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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Received on Tue Sep 27 2011 - 13:30:03 PDT
