By the way, this is the error that came out during the "make serial"
command:
../netcdf/lib/libnetcdf.a(netcdf.o): In function
`__netcdf_MOD_nf90_rename_var':
netcdf.f90:(.text+0x1b73): undefined reference to `nf_rename_var_'
collect2: ld returned 1 exit status
make[1]: *** [sander] Error 1
make[1]: Leaving directory
`/working002b/chem_eng3/dcantu/amber11/src/sander'
make: *** [serial] Error 2
Thanks,
David
On Tue, Mar 15, 2011 at 8:40 PM, David Cantu <dcantu.iastate.edu> wrote:
> 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
>
>
--
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 - 20:30:04 PDT
