Re: [AMBER] [apbs-users] iapbs installation

From: Miguel Ortiz Lombardia <miguel.ortiz-lombardia.afmb.univ-mrs.fr>
Date: Sun, 09 Dec 2012 08:10:43 +0100

Hi Robert,

Thank you, that did the trick, the jobs are now running.

Best,

-- 
Miguel
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
El 09/12/12 02:41, Robert Konecny escribió:
> Hi Miguel,
> 
> there seems to be a typo in $AMBERHOME/bin/MMPBSA_mods/createinput.py which 
> leads to a wrong 'srfm' parameter to be used in the calculation. I'm 
> attaching a small patch to that file which should fix it.
> 
> Best,
> 
> Robert
> 
> 
> On Fri, Dec 07, 2012 at 10:39:12AM +0100, Miguel Ortiz Lombardía wrote:
>> Hi Robert,
>>
>> You are absolutely right concerning compilers. Even if the intel
>> compilers are "gcc compatible", they are so with gcc 4.2.1 and not with
>> gcc 4.6.2, which I was using. To make sure I do not fall in runtime
>> errors due to incompatibilities, I have recompiled the whole thing with
>> the intel compilers (icc version 12.1.6 (gcc version 4.2.1 compatibility))
>>
>> The only changes required are at the configure steps:
>>
>> CC=icc CXX=icpc FC=ifort F77=ifort ./configure (...)
>>
>> I can confirm that this also succeeds compiling APBS / iAPBS / sander.APBS.
>>
>> Thanks!
>>
>> --
>> Miguel Ortiz Lombardía
>>
>> Architecture et Fonction des Macromolécules Biologiques (UMR7257)
>> CNRS, Aix-Marseille Université
>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
>> Tel: +33(0) 491 82 55 93
>> Fax: +33(0) 491 26 67 20
>> mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
>> http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
>>
>> Le 06/12/12 21:28, Robert Konecny a écrit :
>>> Hi Miguel,
>>>
>>> that's a good news. I'm a bit surprised that your compilation succeeded 
>>> since it seems like you are using GNU compilers for APBS and iAPBS 
>>> compilation and then the Intel compilers for Amber. In my experience 
>>> compiler mixing rarely works.
>>>
>> (...)
>>
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Received on Sat Dec 08 2012 - 23:30:01 PST
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