AMBER Archive (2004)

Subject: RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler

From: Ross Walker (
Date: Sun Jul 11 2004 - 13:38:49 CDT

Dear Jiten,

> I would like to AMBER program developers that can I still use
> AMBER modules
> such as sander etc without any problem even if the test run was not
> successful.

What is the exact error in the tests? Are you getting "Program Error" for
every test like in your previous email or are you getting the error Mark
quoted for just dmp?

Is the dmp test the only one that fails? Try commenting it out of the
makefile and then running the tests again. This way you can build up a list
of failed tests. If all the other tests pass then you are probably safe to
use Sander (although with caution) as long as you avoid using polarisable
dipoles. If you plan on using polarisable dipoles (FF02EP) then you are
likely to have problems. If several tests fail then please let me know which
ones and what the error message is in each case and I can try to investigate
it further.

It might be worth testing the values of the various variables in
extra_pts.f. Try adding the following lines around line 223 (those marked
with ** are the original lines DO NOT modify these):

    write(6,'(''max11 = '',i8, '' max12 = '',i8)') max11,max12
    write(6,'(''max13 = '',i8, '' max14 = '',i8)') max13,max14
** maxa = max(max11,max12,max13,max14)
    write(6,'(''maxa = '',i8, '' ier = '',i8)') maxa, ier
** allocate( s3(maxa), stat=ier )
    write(6,'(''ier = '',i8)') ier
** REQUIRE( ier == 0 )

Modify the code here and then recompile and run the dmp test. Here is what I
get on a 32bit P4. You 'SHOULD' get the same. Try it with and without the
-big congfigure option. Unfortunately I don't have access to an Opteron
system at the moment to test this myself.

>cd $AMBERHOME/test/dmp/

>less mdout.dmp

Polarizable options:
     indmeth = 1, maxiter = 20, irstdip = 0, scaldip =
     diptau = 11.00000, dipmass = 0.33000
max11 = 13 max12 = 36
max13 = 60 max14 = 36
maxa = 60 ier = 0
ier = 0



All the best Ross

/\ \/ |\oss Walker

| Department of Molecular Biology TPC15 | | The Scripps Research Institute | | Tel:- +1 858 784 8889 | | EMail:- | | | PGP Key available on request |

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