----- Original Message ----- From: "J. Rui Rodrigues" <[email protected]> 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 <[email protected]>
> 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
