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
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Received on Tue Mar 15 2011 - 17:00:03 PDT
