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 - 13:00:03 PDT
