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 - 12:00:03 PDT
