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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 2:34 PM, Gerald Monard
<Gerald.Monard.univ-lorraine.fr> wrote:
> Ray,
>
> pbsa.SANDER.o (and parms.SANDER.o) should not be compiled (sorry).
> Can you apply this new patch?
>
> Gerald.
>
>
> On 05/26/2016 11:17 PM, Ray Luo wrote:
>>
>> Gerald,
>>
>> Thanks a lot! I'm testing with a "configure -mpi gnu" build in 16
>> threads. Here are the error messages when building "libFpbsa.a".
>>
>> All the best,
>> Ray
>>
>> ++++
>>
>> cd ../pbsa && make libFpbsa.a
>> make[3]: Entering directory
>> `/home/rayl/amber-master-fresh1/AmberTools/src/pbsa'
>> /bin/rm -f decomp.o decomp.mod DECOMP.mod
>> mpif90 -DBINTRAJ -DEMIL -DMPI -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -o density.o density.F90
>> mpif90 -DBINTRAJ -DEMIL -DMPI -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -o gen_dx_file.o
>> gen_dx_file.F90
>> cd ../sander && make decomp.o
>> mpif90 -DBINTRAJ -DEMIL -DMPI -DSANDER -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -I../sander \
>> -o interpX.SANDER.o interpX.F90
>> mpif90 -DBINTRAJ -DEMIL -DMPI -DSANDER -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -I../sander \
>> -o timer.SANDER.o timer.F90
>> mpif90 -DBINTRAJ -DEMIL -DMPI -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -o decomp.o decomp.F90
>> mpif90 -DBINTRAJ -DEMIL -DMPI -DSANDER -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -I../sander \
>> -o parms.SANDER.o parms.F90
>> mpif90 -DBINTRAJ -DEMIL -DMPI -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -o sa_driver.o
>> sa_driver.F90
>> make[4]: Entering directory
>> `/home/rayl/amber-master-fresh1/AmberTools/src/sander'
>> make[4]: `decomp.o' is up to date.
>> make[4]: Leaving directory
>> `/home/rayl/amber-master-fresh1/AmberTools/src/sander'
>> cp -p ../sander/decomp.o ../pbsa
>> cp -p ../sander/decomp.mod ../pbsa
>> mpif90 -DBINTRAJ -DEMIL -DMPI -DSANDER -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -I../sander \
>> -o sa_driver.SANDER.o sa_driver.F90
>> mpif90 -DBINTRAJ -DEMIL -DMPI -DSANDER -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -I../sander \
>> -o pb_p3m.SANDER.o pb_p3m.F90
>> mpif90 -DBINTRAJ -DEMIL -DMPI -DSANDER -c -O3 -mtune=native -fPIC
>> -ffree-form -I/home/rayl/amber-master-fresh1/include
>> -I/home/rayl/amber-master-fresh1/include -I../sander \
>> -o pbsa.SANDER.o pbsa.F90
>> pbsa.F90:88.49:
>>
>> use parms, only : allocate_parms, clean_parms, bcast_parms, cn1, cn2
>>
>> 1
>> Error: Symbol 'bcast_parms' referenced at (1) not found in module 'parms'
>> make[3]: *** [pbsa.SANDER.o] Error 1
>> make[3]: *** Waiting for unfinished jobs....
>> make[3]: Leaving directory
>> `/home/rayl/amber-master-fresh1/AmberTools/src/pbsa'
>> make[2]: *** [libpbsa] Error 2
>> make[2]: Leaving directory
>> `/home/rayl/amber-master-fresh1/AmberTools/src/sander'
>> make[1]: *** [parallel] Error 2
>> make[1]: Leaving directory `/home/rayl/amber-master-fresh1/AmberTools/src'
>> make: *** [install] Error 2
>>
>> --
>> 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
>>
>>
>> _______________________________________________
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>> AMBER-Developers.ambermd.org
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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
>
> ____________________________________________________________________________
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Thu May 26 2016 - 15:00:03 PDT