amber-developers: new sander executable naming scheme

From: David A. Case <case.scripps.edu>
Date: Wed, 25 Jan 2006 15:42:58 -0700

Those of you who have (very) recently updated your CVS tree will note that
we have moved to a new naming scheme for sander executables:

"make.serial" will create sander, sander.LES, sander.PIMD and sander.DFTB

   [The reasons to keep the first three separate outweigh the downside
    of have several execuatble names; we are hoping/planning to fold
    DFTB capability into sander itself, so that sander.DFTB will go away.]

"make.parallel" will create sander.MPI, sander.LES.MPI and sander.PIMD.MPI

   This means that a "make parallel" won't blow away any
previously-created
   serial versions, as it does in Amber 8. We went to this scheme because
   now the capabilities of serial and parallel sander have diverged quite
   a bit: serial sander supports divcon, dftb, amoeba, but NOT
thermodynamic
   integration, evb potentials, etc. Furthermore, even with a single
   cpu workstation or laptop, many users will want a parallel version in
order
   to run TI and evb (which often have just two threads). So, it really
   helps to have different executable names.

The tests have all been updated (I hope!) to match this new scheme. But
some of your local jobs or tests may need to substitute sander.MPI for
"sander" if you are running parallel.

As always, comments and gripes are welcome (as are updates to the Users'
Manual!)

...dac
Received on Wed Apr 05 2006 - 23:49:44 PDT
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