求肋醫學軟體安裝第一和第二步

求肋醫學軟體安裝第一和第二步

This is AMBER9.  All contents are protected by Copyright and Licensing
provisions.  See the Web page below for licensing information; using or
running this code without a valid license is prohibited.

For more information, including tutorials, bug reports, etc., please consult
the Amber Web page:

               http://amber.scripps.edu

Complete documentation, including installation instructions are in the
amber9.pdf file in the "amber9/doc" directory, created in step "0", below.
Here is a brief roadmap for the installation process:


0.  Unpack the files from the CD-ROM:

    Go to a working directory in which you have at least 600 Mb of free
    space; in our example, this will be "/usr/local", but it could be  
    anywhere. Unpack the distribution:

       cd /usr/local
       gunzip -c /mnt/cdrom/amber9.tgz | tar xvf -

    (This assumes that your CD-ROM is mounted at /mnt/cdrom).  This will
    create a /usr/local/amber9 directory.  If you wish, you can also upack
    MOIL-View at this time (cf. step 6 below):

       gunzip -c /mnt/cdrom/mview102.tgz | tar xvf -

    The tutorials are quite large (about 250 Mbytes when uncompressed),
    so we have placed them in a separate tar file, even though disk space
    is cheap these days.  If you have room:

       gunzip -c /mnt/cdrom/tutorial.tgz | tar xvf -

1.  Set up your environment:

    The AMBERHOME environment variable should point to the directory
    you are now in.  For example:

    Using csh, tcsh, etc:   setenv AMBERHOME  /usr/local/amber9

    Using sh, bash, zsh, etc: AMBERHOME=/usr/local/amber9
                              export AMBERHOME

    NOTE:  Be sure to replace the "/usr/local" part above with whatever
    path is appropriate for your machine.

    You must add $AMBERHOME/exe to your PATH environment variable.

2.  Compile the basic AMBER distribution for a single cpu:

    a. Go to the Amber web site, http://amber.scripps.edu, and download
       any bug fixes for version 9.0 that may have been posted.  There will
       be a file called "bugfix.all", which is used as follows:

           cd $AMBERHOME
           patch -p0 -N -r patch-rejects < bugfix.all

    b. go to the src directory below this one.
           cd $AMBERHOME/src

    c. run the configuration script:

           ./configure g95         for the g95 compiler

           (./configure --help will give instructions and options;
           At this point, do not specify any of the parallel options.)

           You may wish to examine (and edit) the config.h file at this point.

    d. compile and install the binaries into $AMBERHOME/exe:

           make serial

3.  Test the basic AMBER distribution

           cd $AMBERHOME/test
           make test.serial

    See the Users' Manual for comments on interpreting the test suite.

4.  (Optional) Compile the code for parallel execution:

    If you want to run sander, sander.LES, or sander.PIMD in a parallel
    environment, do the following:  First, you need to install an MPI
    library, if one is not already present on your machine.  Here are
    instructions for installing openMPI:

            cd /usr/local                (or wherever you want)
            tar xvf openmpi-1.0.tar
            cd /usr/local/openmpi-1.0
            setenv FC /opt/intel_fc_80/bin/ifort  (or your compiler)
            setenv CC /opt/intel_cc_80/bin/icc
            setenv CXX /opt/intel_cc_80/bin/icpc
            ./configure
            make
            make install
            setenv MPI_HOME /usr/local

     Look out for errors, etc., but this should install OPENMPI on your system.
     You should add $MPI_HOME/bin to your PATH and $MPI_HOME/lib to
     your LD_LIBRARY_PATH.  You are now ready to compile a parallel version
     of the Amber programs:

            cd $AMBERHOME/src
            make clean                      (important! don't forget this step)
            ./configure -openmpi -p4 ifort_ia32   (as an example)
            make parallel

    This creates three new executables: sander.MPI, sander.LES.MPI and
    sander.PIMD.MPI.  The serial versions will still be available in
    $AMBERHOME/exe, just without the "MPI" extension.  [Note that this is
    a change from previous releases, where both serial and parallel versions
    were just called "sander".]

    You can then test the parallel version.  Set the DO_PARALLEL environment
    variable to something like 'mpirun -np 4 ' (for a standard mpi run on
    four processors).  Then

            cd $AMBERHOME/test
            make test.parallel

    At this point, you should also compile the PMEMD (particle-mesh Ewald
    molecular dynamics) program.  (Note that, in spite of its name, this code
    now can do implicit solvent GB calculations as well.)  See Chapter 8 of
    the Users' Manual, and $AMBERHOME/src/pmemd/README for instructions.

5.  Documentation

    The Users' manual is in $AMBERHOME/doc/amber9.pdf.  Point your browser
    to $AMBERHOME/tutorials/index.html to access tutorial information.

    A variety of input and output files can also be found in the test
    and examples subdirectories.

6.  MOIL-view

    The CD-ROM also contains a distribution of the MOIL-view program, which
    can be used to visualize Amber structures and trajectories.  Un-tar this
    file and follow the instructions to install.  Note: MOIL-view requires GL
    (not openGL), and so effectively requires an SGI machine.

what are your question?

???到底什麼問題？貼了個INSTALL上來.....

原帖由 soway 於 2006-11-2 13:33 發表
what are your question?

I want know 2...

謝謝！已搞定

原帖由 jxinter 於 2006-11-29 13:10 發表
謝謝！已搞定

How to?

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