Hi Matt,
Check out the website
http://ambermd.org/ubuntu.html. Ubuntu is a pretty
stripped-down Linux distribution (so they can fit everything on to a CD), so
you have to install several packages from apt-get in order to build Amber.
Take a look at the suggested packages for Ubuntu and make sure you install
those first (then re-try the whole thing, but make sure you run "make clean"
in $AMBERHOME/AmberTools/src before trying to recompile).
HTH,
Jason
On Wed, Oct 12, 2011 at 5:07 PM, Matthew D Antalek
<mantale1.binghamton.edu>wrote:
> Hi everyone,
>
> Ok, well I've been able to sort of install the AmberTools package, but
> there seems to be some issues. First when I'm in the AmberTools/src
> directory and type in the
>
> ./configure gnu
>
> command, I immediately get a message that says
>
> "Could not find Xll libraries; you may need to edit config.h to set the
> XHOME and XLIBS variables.
> Warning: the Xll libraries are not in the usal location!
> To search for them try the command: locate libXt"
>
>
>
> it also suggests to install the xorg-dev package which I did. The program
> keeps running, and later on I get another message which says:
>
>
>
> "Checking for libbz2: testp.c:2:19: fatal error: bzlib.h: No such file or
> directory
> compilation terminated"
>
> The program then moves on and keeps on configuring fftw, python and MTK++,
> and I get messages saying that the configures succeeded.
> At the very end I then get a message saying the next step is "make install"
>
>
> I then type "make install" into the terminal and at the end I get a series
> of error messages:
>
> make[3]: *** [ncgen] Error 1
> make[3]: Leaving directory
> '/home/matt/Amber/amber11/AmberTools/src/netcdf/src/ncgen'
>
> make[2]: *** [install-recursive] Error 1
> make[2]: Leaving directory
> 'home/matt/Amber/amber11/AmberTools/src/netcdf/src'
>
> make[1]: leaving directory '/home/matt/Amber/amber11/AmberTools/src/ptraj'
>
> make: *** [serial] Error 2
>
> Are these messages the coming up because during configuration the Xll
> libraries are not found? Once I was back in the terminal I typed in the
> command
>
> locate libXt
>
> and got the output
>
> /usr/lib/libXtst.so.6
> /usr/lib/libXtst.so.6.1.0
> /usr/lib/i-386-linux-gnu/libXt.so.6
> /usr/lib/i-386-linux-gnu/libXt.so.6.0.0
>
>
> I'm guessing that these directories are where the Xll libraries are, but
> what exactly do I do with this info? What should I do to the configure.h
> file?
>
> Last, I ran the "make test" program and got an output of
>
> make[1]: Target 'test.serial' not remade because of errors.
> make[1]: Leaving directory '/home/matt/Amber/amber11/AmberTools/test'
> 195 file comparisons passed
> 3 file comparisons failed
> 157 tests experienced errors
> Test log file saved as .....
> Test diffs file saved as .....
>
> Are there issues because the system can't find the Xll libraries?
>
> Sorry I know this is a lot,
> Matt
>
>
> On Wed, Oct 12, 2011 at 4:11 PM, peker milas <pekermilas.gmail.com> wrote:
>
> > Hi Matt,
> >
> > Ubuntu's primary shell environment is "dash" not "bash". Therefore as a
> > starting point you may want to redirect your shell environment to real
> > "bash". If you like you may use a command as following;
> >
> > sudo rm /bin/sh; sudo ln /bin/bash /bin/sh
> >
> > Hope this helps...
> > best
> >
> > peker
> >
> > On Wed, Oct 12, 2011 at 3:26 PM, Matthew D Antalek
> > <mantale1.binghamton.edu>wrote:
> >
> > > I'm using Ubuntu, with the bash shell.
> > >
> > > -Matt
> > >
> > > On Wed, Oct 12, 2011 at 3:17 PM, Carlos Sosa <sosa0006.r.umn.edu>
> wrote:
> > >
> > > > What Linux shell are using?
> > > >
> > > > On Wed, Oct 12, 2011 at 2:06 PM, Matthew D Antalek
> > > > <mantale1.binghamton.edu>wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I'm an undergrad, and I've never done an MD simulation before,
> nor
> > > have
> > > > I
> > > > > worked much in Linux. I am having some problems with the
> installation
> > > of
> > > > > Amber 11 on my computer. I successfully unpacked the Amber11 and
> > > > AmberTools
> > > > > packages into an amber11 directory. I then follow the instructions
> > > > outlined
> > > > > in the Amber 11 manual (section 1.3), but nothing is happening. I'm
> > > using
> > > > > the bash shell so as outlined in the manual I type:
> > > > >
> > > > > set AMBERHOME=/matt/Amber/amber11
> > > > >
> > > > > but I don't see any output from this command. Likewise, when I type
> > > > >
> > > > > export AMBERHOME
> > > > >
> > > > > nothing happens. It seems that I am not creating a $AMBERHOME
> > > directory,
> > > > > because when I type in a command such as
> > > > >
> > > > > cd $AMBERHOME/src
> > > > >
> > > > > I get an error saying "No such file or directory".
> > > > >
> > > > > I also think that I correctly edited the system's PATH to include
> > the
> > > > > $AMBERHOME/bin directory but I'm not sure.
> > > > >
> > > > >
> > > > > Any help would be much appreciated.
> > > > >
> > > > > Sincerely,
> > > > > Matt
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Carlos P Sosa, Ph.D.
> > > > Adjunct Assistant Professor
> > > > *Biomedical Informatics and Computational Biology* (BICB)
> > > > University of Minnesota Rochester
> > > > 300 University Square<
> > > > http://www1.umn.edu/twincities/maps/UniversitySquare/>
> > > > R0869A
> > > > 111 S Broadway
> > > > Rochester, MN 55904
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Oct 12 2011 - 14:30:03 PDT
