[gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

[Mark Abraham]

----- Original Message -----
From: "J. Rui Rodrigues" <joaquim.rodrigues at estg.ipleiria.pt>
Date: Thursday, April 29, 2010 23:02
Subject: Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi,
> 
> (...)
> > > Output from make:
> > > =================
> > > (...)
> > > /bin/sh ../../libtool --tag=CC   --mode=link 
> cc  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-
> unused -funroll-all-loops  -L/usr/local/lib  -
> > > framework Accelerate -o grompp grompp.o libgmxpreprocess.la 
> ../mdlib/libmd.la ../gmxlib/libgmx.la  -
> lxml2  -L/usr/X11/lib -lfftw3f -lm   -lSM -lICE -lX11
> > > cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-
> unused -funroll-all-loops -framework 
> Accelerate -o grompp grompp.o  -L/usr/local/lib
> > > ./.libs/libgmxpreprocess.a -L/usr/X11/lib 
> ../mdlib/.libs/libmd.a /Users/jrui/Desktop/gromacs-
> 4.0.7/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a
> > > /usr/lib/libxml2.dylib -lpthread -lz -licucore 
> /usr/local/lib/libfftw3f.a -lm /usr/X11/lib/libSM.6.dylib 
> /usr/X11/lib/libICE.6.dylib /usr/X11/lib/libX11.6.dylib
> > > /usr/X11/lib/libXau.6.dylib /usr/X11/lib/libXdmcp.6.dylib
> > > ld warning: in /usr/local/lib/libfftw3f.a, file is not of 
> required architecture
> > 
> > What does (e.g.) "nm /usr/local/lib/libfftw3f.a" have to say? 
> Also, look 
> > at "ls -l /usr/local/lib/libfftw*" to see whether you're 
> picking up 
> > versions with the timestamps you expect... Maybe your FFTW 
> configuration 
> > only installed dynamic libraries, or something. I don't know 
> why 
> > compiling 4.0.5 would have succeeded, however.
> > 
> > Mark
> > 
> 
> Here is the output from ls:
> ls -l /usr/local/lib/libfftw*
> -rw-r--r--  1 root  wheel  2441624 Jul 21  
> 2009 /usr/local/lib/libfftw3.a
> -rwxr-xr-x  1 root  
> wheel      891 Jul 21  2009 
> /usr/local/lib/libfftw3.la-rw-r--r--  1 root  
> wheel  2370752 Jul 21  2009 /usr/local/lib/libfftw3f.a
> -rwxr-xr-x  1 root  
> wheel      894 Jul 21  2009 
> /usr/local/lib/libfftw3f.la
> The output from "nm /usr/local/lib/libfftw3f.a" is so large that 
> it bounced on the mailing list. Here are the first 
> lines:
> nm /usr/local/lib/libfftw3f.a | head
> nm: no name list
> 
> /usr/local/lib/libfftw3f.a(align.o):
> 0000000000000010 s EH_frame1
> 0000000000000000 T _fftwf_alignment_of
> 0000000000000028 S _fftwf_alignment_of.eh
> 
> /usr/local/lib/libfftw3f.a(alloc.o):
> 0000000000000090 s EH_frame1
> 0000000000000082 s LC0
> 000000000000008a s LC1
> 
> 
> Also, "nm -arch i386" returns:
> nm: file: /usr/local/lib/libfftw3f.a does not contain 
> architecture: i386
> 
> while "nm -arch x86_64" returns the same output as nm without options.
> 
> Meanwhile, I went ahead and, by comparing the line where the 
> 4.0.7 compilation fails with the corresponding line 
> in the 4.0.5 compilation, I noticed that only difference is that 
> the latter contains the cc extra options -m64 -
> std=gnu99 
> I guess that 64bit detection is failing. So, I passed these 
> options to configure and the compilation went fine, 
> producing the expected 64bit binaries:
> ./configure CPPFLAGS=-I/usr/local/include LDFLAGS=-
> L/usr/local/lib --prefix=/usr/local/gromacs407 --
> program-suffix=407 CFLAGS="-m64 -std=gnu99"

It may be that the 64 bit detection is failing... comparing the output from configure in the two cases would help diagnose that. Seeing whether a fresh 4.0.5 configuration compiles might be of interest.

The underlying problem might be a change in your system configuration, or the version of the autotools using in constructing 4.0.5 configure vs 4.0.7. If you really care, getting the bootstrap script from a GROMACS git distribution and running that on both your source versions should lead to both being well-formed for your system and the right flags being generated for libtool. Your work-around is probably fine, though.

Mark