AMBER Archive (2008)

Subject: Re: AMBER: ambertools: static linking of user binaries is not supported on Mac OS X

From: Hans Martin Senn (senn_at_chem.gla.ac.uk)
Date: Mon May 19 2008 - 05:35:24 CDT

Dear Alan

Have a look at my recent post and the replies provided (http://amber.ch.ic.ac.uk/archive/200805/0180.html
). Essentially, you should be fine after applying the latest patches,
which fix the static linking problem (by using -static-libgcc instead
of -static, which indeed cannot be used on OS X) and couple of other
bumps.
Bug fixes are available from http://amber.scripps.edu/bugfixes/AmberTools/
.

Cheers
Hans

On 19 May 2008, at 10:39, Alan wrote:
> Hello!
>
> I am a new user of ambertools (1.0) (downloaded from
> http://ambermd.org/AmberTools-get.html, 17 May 08) and I was trying to
> install it in Mac Osx 10.4.11, tiger, gcc version 4.0.1 (Apple
> Computer, Inc. build 5370).
>
> During compilation, almost everything went fine, but sleap failed to
> compile:
>
> g++ -static -o sleap strbuff.o strmain.o plugins.o
> ../plugins/libplugins.a ../mortsrc/libmort.a
> ../freelib/readline/libreadline.a -lm
> /usr/libexec/gcc/i686-apple-darwin8/4.0.1/ld: can't locate file for:
> -lcrt0.o
>
> I didn't try with icc, but I know why this error above, it's explained
> in http://developer.apple.com/qa/qa2001/qa1118.html. Basically static
> linking of user binaries is not supported on Mac OS X. So, removing
> -static (LINK = g++ #-static) in amber10/src/gleap/leapsrc/Makefile
> solved my problem.
>
> I am just wondering how ambertools was compiled in
> http://amberonmac.blogspot.com/. In Leopard? and then Leopard has not
> the problem above anymore or it's because of icc? I am very curious
> about that if someone can clarify me here.
>
> And why sleap need to be linked statically?
>
> And how to get the lastest from the current source tree? I didn't
> apply any patch so far but I saw some discussions about it in this
> list.
>
> About test, ignoring float point differences in some tests (eg.
> sustiva, tp), all fine but:
>
> - c60 (as reported in this list)
>
> - all tests using 'sleap' (Bus error, as reported in this list)
>
> Many thanks in advance,
> Cheers,
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.

.......................................................
Dr. Hans Martin Senn
Lord Kelvin/Adam Smith Research Fellow

E-mail: senn_at_chem.gla.ac.uk
Direct line: +44 (0)141 330 6574
Fax: +44 (0)141 330 4888

Department of Chemistry
Joseph Black Building
University of Glasgow
Glasgow G12 8QQ
Scotland, UK

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