AMBER Archive (2008)

Subject: Re: AMBER: Installation Error

From: Jagan Mohan (o.jagan_at_gmail.com)
Date: Wed Oct 15 2008 - 09:03:04 CDT

thank you for the info... i will keep it in mind... have a good day...

On Wed, Oct 15, 2008 at 6:51 PM, Gustavo Seabra <gustavo.seabra_at_gmail.com>wrote:

> In general, no, you should not apply amber10 bugfixes to amber9 code.
> (And I suppose that's the reason Scott pointed you to this specific
> fix and not to the Amber10 "bugfix.all" file.)
>
> In your case, this was probably a bug that slipped through the net
> during the amber9 time and was detected after amber10 release, but was
> simple enough in that the fix involved just a small change in one
> file. Other amber 10 bugfixes are not that simple.
>
> Gustavo.
>
>
> On Wed, Oct 15, 2008 at 4:51 AM, Jagan Mohan wrote:
> > Thanks a lot scott... It worked... Do AMBER 10 bug fixes be applied to
> AMBER
> > 9 as well... this is a 10 bug fix but it did help me in installing the
> v9...
> > so is it the same case with all fixes...
> >
> > On Wed, Oct 15, 2008 at 1:35 PM, Scott Brozell wrote:
> >>
> >> Hi,
> >>
> >> http://ambermd.org/bugfixes/10.0/bugfix.2
> >>
> >> Scott
> >>
> >> On Wed, 15 Oct 2008, Jagan Mohan wrote:
> >>
> >> > Hello everybody,
> >> > Please help me out to debug this error which appeared while installing
> >> > amber9.
> >> >
> >> > gfortran -o ambpdb ambpdb.o forFIRSTtype.o forFIRSTbond.o
> >> > forFIRSThbond.o
> >> > forFIRSTteth.o forFIRSToutp.o ../lib/amopen.o ../lib/mexit.o
> >> > ../lib/nxtsec.o
> >> > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond nucgen.f
> >
> >> > _nucgen.f
> >> > gfortran -c -O0 -fno-second-underscore -march=nocona -o nucgen.o
> >> > _nucgen.f
> >> > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond ngfil.f >
> >> > _ngfil.f
> >> > gfortran -c -O0 -fno-second-underscore -march=nocona -o ngfil.o
> >> > _ngfil.f
> >> > gfortran -o nucgen nucgen.o ngfil.o ../lib/amopen.o ../lib/mexit.o
> >> > ../lib/nxtsec.o
> >> > g++ -c -o elsize.o elsize.cc
> >> > elsize.cc: In function 'int main(int, char**)':
> >> > elsize.cc:117: error: 'exit' was not declared in this scope
> >> > elsize.cc:124: error: 'strcmp' was not declared in this scope
> >> > elsize.cc:145: error: 'strcmp' was not declared in this scope
> >> > elsize.cc:160: error: 'calloc' was not declared in this scope
> >> > elsize.cc:171: error: 'exit' was not declared in this scope
> >> > elsize.cc:233: error: 'exit' was not declared in this scope
> >> > elsize.cc:295: error: 'exit' was not declared in this scope
> >> > elsize.cc:339: error: 'exit' was not declared in this scope
> >> > elsize.cc: In function 'atom_count GetNumberOfAtoms(const char*,
> int)':
> >> > elsize.cc:504: error: 'exit' was not declared in this scope
> >> > elsize.cc: In function 'atom_count ReadAtomicCoordinates(const char*,
> >> > int,
> >> > atom_count, double*, double*, double*, double*, double*)':
> >> > elsize.cc:565: error: 'exit' was not declared in this scope
> >> > make[1]: *** [elsize.o] Error 1
> >> > make[1]: Leaving directory `/usr/local/amber9/src/etc'
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
-{[O]}-

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu