3. Source Distributions

3. Source Distributions
	Chapter 2. Installation

3.1. General System Requirements

The following 3rd Party Libraries must be available in your development environment for compilation. Links and downloads are here.

Log for C++ 0.3.0 or higher
Netscape Portable Runtime 4.4.1 or higher
TCL 8.0 or higher
Xerces C++ XML Parser 2.3.0 or higher

These libraries are optional depending on your installation choices.

CppUnit 1.10.2 or higher for building/running unit tests
curses (pdcurses 2.6 or ncurses) for the ConsoleCommand plugin
GD Graphics Library for building the POVRayDataLayer tool for the POVRayVideo plugin
Java JNI for the RMI_Control plugin
libcURL 7.14.0 or higher for the SocketsPIC_Control plugin
Massively Parallel Quantum Chemistry (MPQC) 2.2.2 or higher for the MPQC_SClib plugin
Unidata NetCDF for the NetCDF_DataSet plugin and for use with HiveKeeper
Open Babel 1.100.2 for the OpenBabelImportExport plugin (Note: Open Babel version 2.0.0 will not work for this plugin - the API is different.
wxWidgets 2.3.4 or higher, with support for OpenGL (ie, configured with --with-opengl) for building HiveKeeper

3.2. MS Windows

Currently the only IDE supported is MSVC++ 6.0.

Install NanoHive-1 as described in the Windows Installer section - check the Sourcecode boxes for the components you want sourcecode for.
Three batch files were installed with your source installation that are optional, but handy for development.
Edit NanoHive-1\bin\win32-x86\set-env.bat to reflect where you unzipped to. Check the nh-home variable. Check the jdk-path variable if you'll be running the RMI_Control plugin, otherwise you can ignore it.
The nh-devel environment variable controls whether or not to copy (newly compiled) binaries to their respective locations when NanoHive-1 is run. This is handy for development; set this to "ok", ie, set nh-devel=ok
The nh-code environment variable determines whether to copy the files from the Debug directory or the Release directory.
Make the 3rd party libraries available. Open the NanoHive-1 Core VC++ workspace (there's a link to this in the NanoHive-1 program group folder.) Cancel the option to Browse for any missing projects. Choose Tools|Options...|Directories and verify, or add the 3rd party Include and Library directories. The 3rd party libraries you'll need are listed in the General System Requirements section of this chapter.
Build to verify 3rd party library availability. Choose Build|Set Active Configuration...|NanoHive - Win32 Release, and click OK. Hit F7 to build NanoHive-1.

Run NanoHive-1. Open a DOS shell, and change to the NanoHive-1\bin\win32-x86 directory, and run the nh batch file. You should get something like the following:

  C:\Program Files\NanoHive-1\bin\win32-x86>nh
  Setting environment for NanoHive-1
  Setting environment for NanoHive-1
  nh-code: Release
    _ESP_Image.dll
  The system cannot find the path specified.
    AIREBO.dll
          1 file(s) copied.
    BasicCellTraverser.dll
          1 file(s) copied.
    BondCalculator.dll
          1 file(s) copied.
    ConsoleCommand.dll
          1 file(s) copied.
    MeasurementSetToFile.dll
          1 file(s) copied.
    MPQC_SClib.dll
          1 file(s) copied.
    nanoML_ImportExport.dll
          1 file(s) copied.
    nanorexMMP_ImportExport.dll
          1 file(s) copied.
    NetCDF_DataSet.dll
          1 file(s) copied.
    NH_SimStateImportExport.dll
          1 file(s) copied.
    OpenBabelImportExport.dll
          1 file(s) copied.
    POVRayVideo.dll
          1 file(s) copied.
    RAMEntityManager.dll
          1 file(s) copied.
    RC_Traverser.dll
          1 file(s) copied.
    REBO_MBM.dll
          1 file(s) copied.
    RMI_Control.dll
          1 file(s) copied.
    SocketsControl.dll
          1 file(s) copied.
    SocketsPIC_Control.dll
          1 file(s) copied.
    NanoHive.exe
          1 file(s) copied.
    POVRayDataLayer.exe
  The system cannot find the path specified.
    HiveKeeper
  The system cannot find the path specified.
  The system cannot find the path specified.
    CppUnit.exe
  The system cannot find the path specified.
    TestPIP.dll
  The system cannot find the path specified.
    TestPIP-2.dll
  The system cannot find the file specified.

  NanoHive-1 (TM) Version 1.2.0 Copyright (C) 2004,2005 NanoHive-1, LLC
  NanoHive-1 comes with ABSOLUTELY NO WARRANTY; for details run 'NanoHive -l'
  This is free software, and you are welcome to redistribute it under certain
  conditions; run 'NanoHive -l' for details.

  Loading configuration file: C:\Program Files\NanoHive-1\conf\configs.txt
  Logging to C:\Program Files\NanoHive-1/log/NanoHive-1.log
  ConsoleCommand Version 1.2.0 started. (Press Enter to begin interactive mode.)
  SocketsControl Version 1.2.0 started.

Don't worry about any files that the "system cannot find" if they are plugins you haven't installed the sourcecode for.

That's it. Now go back to the ReadMe for its Where To Start section.

3.3. Unix

System Installation

Install any missing supporting libraries. See General System Requirements above for the list of libraries needed. You may find our Supporting Libraries Build and Installation Notes useful for this step.
Unzip/untar the NanoHive-1 package with: gunzip NanoHive-1-x.x.x.tar.gz; tar xvf NanoHive-1-x.x.x.tar
Change to the NanoHive-1-x.x.x/src directory.

The configure script is used to set up the build and installation. You use it to determine where NanoHive-1 will be installed and what plugins to install. If you run configure with no options, it will set NanoHive-1 up to be installed under /usr/local/ and include only the plugins that don't require additional non-standard libraries (BasicCellTraverser, BondCalculator, ConsoleCommand, MeasurementSetToFile, nanoML_ImportExport, nanorexMMP_ImportExport, NH_SimStateImportExport, RAMEntityManager, RC_Traverser, REBO_MBM, and SocketsControl.) See the Plugin Reference for a description of all plugins.

Here's how to build and install the basic configuration:

  $ ./configure
  $ make
  $ su
  $ make install

If you don't want to install as root, or can't, use the --prefix option to install in your home directory:

  $ ./configure --prefix=$HOME

To install the most typically used, standard plugin set (basic plugins plus AIREBO, MPQC_SClib, NetCDF_DataSet, OpenBabelImportExport, and SocketsPIC_Control), use this configure option:

  $ ./configure --enable-standard-plugin-set

The following table shows the list of options for each plugin and component allowing you fine control over what gets built and installed. For example, a popular configuration is the standard plugin set, minus the MPQC_SClib plugin, plus the POVRayVideo plugin:

  $ ./configure --enable-standard-plugin-set --disable-mpqc-sclib --enable-povrayvideo

Table 2.1. NanoHive-1 Configure Script Options

Plugin	Package	Options	Notes
ConsoleCommand	basic	--disable-console-command	Requires a curses library to build.
REBO_MBM	basic	--disable-rebo-mbm	Fails to build with certain compilers, for example, HP's cc/aCC.
AIREBO	standard	--enable-airebo, --disable-airebo	Requires a Fortran compiler to build.
MPQC_SClib	standard	--disable-mpqc-sclib, --enable-mpqc-sclib	Requires MPQC to build.
NetCDF_DataSet	standard	--disable-netcdf-dataset, --enable-netcdf-dataset	Requires netCDF to build.
OpenBabelImportExport	standard	--disable-openbabel, --enable-openbabel	Requires OpenBabel to build.
SocketsPIC_Control	standard	--disable-sockets-pic-control, --enable-sockets-pic-control	Requires libcURL to build.
_ESP_Image	optional	--enable-esp-image	For nanoENGINEER-1 support. Requires the GD graphics library to build.
POVRayVideo	optional	--enable-povrayvideo	If the GD graphics library is found, the POVRayDataLayer tool will also be built.
RMI_Control	optional	--enable-rmi-control	Requires Java to build. Also add the --with-jdk-prefix option to specify where Java is installed.

Execute ./configure --help to get the complete list of configuration customization options.

Here is the directory structure of the installation assuming the default PREFIX of /usr/local.

                   /usr/local/
   _____________________|________________________
  |             |                  |             |
 bin/        include/             lib/    share/NanoHive-1/
  |             |                  |             |
NanoHive        |        NanoHive-1/<plugins>     |
NanoHive-config |        libNanoHiveInterface.*  |
                |        libNanoHiveUtil.*       |
                |                                |
            NanoHiveInterface/*.h                |
            NanoHiveUtil/*.h                     |
                                                 |
             ____________________________________|________________________
            |       |               |     |         |         |           |
        classes/  conf/           data/  doc/   examples/  include/    scripts/
            |       |               |     |         |                     |
            |       |               |   index.html  |                 install-examples
            |       |               |               |                 set-env
            |       |               |          hydrogen-abstraction/  nh
            |       |               |          cytosine-guanine/      pv
            |       |               |          nanotube-5x5/
            |       |               |          cnt-esp/
            |       |               |
            |       |      mpeg_encode.param.tmplt
            |       |      simulation-1.0.1.xsd
            |       |      displayDataLogo.png
            |       |      _________|____________
            |       |     |         |            |
            |       |   local/  MPQC_SClib/  REBO_MBM/
            |       |     |         |            |
            |       |     |         |           *.d
            |       |     |     atominfo.kv
            |       |     |     basis/<basis_sets>
            |       |     |
            |       |  en_resultCodes.txt
            |       |
            |    configs-template.txt
            |
       RMI_Control.jar

User Installation

Install the example simulations with the following command:
```
  PREFIX/share/NanoHive-1/scripts/install-examples
```
This will create a NanoHive-1 folder in the directory where the script is run, then copy the examples directory into it, updating example configuration paths on the fly.
The first time you run NanoHive-1, it creates a .NanoHive-1 directory under your home directory where it puts a conf/configs.txt file and log directory.

That's it. Now go back to the ReadMe for its Where To Start section.

Documentation