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--
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 12:25 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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)
>> >>>
>> >>> _______________________________________________
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>> >>>
>> >>
>> >
>> > --
>> >
>> ____________________________________________________________________________
>> >
>> > 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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Received on Thu May 26 2016 - 13:00:03 PDT