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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 1:18 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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>>
>
> --
> ____________________________________________________________________________
>
> 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