Hi
Should I install X11 library to see xleap after Amber10 installation since xleap has GUI.If so, how I can install it?
> 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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Received on Tue Oct 26 2010 - 23:00:03 PDT
