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
> >
> _______________________________________________
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>
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Received on Wed Oct 12 2011 - 14:30:02 PDT
