Get rid of the -malign-double flag in the config.h (probably in one of the
PMEMD_ variables toward the bottom of the file).
At one point I tested pmemd performance using gcc 4.3, 4.4, and 4.5 on my
Mac on one of the benchmarks (on DHFR), and there was absolutely no
difference in performance, so even if you planned on using a gcc-compiled
pmemd for production simulations, you'll see no difference in different
compiler choices through MacPorts unless you wanted to put the time into
using any newer optimization technologies that may have been built into
newer GCC versions.
Thus, if it's easy enough, I'd suggest just switching to gcc44 to simplify
things.
HTH,
Jason
On Thu, Jul 21, 2011 at 10:34 AM, Jennifer L. Muzyka <
jennifer.muzyka.centre.edu> wrote:
> Should I try GCC 4.4? (I'm running a Mac with OSX 10.5, using gcc45
> selected with MacPorts.) After I was successful in getting AmberTools to
> install, I'm having new troubles with Amber 11. When I type make install, I
> get an error that says
>
> gcc -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -malign-double -DBINTRAJ
> -c pmemd_clib.c
> cc1: error: unknown -malign-XXXXX option specified: 'double'
> cc1: error: unrecognized command line option "-malign-double"
> make[2]: *** [pmemd_clib.o] Error 1
> make[1]: *** [install] Error 2
> make: *** [serial] Error 2
>
> I would appreciate any advice you can offer. Thanks.
> Jennifer
>
>
>
>
> On Jul 20, 2011, at 11:33 PM, Jason Swails wrote:
>
> All of my testing on the Mac is done with GCC 4.4, since that was the
> stable
> version when I first set up my computer (4.5 was experimental at the time),
> and I've never traded up since all my MPIs are compiled with 4.4.
> Therefore, I'm reasonably confident that MTK++ will compile with GCC 4.4,
> even if it is non-compliant under the more strict gcc 4.5+.
>
> I'll try it with some newer versions and see what I get.
>
> All the best,
> Jason
>
> On Wed, Jul 20, 2011 at 2:28 PM, Jennifer L. Muzyka <
> jennifer.muzyka.centre.edu<mailto:jennifer.muzyka.centre.edu>> wrote:
>
> When I type "g++ -v", I get the following:
> kimmy-strees-power-mac-g5:src kimmystree$ g++ -v
> Using built-in specs.
> COLLECT_GCC=g++
>
>
> COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/ppc-apple-darwin9/4.5.3/lto-wrapper
> Target: ppc-apple-darwin9
> Configured with: ../gcc-4.5.3/configure --prefix=/opt/local
> --build=ppc-apple-darwin9
> --enable-languages=c,c++,objc,obj-c++,fortran,java
> --libdir=/opt/local/lib/gcc45 --includedir=/opt/local/include/gcc45
> --infodir=/opt/local/share/info --mandir=/opt/local/share/man
> --datarootdir=/opt/local/share/gcc-4.5 --with-local-prefix=/opt/local
> --with-system-zlib --disable-nls --program-suffix=-mp-4.5
> --with-gxx-include-dir=/opt/local/include/gcc45/c++/ --with-gmp=/opt/local
> --with-mpfr=/opt/local --with-mpc=/opt/local --enable-stage1-checking
> --disable-multilib
> Thread model: posix
> gcc version 4.5.3 (GCC)
>
> Thanks for the suggestion to add "-nomtkpp". It worked!!
> Jennifer
>
>
> On Jul 20, 2011, at 10:57 AM, David A Case wrote:
>
> On Wed, Jul 20, 2011, Jennifer L. Muzyka wrote:
>
> My configure command was ./configure -macAccelerate gnu. I previously
> installed gcc45 using MacPorts and selected it as my gcc port, so that's
> what I was using.
>
> Weird. The workaround is to add "-nomtkpp" to the arguments to configure.
> But just for sanity, can you report the result of typing "g++ -v"?
>
> ....thx...dac
>
>
> _______________________________________________
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> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> Jennifer L. Muzyka
> Professor of Chemistry
> Centre College
> 600 West Walnut Street
> Danville, KY 40422
>
> jennifer.muzyka.centre.edu<mailto:jennifer.muzyka.centre.edu>
> http://web.centre.edu/muzyka/
>
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> Jennifer L. Muzyka
> Professor of Chemistry
> Centre College
> 600 West Walnut Street
> Danville, KY 40422
>
> jennifer.muzyka.centre.edu<mailto:jennifer.muzyka.centre.edu>
> http://web.centre.edu/muzyka/
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jul 21 2011 - 08:30:03 PDT
