On Mon, Oct 04, 2010, Hadrian Djohari wrote:
>
> 1. The instruction in the Amber and AmberTools document seem to direct
> people to have both the source and the compiled binaries in the same
> directory by using only "make" instead of "make install". Is this the only
> way? We prefer to have the source and the compiled binaries in different
> directories (/usr/local/src/amber and /usr/local/amber). If we want separate
> directories, which one should $AMBERHOME point to?
We don't support this: $AMBERHOME is used to point to both
$AMBERHOME/bin (for executables) and $AMBERHOME/dat (for data files).
Furthermore, the test suite relies on having $AMBERHOME/test be in the same
tree as $AMBERHOME/bin. There are probably other problems in having truly
separate directories that I haven't thought of.
Can you achieve your goal through soft links, e.g.
ln -s /usr/local/src/amber /usr/local/amber ?
> (why do I have to install the serial versions first?)
There are many parts of the amber suite that are not parallel codes. They
need to be compiled to make good use of the package.
> how do I link to an existing libraries (fftw, mpi, mkl)?
I wonder if you have really looked carefully at the documentation? All these
are pretty clearly discussed.
> >
> > 4. Once the code is compiled, is there a short test job that use PBS
> > submission, not the "make test" that is available in the directories?
No. PBS commands tend to be specific to individual sites.
...dac
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Received on Mon Oct 04 2010 - 05:00:05 PDT
