On Thu, Apr 8, 2010 at 9:30 PM, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
> Run.jar is not a java jar file: it is an amber test for the Jarzinsky
> facility in Amber:
Yes, but it would appear as though some of the newer Linux
distributions are trying to be a little too *smart*, perhaps, and are
guessing that something suffixed with .jar is a java jar file. Hence
Thorsten's suggestion to change the . to a _ to avoid this confusion?
Of course, even arguably the most commercialized Linux, Ubuntu,
doesn't make this assumption, and OpenSUSE appears to be the only
distro to suffer from this (that I know about) if I correctly
understand Thorsten's first email... Doesn't seem any harm to me to
change Run.jar to Run_jar, or even Run.jarzynski if we don't mind
embracing the future and its wonderful support for long names :).
All the best,
Jason
>
> $ cat Run.jar
> #!/bin/csh -f
>
> set sander = "../../exe/sander"
> if( $?TESTsander ) then
> set sander = $TESTsander
> endif
>
> if( ! $?DO_PARALLEL ) then
> setenv DO_PARALLEL " "
> else
> set numprocs=`echo $DO_PARALLEL | awk -f ../numprocs.awk `
> if ( $numprocs > 19 ) then
> echo " DO_PARALLEL set to $DO_PARALLEL"
> goto toomany
> else if ( $?MP_PROCS)then
> if ($MP_PROCS > 19)then
> # --- For IBM AIX ---
> echo " MP_PROCS set to "$MP_PROCS
> goto toomany
> endif
> endif
> endif
>
> set output = mdout.jar
>
> cat > gbin <<EOF
> test of Jarzynski for a distance in DNA
> &cntrl
> nstlim=1000, cut=12.0, igb=1, saltcon=0.1,
> ntpr=100, ntwr=100000, ntt=3, gamma_ln=5.0,
> ntx=5, irest=1, ntwx=0, ig = 99931,
> ntc=2, ntf=2, tol=0.000001,
> dt=0.002, ntb=0, tempi=300., temp0=300.,
> jar=1,
> /
> &wt type='DUMPFREQ', istep1=1 /
> &wt type='END' /
> DISANG=dist.RST
> DUMPAVE=dist_vs_t
> LISTIN=POUT
> LISTOUT=POUT
> EOF
>
> $DO_PARALLEL $sander -O -i gbin -c dna.crd -p prmtop -o $output <
> /dev/null || goto error
>
> ../dacdif $output.save $output
> ../dacdif dist_vs_t.save dist_vs_t
> /bin/rm -f gbin restrt mdinfo
> exit(0)
>
> error:
> echo " ${0}: Program error"
> exit(1)
>
> toomany:
> echo " too many processors for this test, exiting (Max = 19)"
> echo "============================================================"
> exit(0)
>
>
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7417
>
>
>
> On Thu, Apr 8, 2010 at 8:15 PM, Thorsten M Woelfle <twoelfle.sdsc.edu> wrote:
>> Hi everybody,
>>
>> I get this issue on a opensuse 11.1 system:
>>
>> .....
>> woelfle.beatrix: ~/git_checkout/amber/test/jar $
>>> ./Run.jar
>> executing:
>> java -jar ./Run.jar
>>
>>
>> Invalid or corrupt jarfile ./Run.jar
>> The execution of ./Run.jar failed. The reason is probably that ./Run.jar doesn't contain the MainClass in MANIFEST.MF.
>> If you want to unpack ./Run.jar, call:
>> jar -xf ./Run.jar
>> ....
>>
>>
>> on opensuse 11.2 its gone.
>> Maybe we should rename to Run_jar ...
>>
>> :)
>>
>> All the best
>>
>> Thorsten
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Apr 08 2010 - 19:00:04 PDT
