Re: [AMBER-Developers] Uppercase module filenames

From: MengJuei Hsieh <mengjueh.uci.edu>
Date: Thu, 19 May 2011 16:33:13 -0700

Hi Dr. Goetz,

Okay, I personally like your solution more, since my suggestion was based on
the assumption that copying those module files is required. Nonetheless I
will check if there is some exotic platform/compilers we can think of and
test the sander/Makefile modification you sent.

I have to admit that the only filename conflict I can think of right now is
in our pbsa. That one was a hack, so eventually that will go away.

Best,

-- 
Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.
> From: Andreas Goetz <agoetz.sdsc.edu>
> Date: Thu, 19 May 2011 14:50:02 -0700
> To: MengJuei Hsieh <mengjueh.uci.edu>, AMBER Developers Mailing List
> <amber-developers.ambermd.org>
> Subject: Re: [AMBER-Developers] Uppercase module filenames
> 
> Hi Mengjuei,
> 
> What you describe might work but I would like to avoid copying module files at
> all. There are no conflicts with module names for sander. I just tested this
> and it works with gfortran. Getting rid of copying the .mod files just
> requires replacement of
> 
>   LOCALFLAGS = $(FREEFORMAT_FLAG)
> 
> with
> 
>   LOCALFLAGS = $(FREEFORMAT_FLAG) -I../../AmberTools/src/pbsa
> -I../../AmberTools/src/sqm \
>                                   -I../../AmberTools/src/rism -I../../include
> 
> in sander's Makefile. We really should be using this which is why I was asking
> yesterday for people to test whether this works on platforms I do not have
> access to. If you have access to something else we are supporting apart from
> GNU, Intel or PGI, please try to compile the test I sent and let me know
> whether it works, it just takes a minute.
> 
> We could eventually choose one common place where module files are put when
> the source is compiled, for example $AMBERHOME/include. But this requires a
> little more thinking and testing. I believe that also in this case we woldn't
> have conflicts with module names. If there would be conflicts it probably
> means that module names are not chosen wisely and should changed or that we
> have code duplications or helper routines that should end up in one module.
> 
> All the best,
> Andy
> 
> 
> On May 19, 2011, at 11:33 AM, Mengjuei Hsieh wrote:
> 
>> Hi,
>> 
>> It seems to me that Amber used to support PathScale as a compiler suite,
>> so what was the suggestion by then to deal with module filename with
>> different cases? For example, a module file in gfortran/intel fortran
>> like qmmm_module.mod would become QMMM_MODULE.mod in Open64 and PathScale.
>> 
>> Reading from the archive of the developers' list, the solution was simply
>> cp orig/*.mod dest/ , but that doesn't look very robust. The other way
>> to do it is using "-I" flag, but I can imagine some cases of conflicted
>> module names.
>> 
>> Can we do "find" and then "xargs" in Makefile? They are both POSIX
>> commands, but I am not sure how portable the commands are. Basically it
>> would look like:
>> 
>>        find ../../AmberTools/src/sqm -iname qmmm_module.mod \
>>        -o -iname qmmm_vsolv_module.mod -o -iname qmmm_vsolv_module.mod \
>>        -o -iname qmmm_struct_module.mod -o -iname qmmm_nml_module.mod \
>>        -o -iname qmmm_qmtheorymodule.mod -o -iname qmmm_struct_module.mod \
>>        -o -iname elementorbitalindex.mod | xargs -I xxx cp xxx .
>> 
>> Ideas? :p
>> 
>> Regards,
>> -- 
>> Mengjuei Hsieh, Molecular Bio & Biochem, University of California Irvine
>> 
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> 
> --
> Dr. Andreas W. Goetz
> San Diego Supercomputer Center
> Tel  : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web  : www.awgoetz.de
> 
> 
> 
> 
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Received on Thu May 19 2011 - 17:00:02 PDT