Run.jar is not a java jar file: it is an amber test for the Jarzinsky
facility in Amber:
$ 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
>
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Received on Thu Apr 08 2010 - 19:00:02 PDT
