AMBER Archive (2009)

Subject: Re: [AMBER] problem building AmberTools/sleap on AIX

From: Shan-ho Tsai (tsai_at_hal.physast.uga.edu)
Date: Wed Jan 21 2009 - 15:53:00 CST

Hi Wei,
Skipping the nablib directory did work! sleap built fine
and the tests passed.

I really appreciate all your help, thank you!!
Sincerely,
Shan-Ho

On Fri, 16 Jan 2009, Wei Zhang wrote:

> Hi Shan-ho,
>
> I guess the easiest way it to skip the whole nablib directory,
> current it is not used by sleap yet.
>
> To do this, you have to modify gleap/mortsrc/Makefile,
>
> (1) in the first section:
>
> OBJECTS = \
> .......... \
> nablib/xxx.o ...\
> nablib/xxx.o
>
> remove the those object file in nablist
>
> (2) in the second section:
>
> all:
> .....
> cd nablib; make
> .....
>
> remove the line "cd nablib; make"
>
> Can you try this and let me know the result?
>
> Sincerely,
>
> Wei
>
>
>
>
>
>
>
>
> On Jan 16, 2009, at 2:58 PM, Shan-ho Tsai wrote:
>
>>
>> Hi all,
>>
>> I'm still struggling to get sleap to build on AIX.
>> As my last posting in this thread indicates, I've
>> tried to compile all mortsrc/nablib code (both C
>> and C++ code) with g++. However, I got an error
>> when compiling memutil.c (incorrect C++ syntax
>> in nab.h). Is there a way I can modify nab.h
>> (line 219) to make it compatible with g++ ?
>>
>> I've also tried using the IBM xlC compiler, but
>> got an error compiling one of the C++ programs.
>> As this is not listed as a supported compiler for
>> AmberTools, I didn't pursue this path further.
>>
>> Any other suggestions?
>>
>> Thanks in advance,
>> Shan-Ho
>>
>>
>> On Mon, 12 Jan 2009, Shan-ho Tsai wrote:
>>
>>>
>>> Hi Wei,
>>> Thank you very much for your response. I made the change
>>> in src/gleap/mortsrc/nablib/Makefile that you suggested
>>> and recompiled. I am getting an error compiling memutil.c.
>>> The error message is:
>>>
>>> g++ -c -Dflex -DMORT -O3 -DBINTRAJ -o memutil.o memutil.c
>>> In file included from memutil.c:4:
>>> nab.h:219: error: expected ',' or '...' before '&' token
>>> nab.h:219: error: ISO C++ forbids declaration of 'molecule_t'
>>> with no type
>>> gmake[2]: *** [memutil.o] Error 1
>>>
>>> ---------------------------------------------
>>> Line 219 in nab.h is
>>>
>>> double molsurf(const molecule_t&, double, bool verbose=false );
>>>
>>> I got this error using either g++ 3.3.2 or 4.1.2.
>>>
>>> Thank you!
>>> Shan-Ho
>>>
>>> On Fri, 9 Jan 2009, Wei Zhang wrote:
>>>
>>>> Hi,
>>>>
>>>> It looks like due to C++ name mangling, maybe because we use gcc to
>>>> compile c source
>>>> code, but use g++ to compile c++ code and link them together.
>>>>
>>>> Can you try the following:
>>>>
>>>> find file amber10/src/gleap/mortsrc/nablib/Makefile. Change line 3 to 4
>>>> from:
>>>> .c.o:
>>>> $(CC) -c -Dflex -DMORT $(OCFLAGS) -o $@ $<
>>>>
>>>> to
>>>> .c.o:
>>>> $(CXX) -c -Dflex -DMORT $(OCFLAGS) -o $@ $<
>>>>
>>>> then recompile. This will make sure c code will also compiled by c++
>>>> compiler.
>>>>
>>>> Sincerely,
>>>>
>>>> Wei
>>>>
>>
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