Hi Dan,
Thanks for your comments.
Yes I installed the amber following the link just as you mentioned.
The comfiguration results like:
***************************************************
Your AMBERHOME environment variable should be set to /home/CEAM/amber11
Obtaining the gnu suite version:
gcc -v
The version is 4.3.4
Testing the gcc compiler:
gcc -DCYGWIN -o testp.exe testp.c
OK
Validating the C++ compiler version:
g++ -v
The version is 4.3.4
OK
Testing the gfortran compiler:
gfortran -O0 -o testp.exe testp.f
OK
Testing mixed C/Fortran compilation:
gcc -DCYGWIN -c -o testp.c.o testp.c
gfortran -O0 -c -o testp.f.o testp.f
gcc -o testp.exe testp.c.o testp.f.o -lgfortran
OK
Testing pointer size:
gcc -DCYGWIN -o test_pointer_size.exe test_pointer_size.c
Detected 32 bit operating system.
Testing flex:
OK
Configuring NetCDF; (may be time-consuming)
NetCDF configure succeeded.
Configuring fftw-2.1.5; (may be time-consuming)
fftw-2.1.5 configure succeeded.
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
*******************************************************************
Thanks,
Yan
On Tue, Jul 13, 2010 at 5:44 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I suspect that the issue here is the fact that for some reason you
> have both yacc and yacc.exe. In cygwin, any binary you refer to will
> get the .exe suffix automatically appended to it. So for example if I
> type 'which ptraj' I get:
>
> /home/droe/Amber/AmberTools-1.4/bin/ptraj
>
> When in fact if you actually look at the directory in question there
> is only ptraj.exe.
>
> I assume you are using the Gnu compilers (4.3.4) that come with
> cygwin. What options did you pass to the configure script? Also, have
> you already looked at this page?
>
> http://ambermd.org/mswindows.html
>
> -Dan
>
> On Tue, Jul 13, 2010 at 1:42 AM, Yan Gao <yan.gao.2001.gmail.com> wrote:
> > Hi There,
> >
> > I am trying to install amberTools 1.4 in cygwin 1.7, and had below error:
> >
> >
> ********************************************************************************
> > make[2]: Entering directory
> > `/home/CEAM/amber11/AmberTools/src/gleap/leapsrc'
> > g++ -c -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib
> > -I../plugins -I../freelib -I. -o strmain.o strmain.cpp
> > g++ -c -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib
> > -I../plugins -I../freelib -I. -o strbuff.o strbuff.cpp
> > g++ -c -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib
> > -I../plugins -I../freelib -I. -o plugins.o plugins.cpp
> > g++ -static-libgcc -o sleap.exe strmain.o strbuff.o plugins.o
> > ../freelib/readline/libreadline.a -lm ../plugins/libplugins.a
> > ../mortsrc/libmort.a
> > mv sleap.exe /home/CEAM/amber11/bin
> > make[2]: Leaving directory
> `/home/CEAM/amber11/AmberTools/src/gleap/leapsrc'
> > make[1]: Leaving directory `/home/CEAM/amber11/AmberTools/src/gleap'
> > (cd cifparse && make install )
> > make[1]: Entering directory `/home/CEAM/amber11/AmberTools/src/cifparse'
> > flex -t cifparse.l | sed 's/yy/cifp/g' > lex.cif.c
> > */home/CEAM/amber11/bin/yacc -v -d cifparse.y
> > /home/CEAM/amber11/bin/yacc: /home/CEAM/amber11/bin/yacc: cannot execute
> > binary file*
> > make[1]: Leaving directory `/home/CEAM/amber11/AmberTools/src/cifparse'
> > make[1]: *** [cifp.tab.c] Error 126
> > make[1]: Leaving directory `/home/CEAM/amber11/AmberTools/src/cifparse'
> > make: *** [serial] Error 2
> >
> ********************************************************************************
> >
> > After the install stopped, I manually ran the command:
> > */home/CEAM/amber11/bin/yacc -v -d cifparse.y
> > *it gave the same error;*
> >
> > *Then I ran:*
> > **/home/CEAM/amber11/bin/yacc.exe -v -d cifparse.y*
> >
> > and there is no error report.
> > Also I found both *yacc* and *yacc.exe* in the bin folder.
> >
> > So I thought it might be that the yacc file does not have the exec
> > permission,
> > so I ran:
> > *chmod a=rwx ~/amber11/bin/yacc*
> > and confirmed that the yacc file has the x permission with ls
> > but the red command still gave error
> >
> > I tried another thing: go to the bin folder, and ran:
> > * yacc -v -d ~/amber11/AmberTools/src/cifparse/cifparse.y*
> > This time it gave no error...
> >
> > So I do not understand why one work and another does not. Could you
> please
> > help me? Thanks.
> >
> > I tried to link the yacc.exe to yacc with:
> > *ln -s yacc.exe yacc*
> > and it showed:
> > ln: creating symbolic link `yacc': File exists (it showed even I delete
> the
> > existing yacc file ...)
> >
> > So I am stuck....
> >
> > Any help is appreciated!
> >
> > --
> > 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
> >
>
>
>
> --
> -------------------------
> 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
>
--
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
Received on Tue Jul 13 2010 - 09:30:04 PDT
