should be saved on your system in a text
file with the suffix .lic. You must then choose one of the following
methods which will allow FTrees to access the licenses.
3.1.1 Setting an environment variable to access the licenses
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Set the BIOSOLVE_LICENSE_FILE environmental variable to point to your license
file:
Windows:
Go to the Environment Variables window via:
Control Panel -> System -> Advanced -> Environment Variables
Choose 'New' and enter BIOSOLVE_LICENSE_FILE} as the name and the complete
path to the license file as the value.
Linux/Unix:
Use the setenv or export command -- for example:
setenv BIOSOLVE_LICENSE_FILE /home/user/flexlmlicenses/biosolveit.lic
3.1.2 Running a FlexLM license server
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Instead of specifying a license file directly in the configuation file, it is
also possible to enter the name of a FlexLM license server instead. First,
you must have a FlexLM license system running to which you have access.
A current version of the license manager daemon and the BIOSOLVE vendor daemon
can be downloaded from:
http://www.biosolveit.de/download
To administer your FTrees licenses using a license server, your FlexLM
administrator must take the following steps:
1. Add the FTrees license file to the directory where FlexLM searches for
licenses.
2. Add the BIOSOLVE vendor daemon to the directory where the lmgrd (license
manager daemon) resides.
For more help starting and running FlexLM with BioSolveIT licenses, please
visit our FAQ at:
http://www.biosolveit.de/faq
When using a license server, you must inform FTrees of the server's
name. To do this, you can specify the license server directly in the section
@LICENSE_FILES of file config_ft.dat by adding the line:
Windows:
;@myserver
Linux/Unix:
:@myserver
for a server called 'myserver'.
Alternatively, you can set the environment variable BIOSOLVE_LICENSE_FILE
to @myserver.
If you administer your licenses with FlexLM, it is also possible to use
floating licenses, i.e. licenses that are hosted by a server and distributed
to FTrees clients on demand. Floating licenses have a special layout.
A floating license is always locked to the name or the IP address of the server
and its processor ID (and not of the computer where FTrees will run). Again,
this processor ID can be obtained by running FlexIDgen on the server.
Example of a floating license:
SERVER myserver COMPOSITE=103C749ABB91
USE_SERVER
VENDOR BIOSOLVE
INCREMENT FTrees BIOSOLVE 2.0 28-jun-2005 100 SIGN="00C6 1440 7772
E4A8 116C FFFB EDC8 F400 B648 5413 6ECA 8852 4A2E 29B8 E5D6"
INCREMENT FTrees_ffs BIOSOLVE 2.0 31-mar-2005 10 SIGN="0000 AFBC
4A28 5A3E 4A88 9300 694B 4F00 5B38 4A52 AF98 288E C8BD C322
F063"
In this example the user has 100 FTrees and 10 FTrees-FS (a module)
licenses. Every time a new instance of FTrees is launched the server transfers
the license to the application. When FTrees finishes its computations the
license is returned to the server.
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4. Linux/Unix only: Defining the root directory
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If you are running FTrees on a Linux or Unix system, the configuration file
config_ft.dat must be present in each directory where FTrees will be run (or
see the documentation about how to define an alternative location for a
configuration file).
The second essential entry required in the config_ft.dat after the license
information is the root directory - a line starting @ROOTDIR. All paths
specified later in the file are relative to this path except those starting
with '/' or './'. In the @DIRECTORIES section, you can define default paths
to various data locations. The @STATIC\_DATA section contains paths and
filenames of the static data files of FTrees and the @PROGRAMS section contains
paths and filenames of executables.
For a simple test to get FTrees running in the installation directory, you can
enter the path of the installation directory after the keyword @ROOTDIR and
just leave all the rest as it is. Later, you can customize the configuration
of FTrees for different projects or individually for each user -- detailed
configuration is covered in the documentation.
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5. Starting FTrees: a first simple test
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Windows:
After making the adjustments for licensing (as described above), double
click on the desktop icon for FTrees or start the ftrees.bat which is
located in the installation directory.
Linux/Unix:
Change to the directory where FTrees was unpacked. After making the
adjustments for licensing and definining the root directory (as described
above), enter the command <path>/ftrees at the prompt.
After printing a startup message, FTrees will read the configuration file and
the static data files. You should then see the FTrees prompt:
TOPMENU>
Type 'quit' and 'y' to terminate FTrees.
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6. Basic visualization
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BioSolveIT offer a basic visualization tool FlexV for use with FTrees, which
is already built into the FTrees package.
No license key is needed for FlexV. When started the first time, FlexV generates
a .flexv file in your home directory. This file will be used to store
visualization preferences and should therefore be separate for each user.
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7. Libraries missing?
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We only use standard shared libraries in FTrees. In FlexV, one of the following
libraries may be missing:
OpenGL:
libGL is missing. In this case, OpenGL is not installed on this machine.
Please contact your system vendor or administrator.
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8. Known Issues
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- Runing flexv.exe under Vista and Windows7
If you have problems to run flexv.exe correctly, then activate the
"Compatibility Mode" for Windows XP in the properties of flexe.exe
and try it again.
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Now for any further help or information, we refer you to the User Guide:
doc/ftrees_ug.pdf
© BioSolveIT GmbH, 2013