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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. |
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