AMBER Archive (2009)

Subject: Re: [AMBER] Re: Fw: Help required in Amber10 Installation

From: Sudeep Narayan Banerjee (sudeep_at_bose.res.in)
Date: Thu Oct 15 2009 - 08:30:25 CDT

Dear all,

    I compiled with gcc & now its compiling at present. yes we have gfortran,
f90. And you were correct, I did grep & could not find g95. So i will install
g95 now. I am now running the make file. but its asking for g95 compiler. So
its really needed, i believe.

Best Regards,
Sudeep Narayan Banerjee
Junior Computer Engineer
Email: sudeep_at_bose.res.in
S N Bose National Centre For Basic Sciences
Block JD, Sector III
Saltlake, Kolkata 700098

---------- Original Message -----------
From: Jason Swails <jason.swails_at_gmail.com>
To: Sudeep Narayan Banerjee <sudeep_at_bose.res.in>
Sent: Thu, 15 Oct 2009 09:19:08 -0400
Subject: Re: [AMBER] Re: Fw: Help required in Amber10 Installation

> You should be able to compile amber on any platform that has a
> working fortran and c compiler. (note that is fortran90, not
> fortran77). g77 will not work to install amber, you have to have a
> fortran90 compiler. The GNU(based) compilers you can use are either
> g95 or gfortran (I'm not familiar with f90, but that would appear to
> work as your fortran90 compiler). It appears from your error
> message that either g95 is not installed on your system or it is not
> working (either due to an incomplete environment setup or a binary
> that is incompatible with your hardware/operating system). Does
> your system have g95 or gfortran? (the command 'which' should help
> you find those executables). If not, and you can't successfully use
> f90, then you'll need to install either g95 or gfortran (I'd suggest
> using gfortran) to compile amber. good luck! Jason
>
> On Thu, Oct 15, 2009 at 9:13 AM, Sudeep Narayan Banerjee <sudeep_at_bose.res.in
> > wrote:
>
> >
> > Dear All,
> >
> > Thank you for your continuous help. I really appreciate. Because I am a
> > first
> > user so facing some issues. Well now if I do echo $AMBERHOME it gives the
> > path.
> > new issue
> > we have gcc, g77, f90, mpicc, mpirun, mpich, javac etc compilers and on the
> > other hand we have vasp-path, vasp-path-nc, vasp-path-gama & vasp-mpi to
> > run
> > parallel jobs.
> > when I am doing ./configure_amber -static g95 it gives me few errors like,
> >
> > Unable to compile a Fortran program using g95 -O0 -fno-second-underscore
> > Please check your compiler settings or configure flags.
> >
> > i ran with gcc, g77 but i got same error. What to do.
> > Also is CentOS Operating system compatible with Amber10?
> >
> > Best Regards,
> > Sudeep Narayan Banerjee
> > Junior Computer Engineer
> > Email: sudeep_at_bose.res.in
> > S N Bose National Centre For Basic Sciences
> > Block JD, Sector III
> > Saltlake, Kolkata 700098
> >
> >
> > ---------- Original Message -----------
> > From: Jason Swails <jason.swails_at_gmail.com>
> > To: AMBER Mailing List <amber_at_ambermd.org>
> > Sent: Thu, 15 Oct 2009 09:01:38 -0400
> > Subject: Re: [AMBER] Re: Fw: Help required in Amber10 Installation
> >
> > > Also, the .bash_profile is always sourced at the beginning of each shell
> > > session, but I believe .bashrc is only sourced if your shell is
> > explicitly
> > > told to at some point (either by some global profile script or your
> > > .bash_profile itself). If you believe that your .bashrc is not being
> > > sourced when you launch a new shell, add the following 3 lines to
> > > your .bash_profile if [ -f ~/.bashrc ]; then source ~/.bashrc fi
> > >
> > > This will source your .bashrc in your home directory only if it
> > > exists, and it will do so each time your start a new shell. I
> > > typically find this good practice rather than editing your
> > > .bash_profile since .___rc files are pretty universal across many
> > > different programs, and it prevents the .bash_profile from getting
> > > too cluttered. Lastly, you have to export AMBERHOME before you use
> > > it to expand your PATH variable. Again, 'set' is only used for csh
> > > to set environment variables, so use export only.
> > >
> > > On Thu, Oct 15, 2009 at 8:55 AM, Jason Swails <jason.swails_at_gmail.com
> > >wrote:
> > >
> > > > You're not using bash syntax. It's a mix of cshell and bash. Use
> > export
> > > > instead of set.
> > > > export AMBERHOME=/path/to/amber10
> > > > export PATH=$AMBERHOME/exe:$PATH
> > > >
> > > > Warning-- do not forget the $PATH at the end of the second statement or
> > it
> > > > will completely overwrite your path and you won't be able to find any
> > > > executables (i.e. vi, rm, mv, etc.)!
> > > >
> > > > Good luck!
> > > > Jason Swails
> > > >
> > > >
> > > > On Thu, Oct 15, 2009 at 8:34 AM, Nicolas Sapay <
> > > > nicolas.sapay_at_cermav.cnrs.fr> wrote:
> > > >
> > > >> Hello,
> > > >>
> > > >> Did you source your .bashrc or .bash_profile after your modifications?
> > If
> > > >> not, you have to:
> > > >>
> > > >> source .bashrc
> > > >>
> > > >> Cheers,
> > > >> Nicolas
> > > >>
> > > >>
> > > >> Sudeep Narayan Banerjee a écrit :
> > > >>
> > > >> Dear All,
> > > >>>
> > > >>> I tried to define the environment variables in .bashrc file,
> > opened a
> > > >>> new
> > > >>> shell & typed in echo $AMBERHOME...it gave me nothing. I even tried
> > with
> > > >>> .bash_profile file but still same output, that's nothing, null. In
> > the
> > > >>> Amber10.pdf file its written that "You should then add $AMBERHOME/exe
> > to
> > > >>> your
> > > >>> PATH." I am defining the line in the same file .bashrc and once again
> > i
> > > >>> tried
> > > >>> with .bash_profile like
> > > >>>
> > > >>> set AMBERHOME=/root/amber10
> > > >>> PATH=$PATH:$AMBERHOME/exe
> > > >>> export AMBERHOME=/root/amber10/
> > > >>>
> > > >>> After that whenever I am doing cd $AMBERHOME/src it says "bash: cd:
> > /src:
> > > >>> No
> > > >>> such file or directory". What to do in this case? I am doing from
> > root.
> > > >>> Kindly help!
> > > >>>
> > > >>> Can I install it in CentOS?
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>> Best Regards,
> > > >>> Sudeep Narayan Banerjee
> > > >>> Junior Computer Engineer
> > > >>> Email: sudeep_at_bose.res.in
> > > >>> S N Bose National Centre For Basic Sciences
> > > >>> Block JD, Sector III
> > > >>> Saltlake, Kolkata 700098
> > > >>>
> > > >>>
> > > >>> ---------- Original Message -----------
> > > >>> From: Chris Whittleston <csw34_at_cam.ac.uk>
> > > >>> To: AMBER Mailing List <amber_at_ambermd.org>
> > > >>> Sent: Wed, 7 Oct 2009 18:48:18 +0100
> > > >>> Subject: Re: [AMBER] Re: Fw: Help required in Amber10 Installation
> > > >>>
> > > >>>
> > > >>>
> > > >>>> David is right - you need to use a new shell because .bashrc is only
> > > >>>> read in
> > > >>>> (and the variables set) when you start a shell. If you want to re-
> > > >>>> read .bashrc manually, you can by typing:
> > > >>>>
> > > >>>> source .bashrc
> > > >>>>
> > > >>>> then try:
> > > >>>>
> > > >>>> echo $AMBERHOME
> > > >>>>
> > > >>>> Chris
> > > >>>>
> > > >>>> 2009/10/7 Bill Ross <ross_at_cgl.ucsf.edu>
> > > >>>>
> > > >>>>
> > > >>>>
> > > >>>>> In bash, if .bashrc doesn't work, you can try .profile
> > > >>>>>
> > > >>>>> export AMBERHOME=/some/dir/path
> > > >>>>>
> > > >>>>> Bill
> > > >>>>>
> > > >>>>> _______________________________________________
> > > >>>>> AMBER mailing list
> > > >>>>> AMBER_at_ambermd.org
> > > >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>
> > > >>>>>
> > > >>>>>
> > > >>>> --
> > > >>>> Chris Whittleston
> > > >>>> Department of Chemistry
> > > >>>> University of Cambridge
> > > >>>> Lensfield Road, Cambridge, CB2 1EW
> > > >>>> Email: csw34_at_cam.ac.uk
> > > >>>> Tel: +44 (0)1223 336423
> > > >>>> _______________________________________________
> > > >>>> AMBER mailing list
> > > >>>> AMBER_at_ambermd.org
> > > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>
> > > >>>>
> > > >>> ------- End of Original Message -------
> > > >>>
> > > >>>
> > > >>> _______________________________________________
> > > >>> AMBER mailing list
> > > >>> AMBER_at_ambermd.org
> > > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>
> > > >>>
> > > >>>
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER_at_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
> > > >
> > >
> > > --
> > > ---------------------------------------
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > ------- End of Original Message -------
> >
> >
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
------- End of Original Message -------

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