Re: [AMBER] problem installing AMBER12 on MacOSX

From: Philip Winter <pwinter.ualberta.ca>
Date: Wed, 23 May 2012 14:05:27 -0600

Was any solution to this error found? We get the same error that Robert
Oswald reported when compiling bintraj.F90 during the Amber 12 build
process.

Here was the system: New Mac Pro with Mac OS X 10.7.4 installed. Xcode
4.3.2 was installed. We tried compiling with the gcc/gfortran compilers
from both the MacPorts packages gcc44 and also gcc46. All patches up to
bugfix 7 for AmberTools and for Amber were applied.

Compilation of Amber was successful with the -nobintraj configure option;
but unfortunately we need the bintraj support.

Strangely, I was able to compile successfully (no errors) on a MacBook Pro
(2010 model) with the same versions of Mac OS, Xcode, and the MacPorts
compiler packages listed above.

Regards,
Philip 

--
Philip Winter
Research Assistant, Experimental Oncology, University of Alberta
Email: pwinter.ualberta.ca, Philip.Winter.albertahealthservices.ca
Phone: (office) 780-643-4436, (cell) 780-233-7568
 From: Jason Swails
<jason.swails.gmail.com<jason.swails.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20problem%20installing%20AMBER12%20on%20MacOSX>>
>
> Date: Mon, 14 May 2012 08:38:25 -0700
>
> Just to check, then, what does
>
> gcc --version
> gfortran --version
>
> return?
>
> On Mon, May 14, 2012 at 8:23 AM, Robert Oswald <robert.oswald.gmail.com>wrote:
>
>
> *> Jason, *
> *> As far as I know I am using the exact compilers in the example on the
> wiki: *
> *> *
> *> port select --list gcc *
> *> Available versions for gcc: *
> *> gcc42 *
> *> llvm-gcc42 *
> *> mp-gcc44 (active) *
> *> none *
> *> *
> *> I have applied the bugfix to AmberTools as you suggested. *
> *> Robert *
> *> *
> *> On Mon, May 14, 2012 at 11:11 AM, Jason Swails <jason.swails.gmail.com
> *
> *> >wrote: *
> *> *
> *> > What version of the GNU compilers are you using? *
> *> > *
> *> > My suggestion is to use the exact compilers used in the example on
> the *
> *> wiki *
> *> > you were following. *
> *> > *
> *> > Also, the real8 problem should have been fixed by a bugfix to
> AmberTools. *
> *> > Please check that you have all bugfixes applied. (Since you applied
> one *
> *> by *
> *> > hand, use the command: *
> *> > *
> *> > ./patch_amber.py --update --ignore-fails *
> *> > ) *
> *> > *
> *> > HTH, *
> *> > Jason *
> *> > *
> *> > On Mon, May 14, 2012 at 8:06 AM, Robert Oswald <
> robert.oswald.gmail.com *
> *> > >wrote: *
> *> > *
> *> > > I am trying to install AmberTools12 and Amber12 on Mac OS X
> (10.7.3) *
> *> > > following exactly the procedure described in: *
> *> > > *
> *> > > http://jswails.wikidot.com/installing-amber12-and-ambertools-12 *
> *> > > *
> *> > > I had no problem installing AmberTools12 alone (except for having
> to *
> *> fix *
> *> > > the real8 problem in psfprm.F90). Installing with Amber 12, I have
> run *
> *> > into *
> *> > > the following issue: *
> *> > > *
> *> > > gfortran -DBINTRAJ -c -O3 -mtune=native -ffree-form *
> *> > > -I../../AmberTools/src/pbsa -I../../AmberTools/src/sqm *
> *> > > -I../../AmberTools/src/rism -I../../include *
> *> > > -I/Users/reo1/Documents/amber12/include *
> *> > > -I/Users/reo1/Documents/amber12/include -o bintraj.o bintraj.F90 *
> *> > > bintraj.F90:119.27: *
> *> > > *
> *> > > call checkNCerror(nf90_put_att(vel_ncid, VelocVarID, *
> *> > > "scale_factor", & *
> *> > > 1 *
> *> > > Error: Generic function 'nf90_put_att' at (1) is not consistent
> with a *
> *> > > specific intrinsic interface *
> *> > > make[2]: *** [bintraj.o] Error 1 *
> *> > > make[1]: *** [serial] Error 2 *
> *> > > make: *** [install] Error 2 *
> *> > > *
> *> > > I'd be grateful for any help in resolving this problem. *
> *> > > Thanks, *
> *> > > Robert Oswald *
> *> > > *
> *> > > *
> *> > > -- *
> *> > > ******************************************** *
> *> > > Robert Oswald *
> *> > > Department of Molecular Medicine *
> *> > > Cornell University *
> *> > > Ithaca, NY 14850 *
> *> > > _______________________________________________ *
> *> > > AMBER mailing list *
> *> > > AMBER.ambermd.org *
> *> > > http://lists.ambermd.org/mailman/listinfo/amber *
> *> > > *
> *> > *
> *> > *
> *> > *
> *> > -- *
> *> > Jason M. Swails *
> *> > Quantum Theory Project, *
> *> > University of Florida *
> *> > Ph.D. Candidate *
> *> > 352-392-4032 *
> *> > _______________________________________________ *
> *> > AMBER mailing list *
> *> > AMBER.ambermd.org *
> *> > http://lists.ambermd.org/mailman/listinfo/amber *
> *> > *
> *> *
> *> *
> *> *
> *> -- *
> *> ******************************************** *
> *> Robert Oswald *
> *> Department of Molecular Medicine *
> *> Cornell University *
> *> Ithaca, NY 14850 *
> *> _______________________________________________ *
> *> AMBER mailing list *
> *> AMBER.ambermd.org *
> *> http://lists.ambermd.org/mailman/listinfo/amber *
> *> *
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
>
> Received on Mon May 14 2012 - 09:00:04 PDT
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 23 2012 - 13:30:02 PDT
Custom Search