AMBER Archive (2008)

Subject: Re: AMBER: Installation Error

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Oct 15 2008 - 08:21:14 CDT

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'
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