Dear Jason,
Thank you for your suggestions. It solved the problem with AmberTools. Now
the XLEaP is working.
While I am compiling amber10 afterwards,I got errors:
The command I used :
*./configure_amber -cygwin -nosanderidc gfortran
make install
*
The errors I got:
******************************
*************************************************************************************************************
make[2]: Leaving directory `/home/CEAM/amber10/src/lib'
gfortran -o ambpdb.exe ambpdb.o forFIRSTtype.o forFIRSTbond.o
forFIRSThbond.o forFIRSTteth.o forFIRSToutp.o forFIRSTsugar.o
../lib/amopen.o ../lib/mexit.o ../lib/nxtsec.o
cpp -traditional -P -DNO_SANDER_DIVCON -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ nucgen.f > _nucgen.f
gfortran -c -O0 -fno-range-check -fno-second-underscore -o nucgen.o
_nucgen.f
cpp -traditional -P -DNO_SANDER_DIVCON -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ ngfil.f > _ngfil.f
gfortran -c -O0 -fno-range-check -fno-second-underscore -o ngfil.o
_ngfil.f
gfortran -o nucgen.exe nucgen.o ngfil.o ../lib/amopen.o ../lib/mexit.o
../lib/nxtsec.o
g++ -c -DBINTRAJ -I../netcdf/include -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 `/home/CEAM/amber10/src/etc'
make: *** [serial] Error 2
*******************************************************************************************************************************************
Could you please guide me what should I do ? Thanks!
It looks that some c/c++ commands were not recognized/declared during the
compiling of the code elsize.
While since the amber compilation does compiles many codes before this stop,
can I assume that the compilers (g++, gfortran) are good? I installed cygwin
1.7 with full install. Should I re-install it?
Do I need to supply additional lib files?
Also I ran several commands (xleap,nab) from AmberTools after its
compilation to see if it is successful. Does it matter the compilation of
amber?
I tried configure without *-nosanderidc*, but the error remains.
Regards,
Yan
On Wed, Jun 30, 2010 at 10:59 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Assuming that you have the proper X components from the cygwin install...
> see line 182 of configure_at. This is where xhome is set. You can change
> the value here to point to the location on your system. xhome should be
> set
> such that libXt.a is in $xhome/lib.
>
> On Wed, Jun 30, 2010 at 11:12 PM, Yan Gao <yan.gao.2001.gmail.com> wrote:
>
> > Hi there,
> >
> > I am installing AmberTool1.2 in Cygwin 1.7 (I installed everything for
> > Cygwin).
> >
> > After setting the environment,
> > I use below command:
> > *./configure_at -cygwin gcc*
> >
> > I got below warnings:
> > *Warning: the X11 libraries are not in the usual location !
> > To search for them try the command: locate libXt
> > On Fedora Core 5 install an xorg-x11-devel package.
> > On RedHat8 install an XFree86-devel package.
> > For the moment Amber will be configured not to build XLEaP. *
> >
> > (It compiled ok though for AmberTool1.2 and Amber10 afterwards)
> >
> > May I know how can I compile/build XLEaP? Thanks! I am learning amber
> using
> > tutorials, and it seems that XLEaP is an important tool.
> >
> > I checked and found that I have in my cygwin (I idid a full installation
> > for
> > cygwin)
> > libXt at /cygwin/lib
> > libXext at /cygwin/lib
> >
> > I have tried followings:
> > 1.re-installed cygwin, nothing changes
> > 2.link the libXt and linXext files, but it does not work
> > *ln -s /lib/libXt /usr/lib/libXt.so
> > ln -s /lib/libXext /usr/lib/libXext.so*
> >
>
> These link statements won't work according to what you've said earlier in
> your email. First of all, libXt doesn't exist at all, only libXt.a and
> libXt.so do. Second of all, the directory you've given above is
> /cygwin/lib, not /lib. Finally, the X-libraries are not searched for in
> /usr/lib, they're searched for in /usr/X11R6/lib. I think your best bet is
> to follow my suggestion above.
>
> Good luck!
> Jason
>
>
> >
> >
> > Regards,
> > --
> > Yan Gao
> > Jacobs School of Engineering
> > University of California, San Diego
> > Tel: 858-952-2308
> > Email: Yan.Gao.2001.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Thu Jul 01 2010 - 12:00:08 PDT
