AMBER Archive (2008)

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

From: Hans Martin Senn (
Date: Mon May 19 2008 - 05:35:24 CDT

Dear Alan

Have a look at my recent post and the replies provided (
). 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
Bug fixes are available from


On 19 May 2008, at 10:39, Alan wrote:
> Hello!
> I am a new user of ambertools (1.0) (downloaded from
>, 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 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
> 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

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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)