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
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Received on Tue Mar 15 2011 - 16:30:02 PDT
