On Wed, Oct 27, 2010 at 1:49 AM, Shaandar Nyamtulga <nyam100.hotmail.com>wrote:
>
> Hi
> Should I install X11 library to see xleap after Amber10 installation since
> xleap has GUI.If so, how I can install it?
>
This depends on your system. You should install the xorg and xorg-dev (or
whatever package has the x11 header files) packages from your favorite
package manager (i.e. yum or aptitude).
Hope this helps,
Jason
> > From: nyam100.hotmail.com
> > To: amber.ambermd.org
> > Date: Tue, 26 Oct 2010 12:55:08 +0000
> > Subject: Re: [AMBER] xleap, xaLeap is missing after Amber10 installation
> >
> >
> > Thanks for your prompt response.All tests before "killed" went fine.
> > Strange thing here is that xleap and xaLeap are omitted from exe
> directory after installation. I know they should be there because I
> successfully installed 10 months ago on different computer and were using
> them.I tried copying these two files from the previous installation without
> success.I used gfortran as compiler and installed flex, byacc, g77, csh.
> >
> > > From: ross.rosswalker.co.uk
> > > To: amber.ambermd.org
> > > Date: Mon, 25 Oct 2010 23:07:15 -0700
> > > Subject: Re: [AMBER] xleap, xaLeap is missing after Amber10
> installation
> > >
> > > Hi Shaandar,
> > >
> > > > I installed Ambertools 3.1, Amber10 on Ubuntu 8.10. Ambertools
> > > installation
> > > > went fine.Tests are passed.
> > > > The following is last lines of Amber10 installation script messages.
> Since
> > > it
> > > > says that test is completed, I guessed installation is fine.(But here
> I
> > > suspect it
> > > > halted)
> > > >
> > > > cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond -DBINTRAJ
> > > > ngfil.f > _ngfil.f
> > > > gfortran -c -O0 -fno-range-check -fno-second-underscore -o ngfil.o
> > > _ngfil.f
> > > > gfortran -static -o nucgen nucgen.o ngfil.o ../lib/amopen.o
> > > ../lib/mexit.o
> > > > ../lib/nxtsec.o
> > > > g++ -c -DBINTRAJ -I../netcdf/include -o elsize.o elsize.cc
> > > > g++ -DBINTRAJ -I../netcdf/include -o elsize elsize.o -lm
> > > > /bin/mv ambpdb nucgen elsize ../../exe/
> > > > /bin/cp calcpka.pl cpinutil.pl CPin.pm ../../exe
> > > > make[1]: Leaving directory `/home/nyamaa/amber10/amber11/src/etc'
> > > >
> > > > Installation of Amber10 (serial) is complete at Tue Oct 26 12:18:38
> EDT
> > > 2010.
> > >
> > > This looks fine to me. Take a look in $AMBERHOME/exe/ you should see
> all the
> > > executables including sander.LES.
> > >
> > > > But when I test installation it exits with the following error.
> > > >
> > > > cd LES && ./Run.PME_LES
> > > >
> > > > Amber 8 ADDLES and SANDER.LES test:
> > > >
> > > > addles:
> > > > Killed
> > > > ./Run.PME_LES: Program error
> > > > make: *** [test.sander.LES] Error 1
> > >
> > > This is not the first test case so I assume the tests before this all
> ran
> > > fine?
> > >
> > > Try running:
> > >
> > > ulimit -a
> > >
> > > What does it list for "stack size" and "max memory size" - Typically
> when
> > > you see a message just saying killed it means you either requested too
> much
> > > memory than the machine either has or you are allowed to request or you
> used
> > > too much stack space.
> > >
> > > Try
> > >
> > > ulimit -s 0
> > > ulimit -m 0
> > >
> > > Then ulimit -a again to see if the settings stuck. If they don't you
> may
> > > need to do it as root or have someone who is root adjust the system
> limits
> > > for users.
> > >
> > > All the best
> > > Ross
> > >
> > > /\
> > > \/
> > > |\oss Walker
> > >
> > > ---------------------------------------------------------
> > > | Assistant Research Professor |
> > > | San Diego Supercomputer Center |
> > > | Adjunct Assistant Professor |
> > > | Dept. of Chemistry and Biochemistry |
> > > | University of California San Diego |
> > > | NVIDIA Fellow |
> > > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> > > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > > ---------------------------------------------------------
> > >
> > > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not
> > > be read every day, and should not be used for urgent or sensitive
> issues.
> > >
> > >
> > >
> > >
> > >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Oct 27 2010 - 10:30:04 PDT
