Re: [AMBER-Developers] Parallel make failing

From: Gerald Monard <Gerald.Monard.univ-lorraine.fr>
Date: Thu, 26 May 2016 23:34:47 +0200

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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>

-- 
____________________________________________________________________________
  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 - 15:00:02 PDT
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