Hi Davide (and others),
Further to this email, there is now a patch available for Amber 10 to
add support for PUPIL 1.3.
This patch is available here: http://ambermd.org/bugfixes/10.0/bugfix.30
Before applying this patch, I recommend you apply any of those from 1 to
29 that you haven't done already.
Please let me know if you have any questions.
Best regards,
Ben Roberts
Ben Roberts wrote:
> Hi Davide,
>
> I think you may have stumbled across an incomplete patch. -jxms, -jxmx etc
> are present in Amber 11 but not yet Amber 10. They exist to provide better
> user control over maximum memory allocation to JVMs launched from within
> sander.PUPIL.
>
> I think the best solution is for my PUPIL colleagues and I to prepare a
> further patch for Amber 10. I can't say when that will be done; I'm out of
> the office at the moment and return to work in early January. I'm happy to
> notify you of the new patch if you would find that helpful. If a new patch
> isn't possible, I'll try to come up with another way forward for you.
>
> Best regards,
>
> Ben Roberts
>
> ----- Original Message -----
> From: "davide branduardi" <davide.branduardi.gmail.com>
> To: <amber.ambermd.org>
> Sent: Wednesday, December 23, 2009 7:29 AM
> Subject: [AMBER] pupil and amber
>
>
>> Dear All,
>> I'm trying to use AMBER10 together with PUPIL to do a qmmm calculation.
>> The setup of amber10 (bugfixed with the latest patch) with make
>> sander.PUPIL
>> works fine and the setup of pupil runs fine as well.
>> Unfortunately when I run the tests (ala3 with g03)
>> I got some problems specifically connected with the amber code
>> The line that pupil call is
>>
>> ./sanderLinux -O -i mdin -p ala3.parm7 -c ala3.inpcrd -ORBInitialPort 3001
>> -ORBInitialHost baldios -OptPrint 5 -jxms 64 -jxmx 4096 -jxss 16
>>
>> (where sanderLinux is a link to sander.PUPIL )
>> but sander ends up with an error which is
>>
>> mdfil: Error unknown flag: -jxms
>>
>> usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
>> [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
>> rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo
>> -radii radii -y inptraj]
>> Consult the manual for additional options.
>>
>> In fact mdfil.f (After being patched with pupil) routine does contain
>> ORBInitialPort -ORBInitialHost -OptPrint options but not -jxms
>> -jxmx -jxss.
>> I suspect that these are connected with CORBA and this make me think that
>> probably my java installation or the runtime
>> environment is not properly set.
>> Anyone can help me?
>> Best regards
>>
>> Davide
>
>
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--
Dr. Benjamin P. Roberts
Postdoctoral Research Associate
Quantum Theory Project
University of Florida
2301 New Physics Building #92
PO Box 118435
Gainesville FL 32611-8435
USA
Phone: +1 352 392 6712
Cell: +1 352 222 3677
Member of the Royal Australian Chemical Institute
and of the American Chemical Society
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Received on Thu Jan 14 2010 - 07:30:01 PST
