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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 1:30 PM, Ray Luo <rluo.uci.edu> wrote:
> Gerald,
>
> Will try your patch next ...
>
> 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 1:18 PM, Gerald Monard
> <Gerald.Monard.univ-lorraine.fr> wrote:
>> Ray, Dan (+any volunteer): can you try (and test) that patch?
>>
>> I can do the same for LIBPBSA dependencies...;-)
>>
>> Gerald.
>>
>>
>> On 05/26/2016 09:41 PM, Gerald Monard wrote:
>>>
>>> Ray,
>>>
>>> Yes, my mistake: pb_force.o has a dependency for sa_driver.o.
>>> But it's weirder(?) than this: if I track the compilation, a problem
>>> appears for libFpbsa.a (pbsa library for sander). I can see this (in
>>> serial order):
>>>
>>> gfortran [...] -DSANDER [...] -I../sander \ -o sa_driver.SANDER.o
>>> sa_driver.F90
>>> gfortran [...] -DSANDER [...] -I../sander \ -o pb_force.SANDER.o
>>> pb_force.F90
>>> gfortran [...] -DSANDER [...] -I../sander \ -o pb_p3m.SANDER.o pb_p3m.F90
>>> gfortran [...] -DSANDER [...] -I../sander \ -o interpX.SANDER.o
>>> interpX.F90
>>> gfortran [...] [...] -o pb_force.o pb_force.F90
>>> gfortran [...] [...] -o pb_direct.o pb_direct.F90
>>>
>>> It means that pb_force is compiled twice (thus the error for the
>>> parallel make: pb_direct needs pb_force that needs sa_driver which will
>>> create the solvent_accessibility module; while pb_force.SANDER.o needs
>>> sa_driver.SANDER.o that will create the solvent_accessibility module!).
>>>
>>> Origin: makedepend has a definition for pb_direct.SANDER.o, but Makefile
>>> compiles pb_direct.o as requested by SANDERPBSAOBJS.
>>> Two options
>>> 1) It should be said pb_direct.SANDER.o in the Makefile (to be
>>> consistent with makedepend)
>>> 2) makedepend should not contain the $SANDER{"pb_direct"} directive (to
>>> be consistent with Makefile)
>>>
>>> I'm checking the discrepancy between Makefile and makedepend and will
>>> commit a patch asap.
>>>
>>> Ray: you know more than me what is needed: to patch Makefile or to patch
>>> makedepend? (I guess it depends where #ifdef SANDER are present)
>>>
>>> Gerald.
>>>
>>> On 05/26/2016 09:21 PM, Ray Luo 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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>>>>
>>>>
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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 - 14:00:03 PDT