It sounds like the permissions where not preserved when the archive was
unpacked. Thus, every test script needs to be made executable as well.
Try these commands:
cd $AMBERHOME/AmberTools/test
chmod +x `find . -name "Run*"` `find . -name "*.sh"`
cd $AMBERHOME/test
chmod +x `find . -name "Run*"` `find . -name "*.sh"`
In the future, I would suggest using the "-p" or "--preserve-permissions"
flag when untarring an archive on that machine, since it seems like they're
not preserved by default for you.
HTH,
Jason
On Thu, Jan 19, 2012 at 2:20 PM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:
> Thanks a lot for replying dac.
>
> I have just checked the availability of /bin/sh and I have it.
>
> Moreover I had already tried to change the permissions of that bash script
> as follows:
>
> chmod a+x test_amber_serial.sh
>
> and I get the following error(s):
>
> ###################################################################
> make[1]: Entering directory `/home/max/amber11/test'
> cd dmp && ./Run.dmp
> /bin/sh: ./Run.dmp: Permission denied
> make[1]: [test.sander.BASIC.nopar] Error 126 (ignored)
> cd adenine && ./Run.adenine
> /bin/sh: ./Run.adenine: Permission denied
> make[1]: [test.sander.BASIC.nopar] Error 126 (ignored)
> cd variable_14 && ./Run.variable_14_igb1
> /bin/sh: ./Run.variable_14_igb1: Permission denied
> ***
> ***
> ***
> make[1]: [test.serial.pmemd] Error 126 (ignored)
>
> Finished serial test suite for Amber 11 at Thu Jan 19 19:12:40 GMT 2012.
>
> make[1]: Target `test.serial' not remade because of errors.
> make[1]: Leaving directory `/home/max/amber11/test'
> 0 file comparisons passed
> 0 file comparisons failed
> 354 tests experienced errors
> ####################################################################
>
> which still seems related to a permissions matter.
>
> Even though I can not figure out why I have these problems, as I did not
> modify any permission of any file/directory and AT1.5 did not create
> any trouble.
>
> Best,
>
>
>
> Il 19 gennaio 2012 19:06, David A Case <case.biomaps.rutgers.edu> ha
> scritto:
> > On Thu, Jan 19, 2012, Massimiliano Porrini wrote:
> >
> >> ./test_amber_serial.sh
> >> make: execvp: ./test_amber_serial.sh: Permission denied
> >
> > Check the permissions on the file amber11/test/test_amber_serial.sh: it
> needs
> > to have execute permission. [It is theoretically possible that /bin/sh
> is
> > not available on your system, but that seems rather unlikely....]
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jan 19 2012 - 12:00:03 PST
