Re: [AMBER-Developers] Parallel make failing

From: Ray Luo <rluo.uci.edu> Date: Thu, 26 May 2016 14:17:13 -0700

--
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 1:53 PM, Gerald Monard
<Gerald.Monard.univ-lorraine.fr> wrote:
> Ray,
>
> The patch was generated with git format-patch, so you should use git am
> instead of git apply.
>
> Gerald.
>
> On 05/26/2016 10:49 PM, Ray Luo wrote:
>> Gerald,
>>
>> Somehow I got the following error messages when applying it ...
>>
>> git apply ~/0001-libFpbsa-PBSA-library-for-sander-dependency-modifica.patch
>> /home/rayl/0001-libFpbsa-PBSA-library-for-sander-dependency-modifica.patch:32:
>> trailing whitespace.
>> # in alphabetical order (GM/2016-05-26)
>> /home/rayl/0001-libFpbsa-PBSA-library-for-sander-dependency-modifica.patch:33:
>> trailing whitespace.
>> SANDERPBSAOBJS= curv.o density.o dsvdc.o gen_dx_file.o GrToPr.o \
>> /home/rayl/0001-libFpbsa-PBSA-library-for-sander-dependency-modifica.patch:34:
>> trailing whitespace.
>>          iimod.o interpX.SANDER.o memory_module.o miniop.o np_force.SANDER.o  \
>> /home/rayl/0001-libFpbsa-PBSA-library-for-sander-dependency-modifica.patch:35:
>> trailing whitespace.
>>          parms.SANDER.o pb_bldsys.o pb_crgview.o pb_direct.o pb_fddrv.o  \
>> /home/rayl/0001-libFpbsa-PBSA-library-for-sander-dependency-modifica.patch:36:
>> trailing whitespace.
>>          pb_fdfrc.SANDER.o pb_force.SANDER.o pb_init.SANDER.o pb_list.o
>> pb_lsolver.o  \
>> error: patch failed: AmberTools/src/pbsa/Makefile:67
>> error: AmberTools/src/pbsa/Makefile: patch does not apply
>> error: patch failed: AmberTools/src/pbsa/depend:37
>> error: AmberTools/src/pbsa/depend: patch does not apply
>> error: patch failed: AmberTools/src/pbsa/makedepend:16
>> error: AmberTools/src/pbsa/makedepend: patch does not apply
>>
>> 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 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)
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER-Developers mailing list
>>>>>>>>> AMBER-Developers.ambermd.org
>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER-Developers mailing list
>>>>>>>>> AMBER-Developers.ambermd.org
>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> ____________________________________________________________________________
>>>>>>>
>>>>>>>      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
>>>>>>>
>>>>>>>
>>>>>>> ____________________________________________________________________________
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER-Developers mailing list
>>>>>>> AMBER-Developers.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER-Developers mailing list
>>>>>> AMBER-Developers.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>>>
>>>>>
>>>>
>>>> --
>>>> ____________________________________________________________________________
>>>>
>>>>   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
>>>>
>>>> ____________________________________________________________________________
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER-Developers mailing list
>>>> AMBER-Developers.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
> --
> ____________________________________________________________________________
>
>   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
>
> ____________________________________________________________________________
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers