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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 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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Received on Thu May 26 2016 - 12:30:03 PDT