Hi Tyler,
> > So it is something in the FFTW build that is stopping make -j4 from
> working.
> > Make -j4 inside FFTW manually works so I suspect it is in the
> building of
> > Sander.RISM where make sends off one thread to do FFTW while
> continuing to
> > compile within src/sander and this leads to the link occurring before
> the
> > FFTW compile has completed.
> >
>
> I didn't realize the RISM section of the makefile was the problem.
> I'll look into it now.
I suspect this will be the first of many problems - I.e. problems lie
elsewhere as well. E.g. I have seen transient issues with make -j4 with
qmmm_module.mod not being found. The issue is there are several problems and
they move around due to machine load etc but the FFTW one seems to be a
recurring problem so if you can look at it that would be great. A couple of
things I tried were:
1) Edit src/sander/Makefile
Change:
sander.RISM$(SFX): $(NETCDF) libsqm librism $(RISMOBJ) $(QMOBJ) \
$(FULLPIMDOBJ) $(LSCIVROBJ) force.RISM.o syslib \
nxtsec netlib libpbsa configured_serial \
$(NCSU_OBJECTS) $(XRAY_OBJS) $(FLIBS_FFTW2)
$(FC) $(FFLAGS) $(AMBERFFLAGS) -o sander.RISM$(SFX) $(RISMOBJ)
$(QMOBJ) \
$(FULLPIMDOBJ) $(LSCIVROBJ) force.RISM.o \
../../AmberTools/src/rism/amber_rism_interface.o \
../lib/nxtsec.o \
$(LIBDIR)/librism.a $(LIBDIR)/libsqm.a $(LIBDIR)/libFpbsa.a \
$(NCSU_OBJECTS) $(XRAY_OBJS) $(FLIBS_FFTW2) $(FLIBSF) \
../lib/sys.a $(NETCDFLIB) $(LDFLAGS) $(AMBERLDFLAGS)
to
sander.RISM$(SFX): $(NETCDF) $(FLIBS_FFTW2) libsqm librism $(RISMOBJ)
$(QMOBJ) \
$(FULLPIMDOBJ) $(LSCIVROBJ) force.RISM.o syslib \
nxtsec netlib libpbsa configured_serial \
$(NCSU_OBJECTS) $(XRAY_OBJS) $(FLIBS_FFTW2)
$(FC) $(FFLAGS) $(AMBERFFLAGS) -o sander.RISM$(SFX) $(RISMOBJ)
$(QMOBJ) \
$(FULLPIMDOBJ) $(LSCIVROBJ) force.RISM.o \
../../AmberTools/src/rism/amber_rism_interface.o \
../lib/nxtsec.o \
$(LIBDIR)/librism.a $(LIBDIR)/libsqm.a $(LIBDIR)/libFpbsa.a \
$(NCSU_OBJECTS) $(XRAY_OBJS) $(FLIBSF) \
../lib/sys.a $(NETCDFLIB) $(LDFLAGS) $(AMBERLDFLAGS)
Doesn't work.
2) Change
librism librism_mpi:
cd ../../AmberTools/src/rism && $(MAKE) $.
cd ../../AmberTools/src/rism && rm -f amber_rism_interface.o &&
$(MAKE) SPEC_FPP=-DSANDER amber_rism_interface.o
to
librism librism_mpi:
cd ../../AmberTools/src/fftw-2.1.5 && $(MAKE)
cd ../../AmberTools/src/rism && $(MAKE) $.
cd ../../AmberTools/src/rism && rm -f amber_rism_interface.o &&
$(MAKE) SPEC_FPP=-DSANDER amber_rism_interface.o
This didn't work either.
I also tried a bunch of other minor changes related to the way
$(FLIBS_FFTW2) is defined. Actually explicitly adding the library to the
Makefile etc but this also didn't work.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Sat Nov 12 2011 - 15:30:02 PST
