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 - 08:13:27 CDT

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 -------

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