Another comment: You can hack the configure script itself and replace all
instances of gcc -> gcc44, g++ -> g++44, and gfortran -> gfortran44.
This should work. The problem is that if you do this in the config.h file,
then netcdf and other packages will be built with the other versions. This
wouldn't normally be a problem, I don't think, except that Amber11 copies
the netcdf module files (netcdf.mod) into each directory instead of
interacting with the API through the library files and header files only (as
will be done in future releases, I believe). In any case, I would not trust
module file compatibilities between gfortran 4.1 and gfortran 4.4.
Hope this helps,
Jason
On Tue, Mar 15, 2011 at 4:58 PM, David Cantu <dcantu.iastate.edu> wrote:
> Hi Dan,
>
> I started over. Deleted the $AMBERHOME directory and started everything
> again.
>
> David
>
> On Tue, Mar 15, 2011 at 6:55 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Did you do a 'make clean' before trying to remake? In order to succeed
> > with a new compiler all of amber must be recompiled.
> >
> > -Dan
> >
> > On Tue, Mar 15, 2011 at 7:16 PM, David Cantu <dcantu.iastate.edu> wrote:
> > > Hi,
> > >
> > > As a follow up to the mail I posted a couple hours ago. I am trying to
> > > install the serial amber.
> > >
> > > The following error shows up in the terminal:
> > >
> > > Fatal Error: Parse error when checking module version for file
> > 'netcdf.mod'
> > > opened at (1)
> > > make[1]: *** [ncsu-umbrella.o] Error 1
> > > make[1]: Leaving directory
> > > `/working002b/chem_eng3/dcantu/amber11/src/sander'
> > > make: *** [serial] Error 2
> > >
> > > I should say that I modified the config.h file (from gcc to gcc44, g++
> to
> > > g++44, and gfortran to gfortran44). The computer I am using uses GNU
> > 4.1.2
> > > as the defaults compiler. When I compile with 4.1.2 I get test failures
> > with
> > > NCSU.
> > >
> > > So I tried with the GNU 4.4.4 compiler that is also in the computer and
> I
> > > get the errors shown above. Any ideas?
> > >
> > > Thanks!
> > >
> > > David
> > >
> > > On Mon, Mar 14, 2011 at 9:08 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> > >
> > >> Hi David,
> > >>
> > >> NCSU is a block of code that is responsible for advanced sampling
> > >> techniques, such as ABMD, umbrella sampling, steered MD, etc. done in
> a
> > >> very
> > >> general way. If you don't think you'll ever use this functionality,
> > then
> > >> you don't have to do anything else. However, if you want to use the
> > NCSU
> > >> functionality then you'll have to upgrade the compiler as Dan
> mentioned
> > in
> > >> his response.
> > >>
> > >> Upgrading compilers are system-dependent. In this case, Google is
> your
> > >> friend. If you are running RHEL or a variant (CentOS for example),
> then
> > >> there have been numerous posts on upgrading the compiler on this
> mailing
> > >> list; a quick search should reveal them.
> > >>
> > >> Hope this helps,
> > >> Jason
> > >>
> > >> On Mon, Mar 14, 2011 at 12:16 AM, David Cantu <dcantu.iastate.edu>
> > wrote:
> > >>
> > >> > Hi Dan,
> > >> >
> > >> > Thanks for your help. I'm a beginner here, what is ncsu? If I do
> need
> > to
> > >> > use
> > >> > ncsu, how can I upgrade a complier.
> > >> >
> > >> > Thanks,
> > >> >
> > >> > David
> > >> >
> > >> > On Sun, Mar 13, 2011 at 9:21 PM, Daniel Roe <daniel.r.roe.gmail.com
> >
> > >> > wrote:
> > >> >
> > >> > > Hi,
> > >> > >
> > >> > > If I remember correctly this was an issue that occurred only with
> > the
> > >> > > ncsu stuff and gnu compilers version 4.1.2. If you are using those
> > >> > > compilers I think you have to upgrade to a more recent version to
> > use
> > >> > > the ncsu stuff. If you don't need the ncsu stuff the rest of amber
> > >> > > should work fine.
> > >> > >
> > >> > > -Dan
> > >> > >
> > >> > > On Sunday, March 13, 2011, David Cantu <dcantu.iastate.edu>
> wrote:
> > >> > > > Dear Amber Developers,
> > >> > > >
> > >> > > > I successfully installed AmberTools and now am installing
> Amber11.
> > >> > > > After 'make serial', I did 'make test'. I got 14 test failures.
> In
> > >> > > several
> > >> > > > '.dif' files I got the folllowing error:
> > >> > > >
> > >> > > >> ** NCSU-Error ** : expected list value for key 'i', got
> > '<EMPTY>'
> > >> > > instead
> > >> > > >
> > >> > > > How can I correct this?
> > >> > > >
> > >> > > > Thank you,
> > >> > > >
> > >> > > > David
> > >> > > >
> > >> > > >
> > >> > > >
> > >> > > >
> > >> > > > --
> > >> > > > David Cantu
> > >> > > > Graduate Research Assistant
> > >> > > > Chemical and Biological Engineering
> > >> > > > 3055 Sweeney Hall
> > >> > > > Iowa State University
> > >> > > > Ames IA, 50011
> > >> > > > _______________________________________________
> > >> > > > AMBER mailing list
> > >> > > > AMBER.ambermd.org
> > >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > >
> > >> > >
> > >> > > --
> > >> > > -------------------------
> > >> > > Daniel R. Roe
> > >> > > Postdoctoral Associate
> > >> > > SAS - Chemistry & Chemical Biology
> > >> > > 610 Taylor Road
> > >> > > Piscataway, NJ 08854
> > >> > >
> > >> > > _______________________________________________
> > >> > > AMBER mailing list
> > >> > > AMBER.ambermd.org
> > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > >
> > >> >
> > >> >
> > >> >
> > >> > --
> > >> > David Cantu
> > >> > Graduate Research Assistant
> > >> > Chemical and Biological Engineering
> > >> > 3055 Sweeney Hall
> > >> > Iowa State University
> > >> > Ames IA, 50011
> > >> > _______________________________________________
> > >> > 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
> > >>
> > >
> > >
> > >
> > > --
> > > David Cantu
> > > Graduate Research Assistant
> > > Chemical and Biological Engineering
> > > 3055 Sweeney Hall
> > > Iowa State University
> > > Ames IA, 50011
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> David Cantu
> Graduate Research Assistant
> Chemical and Biological Engineering
> 3055 Sweeney Hall
> Iowa State University
> Ames IA, 50011
> _______________________________________________
> 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
Received on Tue Mar 15 2011 - 17:30:03 PDT
