Hi,
Try ./configure linux_em64t ifort mpich2 ... I think that kills it
before the compilers are even tested, so you should be able to see the
error even if you don't have the intel compilers.
I'll look for the violation and try to check in that change instead of
using bash explicitly.
Thanks!
Jason
On Sun, Dec 13, 2009 at 2:10 AM, Scott Brozell <sbrozell.rci.rutgers.edu> wrote:
> Hi,
>
> pmemd's configure works for me with dash on my ubuntu.
> I agree that line 471 does not look suspicious.
> I recommend that it goes back to bin/sh and you debug the failure
> (Id start by weeding away at the if statement starting on line 331).
>
> thanks,
> Scott
>
> ps details:
>
> DISTRIB_DESCRIPTION="Ubuntu 8.10"
>
> Dec 12 10:59:06pm ubuntu 121> ~/amber/amber11/src/pmemd ./configure linux_em64t gfortran nopar
> File config_data/fft.pubfft being used...
> File config_data/linux_em64t.gfortran being used...
> File config_data/interconnect.nopar being used...
> PMEMD Configurate successfully completed.
> Dec 12 10:59:20pm ubuntu 122> ~/amber/amber11/src/pmemd head ./configure
> #!/bin/dash
>
> Dec 12 10:59:30pm ubuntu 123> ~/amber/amber11/src/pmemd man dash
> ...
> BSD January 19, 2003 BSD
>
>
> Scott
>
> On Fri, Dec 11, 2009 at 02:08:52PM -0500, Jason Swails wrote:
>> The pmemd configure script fails when I have /bin/sh directed to dash.
>> However, when I replace #!/bin/sh with #!/bin/bash, it works just
>> fine (it complains at line 471, though a quick glance couldn't tell me
>> the offending part). I've changed it and committed the changes to CVS
>> (all I changed was sh to bash). If there's another way you want to
>> address this then by all means, I just thought I'd reply here since it
>> was applicable to the discussion topic of dash vs. bash and sh
>> compatibility.
>>
>> --Jason
>>
>> On Wed, Dec 9, 2009 at 10:15 PM, Jason Swails <jason.swails.gmail.com> wrote:
>> > On Wed, Dec 9, 2009 at 9:53 PM, case <case.biomaps.rutgers.edu> wrote:
>> >>
>> >> On Wed, Dec 09, 2009, Jason Swails wrote:
>> >> >
>> >> > the command i was using was "ptraj prmtop script >& output"
>> >>
>> >> This is not a good command, that is, it is not part of the POSIX standard for
>> >> shells.
>> >>
>> >> what you want is this (I think!) : "ptraj prmtop script > output 2>&1"
>> >
>> > that is in fact what I wanted, but I picked up the habit as I was
>> > learning unix and it never slipped (i don't even know if >& redirects
>> > both stderr and stdout to the same place in bash). I'm not too
>> > worried about redirecting stderr, so the simple > is good enough (I
>> > changed all occurrences in the script). Hopefully the rest of my
>> > commands are POSIX compliant :)
>> >
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Dec 13 2009 - 07:30:04 PST
