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 |
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Received on Mon Oct 25 2010 - 23:30:03 PDT
