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
>>>
>
> _______________________________________________
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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 - 14:00:04 PDT
