Re: [AMBER-Developers] CVS Tree Locked

From: Daniel Roe <>
Date: Sun, 7 Mar 2010 09:45:49 -0500

Hi Gustavo,

Are you sure you aren't just running the sander.MPI in your $AMBERHOME/bin
directory? If I do something like

export TESTsander=ThisWontWork

and run:

make test

I indeed get something like:

cd cytosine && ./Run.cytosine
ThisWontWork: Command not found.
  ./Run.cytosine: Program error
make: *** [test.sander.BASIC] Error 1

However, if I do the same thing and run:

make test.parallel

(after setting DO_PARALLEL and setting up MPI etc) I get:

cd cytosine && ./Run.cytosine
diffing with cytosine.out

the reason being that in the makefile the parallel tests are set up in this

        export TESTsander=$(AMBERHOME)/exe/sander.MPI; $(MAKE) -k
        export TESTsander=$(AMBERHOME)/exe/sander.MPI; cd 4096wat &&

So whatever you set as TESTsander gets overwritten to be what is in
$AMBERHOME/exe. I have done a cvs update on the makefile and its current -
is it set up differently in your makefile? Or am I missing your point?


On Sat, Mar 6, 2010 at 10:58 AM, Gustavo Seabra <>wrote:

> On Sat, Mar 6, 2010 at 1:36 AM, Daniel Roe <> wrote:
> > I will take responsibility for this. I was testing the code for Carlos,
> but
> > I forgot that the test Makefile overwrites the TESTsander variable for
> the
> > parallel tests. So when I ran the parallel tests I wasn't testing what I
> set
> > TESTsander to, I was testing the default ($(AMBERHOME)/exe/sander.MPI).
> As a
> > bonus the error doesn't show up when the fdist subroutine isnt called
> (i.e
> > REM runs etc with 1 thread per group still passed the parallel tests).
> Sorry
> > everyone.
> That's weird... Something else may be broken. For me, it has always
> worked to set TESTsander to point to any executable I wanted, (serial
> or parallel, sander or pmemd) and the tests used the correct
> executable.
> > Can anyone suggest an easy way to modify the parallel tests so that you
> can
> > set a variable to point to the binary you want to test (like TESTsander
> in
> > the serial tests). I suppose you could have a SANDERMPI variable in the
> > makefile or something that TESTsander gets set to, like
> If just using:
> $ export TESTsander=/path/to/the/parallel/executable/I/want/to/test
> isn't working, something else must be wrong.
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7450 Ext. 5021
> _______________________________________________
> AMBER-Developers mailing list
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Received on Sun Mar 07 2010 - 07:00:02 PST
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