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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 12:38 PM, Ray Luo <rluo.uci.edu> wrote:
> Okay ... let me finish "make -j 4 install" without skipping python ...
> Installing python before building is small on centos so I usually skip
> this part when building ...
>
> 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 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)
>>> >>>
>>> >>> _______________________________________________
>>> >>> AMBER-Developers mailing list
>>> >>> AMBER-Developers.ambermd.org
>>> >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>> >>> _______________________________________________
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>>> >>> 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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Received on Thu May 26 2016 - 14:00:02 PDT