AMBER Archive (2009)

Subject: Re: [AMBER] amber9 in fedora10

From: Eric (eabsgarten_at_gmail.com)
Date: Tue Jan 13 2009 - 12:28:33 CST

Hey Bala,

Did you apply the bugfix.all patch from ambermd.org for your version of
amber?

I think you're missing the X11 development libraries.

If you google your errors you will see question has come up on the list
before.

I'm not sure what fedora/yum names the libraries exactly,but you could try
(as root):
yum install libxt-dev

-Eric

On Tue, Jan 13, 2009 at 1:16 PM, Bala subramanian <bala.biophysics_at_gmail.com
> wrote:

> Thank you for the help. I installed c shell, the make was proceeding fine
> but i got a new error this time which i have pasted below.
>
> WcActCB.c: In function 'WcSystemACT':
> WcActCB.c:1440: error: expected declaration specifiers before 'Widget'
> WcActCB.c:1440: error: expected declaration specifiers before 'XEvent'
> WcActCB.c:1440: error: expected declaration specifiers before 'Cardinal'
> WcActCB.c: In function 'WcAddCallbacksACT':
> WcActCB.c:1442: error: expected declaration specifiers before 'Widget'
> WcActCB.c:1442: error: expected declaration specifiers before 'XEvent'
> WcActCB.c:1442: error: expected declaration specifiers before 'Cardinal'
> WcActCB.c: In function 'WcRemoveCallbacksACT':
> WcActCB.c:1444: error: expected declaration specifiers before 'Widget'
> WcActCB.c:1444: error: expected declaration specifiers before 'XEvent'
> WcActCB.c:1444: error: expected declaration specifiers before 'Cardinal'
> WcActCB.c: In function 'WcOnceOnlyACT':
> WcActCB.c:1446: error: expected declaration specifiers before 'Widget'
> WcActCB.c:1446: error: expected declaration specifiers before 'XEvent'
> WcActCB.c:1446: error: expected declaration specifiers before 'Cardinal'
> WcActCB.c: In function 'WcTranslationsACT':
> WcActCB.c:1448: error: expected declaration specifiers before 'Widget'
> WcActCB.c:1448: error: expected declaration specifiers before 'XEvent'
> WcActCB.c:1448: error: expected declaration specifiers before 'Cardinal'
> WcActCB.c: In function 'WcDynamicActionACT':
> WcActCB.c:1450: error: expected declaration specifiers before 'Widget'
> WcActCB.c:1450: error: expected declaration specifiers before 'XEvent'
> WcActCB.c:1450: error: expected declaration specifiers before 'Cardinal'
> WcActCB.c: In function 'WcDynamicCallbackACT':
> WcActCB.c:1452: error: expected declaration specifiers before 'Widget'
> WcActCB.c:1452: error: expected declaration specifiers before 'XEvent'
> WcActCB.c:1452: error: expected declaration specifiers before 'Cardinal'
> WcActCB.c: In function 'WcRegisterWcActions':
> WcActCB.c:1461: error: expected declaration specifiers before
> 'XtAppContext'
> WcActCB.c:1463: error: expected '=', ',', ';', 'asm' or '__attribute__'
> before 'WcActions'
> WcActCB.c:1463: error: 'WcActions' undeclared (first use in this function)
> WcActCB.c:1463: error: expected expression before ']' token
> WcActCB.c:1536: error: expected '=', ',', ';', 'asm' or '__attribute__'
> before 'already'
> WcActCB.c:1536: error: 'already' undeclared (first use in this function)
> make[2]: *** [WcActCB.o] Error 1
> make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Wc'
> make[1]: *** [install] Error 2
> make[1]: Leaving directory `/usr/local/amber9/src/leap'
> make: *** [serial] Error 2
>
>
> On Tue, Jan 13, 2009 at 7:00 PM, Ross Walker <ross_at_rosswalker.co.uk>
> wrote:
>
> > Dear Bala,
> >
> > Searching for the following portion of the error message
> >
> > /bin/csh: bad interpreter Fedora
> >
> > on http://archive.ambermd.org/ turns up a number of hits that address
> this
> > problem, the most useful one being from Scott:
> >
> > http://archive.ambermd.org/200812/0292.html
> >
> > Who points out that you need to have the csh shell installed to compile
> > amber. For some strange reason Fedora 10 chooses not to install this by
> > default.
> >
> > All the best
> > Ross
> >
> > > -----Original Message-----
> > > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> > > Behalf Of Bala subramanian
> > > Sent: Tuesday, January 13, 2009 9:52 AM
> > > To: amber_at_ambermd.org
> > > Subject: [AMBER] amber9 in fedora10
> > >
> > > Hello all,
> > >
> > > I am installing amber on a machine with fedora10. The configure.h was
> > > created successfully. But make serial gives me the following error.
> > Kindly
> > > help me to solve it.
> > >
> > > Starting installation of Amber9 (serial) at Tue Jan 13 18:40:29 CET
> 2009.
> > > cd lib; make install
> > > make[1]: Entering directory `/usr/local/amber9/src/lib'
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond
> > new2oldparm.f
> > > >
> > > _new2oldparm.f
> > > gfortran -c -O0 -fno-second-underscore -o new2oldparm.o
> _new2oldparm.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond nxtsec.f >
> > > _nxtsec.f
> > > gfortran -c -O0 -fno-second-underscore -o nxtsec.o _nxtsec.f
> > > gfortran -o new2oldparm new2oldparm.o nxtsec.o
> > > mv new2oldparm ../../exe
> > > /bin/rm _*.f
> > > make[1]: Leaving directory `/usr/local/amber9/src/lib'
> > > cd addles; make install
> > > make[1]: Entering directory `/usr/local/amber9/src/addles'
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond lesmain.f
> >
> > > _lesmain.f
> > > gfortran -c -O0 -fno-second-underscore -o lesmain.o _lesmain.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond addspace.f
> >
> > > _addspace.f
> > > gfortran -c -O0 -fno-second-underscore -o addspace.o _addspace.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond readprm.f
> >
> > > _readprm.f
> > > gfortran -c -O0 -fno-second-underscore -o readprm.o _readprm.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond writprm.f
> >
> > > _writprm.f
> > > gfortran -c -O0 -fno-second-underscore -o writprm.o _writprm.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond readcrd.f
> >
> > > _readcrd.f
> > > gfortran -c -O0 -fno-second-underscore -o readcrd.o _readcrd.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond writcrd.f
> >
> > > _writcrd.f
> > > gfortran -c -O0 -fno-second-underscore -o writcrd.o _writcrd.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond pick.f >
> > > _pick.f
> > > gfortran -c -O0 -fno-second-underscore -o pick.o _pick.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond rline.f >
> > > _rline.f
> > > gfortran -c -O0 -fno-second-underscore -o rline.o _rline.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond nxt.f >
> > > _nxt.f
> > > gfortran -c -O0 -fno-second-underscore -o nxt.o _nxt.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond intgr.f >
> > > _intgr.f
> > > gfortran -c -O0 -fno-second-underscore -o intgr.o _intgr.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond find.f >
> > > _find.f
> > > gfortran -c -O0 -fno-second-underscore -o find.o _find.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond of.f >
> _of.f
> > > gfortran -c -O0 -fno-second-underscore -o of.o _of.f
> > > _of.f:184.8:
> > >
> > > 1 1x,'*** IF EXISTS MUST SPECIFY read OR wovr ',/)
> > > 1
> > > Warning: Extension: Tab character in format at (1)
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond geti.f >
> > > _geti.f
> > > gfortran -c -O0 -fno-second-underscore -o geti.o _geti.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond unit.f >
> > > _unit.f
> > > gfortran -c -O0 -fno-second-underscore -o unit.o _unit.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond getc.f >
> > > _getc.f
> > > gfortran -c -O0 -fno-second-underscore -o getc.o _getc.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond alert.f >
> > > _alert.f
> > > gfortran -c -O0 -fno-second-underscore -o alert.o _alert.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond echo.f >
> > > _echo.f
> > > gfortran -c -O0 -fno-second-underscore -o echo.o _echo.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond get4c.f >
> > > _get4c.f
> > > gfortran -c -O0 -fno-second-underscore -o get4c.o _get4c.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond getd.f >
> > > _getd.f
> > > gfortran -c -O0 -fno-second-underscore -o getd.o _getd.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond wlesprm.f
> >
> > > _wlesprm.f
> > > gfortran -c -O0 -fno-second-underscore -o wlesprm.o _wlesprm.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond lesprm.f >
> > > _lesprm.f
> > > gfortran -c -O0 -fno-second-underscore -o lesprm.o _lesprm.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond les2prm.f
> >
> > > _les2prm.f
> > > gfortran -c -O0 -fno-second-underscore -o les2prm.o _les2prm.f
> > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond checksz.f
> >
> > > _checksz.f
> > > gfortran -c -O0 -fno-second-underscore -o checksz.o _checksz.f
> > > cd ../lib; ./Makelist ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o
> > > /bin/sh: ./Makelist: /bin/csh: bad interpreter: No such file or
> directory
> > > make[1]: *** [libobj] Error 126
> > > make[1]: Leaving directory `/usr/local/amber9/src/addles'
> > > make: *** [serial] Error 2
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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