Ray,
have you tried `-mpi` too? I think Dan's attempt in hist 1st post was with
MPI.
> mpif90 -DBINTRAJ -DMPI -c -O3 -mtune=native -fPIC -ffree-form
> -I/home/droe/Amber/GIT/amber/include
> -I/home/droe/Amber/GIT/amber/include -o pb_force.o pb_force.F90
> pb_force.F90:292:77:
Hai
On Thu, May 26, 2016 at 3:21 PM, Ray Luo <rluo.uci.edu> wrote:
> Gerald,
>
> Somehow in my "depend", as generated by "makedepend", "pb_force.o"
> lists "sa_driver.o" as one of the depends in all three cases, i.e. for
> PBSA, SANDER, and LIBPBSA ... I suppose "makedepend" is okay?
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Thu, May 26, 2016 at 11:31 AM, Gerald Monard
> <Gerald.Monard.univ-lorraine.fr> wrote:
> > Hello,
> >
> > FYI, based on Dan's error report: pbsa/pb_force.F90 needs the
> > solvent_accessibility module from sa_driver.F90, but makedepend does not
> > recognize this dependency. So if you're lucky the first one get compiled
> > before the second one (the files are in "correct" order in the
> > Makefile), if not, then you're doomed for a compile error.
> >
> > Gerald.
> >
> > On 05/26/2016 07:37 PM, Gerald Monard wrote:
> >> Hello,
> >>
> >> This issue was raised some weeks/months ago (see thread
> >> [AMBER-Developers] Sander parallel build broken by PBSA updates). If
> >> it's still the same problem, it's a dependency problem in PBSA
> >> (makedepend not making its work correctly). You can't see it with make
> >> -j1 and it's a random problem with make -jX (X>1).
> >> I (partially) solved it last time. I'll check into it asap.
> >>
> >> Gerald.
> >>
> >> On 05/26/2016 07:23 PM, Ray Luo wrote:
> >>> First thing first, I always "git clean -xfd" before rebuilding. I'll
> try
> >>> different thead values to see whether I can reproduce the problem.
> >>>
> >>> Also all object files for sander are separately defined and built so
> this
> >>> could be something higher up.
> >>>
> >>> Ray
> >>> On May 26, 2016 10:04 AM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> >>>
> >>> On Thu, May 26, 2016, Ray Luo wrote:
> >>>> Okay, I've just confirmed again that I can
> >>>> make -j 32 install
> >>>> if I turned off python building. I don't know too much how the python
> >>>> part is built ... Please take a look of the dependence relations
> >>>> related to python building.
> >>>
> >>> Nope - still fails for me with '--skip-python'. It's almost certainly
> >>> an issue with pbsa/libpbsa dependencies since that is where the build
> >>> always fails for me ('make -j4'):
> >>>
> >>> ```
> >>> mpif90 -DBINTRAJ -DMPI -c -O3 -mtune=native -fPIC -ffree-form
> >>> -I/home/droe/Amber/GIT/amber/include
> >>> -I/home/droe/Amber/GIT/amber/include -o pb_force.o pb_force.F90
> >>> pb_force.F90:292:77:
> >>>
> >>> sa_init, sa_driver, sa_free,
> >>> sa_free_mb, &
> >>>
> >>> 1
> >>> Error: Symbol ‘saslave_init’ referenced at (1) not found in module
> >>> ‘solvent_accessibility’
> >>> Makefile:226: recipe for target 'pb_force.o' failed
> >>> make[3]: *** [pb_force.o] Error 1
> >>> ```
> >>>
> >>> -Dan
> >>>
> >>> --
> >>> -------------------------
> >>> Daniel R. Roe, PhD
> >>> Department of Medicinal Chemistry
> >>> University of Utah
> >>> 30 South 2000 East, Room 307
> >>> Salt Lake City, UT 84112-5820
> >>> http://home.chpc.utah.edu/~cheatham/
> >>> (801) 587-9652
> >>> (801) 585-6208 (Fax)
> >>>
> >>> _______________________________________________
> >>> AMBER-Developers mailing list
> >>> AMBER-Developers.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>> _______________________________________________
> >>> AMBER-Developers mailing list
> >>> AMBER-Developers.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>
> >>
> >
> > --
> >
> ____________________________________________________________________________
> >
> > Prof. Gerald MONARD
> > SRSMC, Université de Lorraine, CNRS
> > Boulevard des Aiguillettes B.P. 70239
> > F-54506 Vandoeuvre-les-Nancy, FRANCE
> >
> > e-mail : Gerald.Monard.univ-lorraine.fr
> > tel. : +33 (0)383.684.381
> > fax : +33 (0)383.684.371
> > web : http://www.monard.info
> >
> >
> ____________________________________________________________________________
> >
> >
> > _______________________________________________
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> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Thu May 26 2016 - 12:30:05 PDT
