Do you see a file $AMBERHOME/lib/libFpbsa.a? If not, try re-building Amber
11 in serial. That's what's causing the error, is that PBSA's Makefile
isn't finding libFpbsa.a (as built in the serial version of Amber11). Note
that libFpbsa.a is only built (as far as I can tell) during the serial Amber
build, NOT during the serial AmberTools 1.5 build.
This will be remedied in the next AmberTools/Amber release.
HTH,
Jason
On Tue, Sep 27, 2011 at 4:24 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> A couple of days ago I installed from scratch AmberTools 1.4 and Amber 11 -
> parallel.
>
> My system is a 12 core Mac Pro running on OSX 10.6.8
>
> My fortan compiler was gcc44 downloaded from MacPorts and my mpi MPICH2.
>
> The installation works fine
>
> Today I tried to install AmberTool 1.5 / Amber 11 in a different directory
> (NOT ON TOP of the 1.4 installation).
>
> make parallel gives an error message (see at the end)
>
> The serial AmberTools 1.5 installation works:
>
> Finished test suite for AmberTools at Tue Sep 27 21:34:41 CEST 2011.
>
> 489 file comparisons passed
> 9 file comparisons failed
> 0 tests experienced errors
>
> The mpi configuration works
> Configuring fftw-3.2.2 (may be time-consuming)...
>
> fftw-3.2.2 configure succeeded.
>
> The configuration file, config.h, was successfully created.
>
> If you have amber11, the most common next step is to
> 'cd ../../src; make clean; make parallel'.
>
> $ ./AT15_Amber11.py
> ........
> Patching pmemd's Makefile
>
> Amber 11 patched for AmberTools 1.5. Run
> cd src; make parallel
> to build amber11
>
> NOTE: Because PBSA has changed since Amber 11 was released, some
> tests are known to fail and others are known to quit in error. These
> can be safely ignored.
>
> Tests that error: Tests in $AMBERHOME/test/sander_pbsa_frc
> Run.argasp.min Run.dadt.min Run.dgdc.min
> Run.lysasp.min Run.polyALA.min Run.polyAT.min
> Run.argasp.min Run.dadt.min Run.dgdc.min
> Run.lysasp.min Run.polyALA.min Run.polyAT.min
> Run.argasp.min Run.dadt.min Run.dgdc.min
> Run.lysasp.min Run.polyALA.min Run.polyAT.min
>
> Tests that produce possible FAILUREs:
> cd sander_pbsa_ipb2 && ./Run.110D.min
> cd sander_pbsa_lpb && ./Run.lsolver.min (only some of them fail here)
> cd sander_pbsa_tsr && ./Run.tsrb.min
> cd sander_pbsa_decres && ./Run.pbsa_decres
> mm_pbsa.pl tests 02, 03, and 05
>
> $ cd src
>
> $ make clean
>
> $ make parallel
>
> Warning: Deleted feature: PAUSE statement at (1)
> cpp -traditional -P -DBINTRAJ -DMPI svbksb.f > _svbksb.f
> mpif90 -c -O3 -mtune=generic -ffree-form -o svbksb.o _svbksb.f
> cpp -traditional -P -DBINTRAJ -DMPI pythag.f > _pythag.f
> mpif90 -c -O3 -mtune=generic -ffree-form -o pythag.o _pythag.f
> Error: a serial version of libFpbsa.a must be built before parallel build.
> make[2]: *** [libFpbsa.parallel] Error 2
> make[1]: *** [libpbsa] Error 2
> make: *** [parallel] Error 2
>
> Thanks in advance for any assistance in trouble shooting this.
>
> George
>
>
> _______________________________________________
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> AMBER.ambermd.org
> 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 Tue Sep 27 2011 - 17:30:02 PDT
