Re: [AMBER] AMBER Digest, Vol 162, Issue 3

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 29 May 2012 08:41:54 +1000

What version of Xcode was used to compile the MacPort compilers that actually worked for Amber?

If you upgraded your Mac OS X to Lion without formatting (like I did), your ports are still likely built with the older Xcode, which should not be experiencing these issues.

Also, you can configure without -nobintraj and just remove the -DBINTRAJ from the Fortran compiler and preprocessor variables (but leave it for the C compiler and flags) to build AmberTools with NetCDF support but Amber without it.

That way you can use cpptraj and ptraj with NetCDF trajectories even if sander/pmemd can't create them on your Mac.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On May 25, 2012, at 1:48 AM, Julio Dominguez <acheron24.hotmail.com> wrote:
> Dear Philip Winter
> 
> Maybe the MacBookPro has a previous Xcode version installed? Quite a few things changed with the new Xcode 4.3.2. Check with xcode-select -version which one is really running. For 4.3.2 I get 2309 and down to 895 for 3.6
> 
> My compilation went fine using intel compilers, xcode 3.6 through 4.3.2. 
> 
> Best regards.
> 
> 
>> Message: 1
>> Date: Wed, 23 May 2012 14:05:27 -0600
>> From: Philip Winter <pwinter.ualberta.ca>
>> Subject: Re: [AMBER] problem installing AMBER12 on MacOSX
>> To: amber.ambermd.org
>> Message-ID:
>>    <CA+z7t8QD8Hi=mrZXtm+xkpJdazx3YCV811WFgz=cukwbLUay7A.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>> 
>> 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
>>> 
> 
> 
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Received on Mon May 28 2012 - 16:00:03 PDT
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