Dear Jason,
Thanks very much for your detailed explanations. I have tried as what you
told me, but I can not still build ambertools-1.5 successfully.
Related to the gnu version, they are gfortran/gcc (Ubuntu/Linaro
4.5.2-8ubuntu4) 4.5.2. And the attached file is the log file what you want.
Thanks very much!
Once again, I am really sorry for sending the e-mails twice.
Best Regards,
Qinghua
On Mon, Nov 7, 2011 at 2:37 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Nov 7, 2011 at 8:19 AM, Qinghua Liao <fantasticqhl.gmail.com>
> wrote:
>
> > Dear amber users,
> >
> > I am trying to install amber11 and ambertools-1.5 on ubuntu 64 bit, but I
> > failed. I can do the configure successfully without any errors except the
> > X11, however I installed the xorg-dev package just as the instruction.
> The
> > attached file is generated from ./configure gnu, and here are the output
> of
> > the ./configure gnu:
> >
>
> Try replacing "/usr/X11R6" in your $AMBERHOME/AmberTools/src/configure
> script with "/usr". I think that's where the X11 libraries are located for
> these later Ubuntu releases.
>
>
> > ../libsrc/.libs/libnetcdf.a(v1hpg.o): In function `nc_get_NC':
> > v1hpg.c:(.text+0x1d81): undefined reference to `ncx_getn_schar_schar'
> > v1hpg.c:(.text+0x1e14): undefined reference to `ncx_get_size_t'
> > collect2: ld returned 1 exit status
> > make[3]: *** [ncgen] Error 1
> > make[3]: Leaving directory
> > `/home/qinghua/amber11/AmberTools/src/netcdf/src/ncgen'
> > make[2]: *** [install-recursive] Error 1
> > make[2]: Leaving directory
> > `/home/qinghua/amber11/AmberTools/src/netcdf/src'
> > make[1]: *** [/home/qinghua/amber11/lib/libnetcdf.a] Error 2
> > make[1]: Leaving directory `/home/qinghua/amber11/AmberTools/src/ptraj'
> > make: *** [serial] Error 2
> >
>
> This looks like NetCDF failed during the build process for some reason.
> What version of the GNU compilers are you using? (gcc --version -or-
> gfortran --version).
>
> One thing you could try is to go to $AMBERHOME/AmberTools/src/netcdf/src
> and run the command
>
> make distclean
>
> and then try to rebuild (you'll have to reconfigure).
>
> Also, could you attach your netcdf.log file? That may help us determine
> what went wrong.
>
> HTH,
> Jason
>
> P.S. You should also allow us more than 5 hours to respond to your request
> before bumping it with another email. Many of us have ~12 hour time
> difference relative to you, so we can't respond very soon after you email
> us.
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 07 2011 - 07:00:03 PST
