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
>
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Received on Tue Mar 15 2011 - 17:00:02 PDT
