Hi Jason,
Thanks for the tip. That worked fine when running the configure script, but
failed again with the "make serial". I have no clue why.
Do you (or anyone reading) know more about the ncsu? I do not know if I'll
use it. I am planning to use replica exchange md, and do not know if ncsu is
used there. Is there any documentation about it?
Thanks,
David
On Tue, Mar 15, 2011 at 7:14 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
>
--
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
Received on Tue Mar 15 2011 - 20:30:03 PDT
