I just tried "make -j 8 install" for serial build and ok with my machine
too.
Hai
On Thu, Feb 18, 2016 at 3:36 PM, Ray Luo <rluo.uci.edu> wrote:
> Gerald,
>
> Your fix also worked on my side! Thanks a lot!
>
> I used "make -j 8 install" though I skipped python install in both the
> serial and parallel tests.
>
> 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, Feb 18, 2016 at 11:23 AM, Ray Luo <rluo.uci.edu> wrote:
> > Thanks, I'm downloading your fix ...
> >
> > Also, the python-related installation seems to mess up the dependence
> > issue whether I use single or multi-thread make ... I don't know why
> > my changes in pbsa and sander have caused this to break.
> >
> > 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, Feb 18, 2016 at 11:08 AM, Gerald Monard
> > <Gerald.Monard.univ-lorraine.fr> wrote:
> >> Hi,
> >>
> >> I think that I found a fix. The problem was in the makedepend program in
> >> pbsa/ that had not been updated. That should work now. Can anybody test?
> >>
> >> Best,
> >>
> >> Gerald.
> >>
> >> On 02/18/2016 07:01 PM, Ross Walker wrote:
> >>> I second this - I tried to disable PBSA building for now but of course
> it is linked into Sander etc so we'd disabling Sander as well.
> >>>
> >>> I'd suggest spending a few hours trying to fix it and if you can't the
> checkin should be reversed until this is fixed.
> >>>
> >>> Serial builds really aren't a viable option these days - try doing a
> serial build on a Xeon Phi and you'll understand. :-(
> >>>
> >>> All the best
> >>> Ross
> >>>
> >>>> On Feb 18, 2016, at 9:13 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >>>>
> >>>> On Wed, Feb 17, 2016 at 6:04 PM, Ray Luo, Ph.D. <ray.luo.uci.edu>
> wrote:
> >>>>> Ross,
> >>>>>
> >>>>> Please pull again to see whether it fixed the build problem on your
> >>>>> side. Looks like multi-thread make does not work ... Too many
> >>>>> dependence issues ...
> >>>>
> >>>> The multi-threaded build definitely doesn't work for me when I hit
> pbsa stuff:
> >>>>
> >>>> $ make -j6 install
> >>>> ...
> >>>> make[2]: Entering directory
> '/home/droe/Amber/GIT/amber/AmberTools/src/pbsa'
> >>>> gcc -c -O3 -mtune=native -fPIC ...
> >>>> ...
> >>>> Makefile:238: recipe for target 'pb_p3m.LIBPBSA.o' failed
> >>>> Makefile:238: recipe for target 'pb_fdfrc.LIBPBSA.o' failed
> >>>>
> >>>> Amber is pretty large nowadays, and not being able to build in
> >>>> parallel is a real drawback. We can currently get around this by
> >>>> adding a '.NOTPARALLEL' target to the pbsa Makefile (or forcing -j1),
> >>>> but ideally I think the multi-threaded build should be fixed.
> >>>>
> >>>> -Dan
> >>>>
> >>>>>
> >>>>> 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 Wed, Feb 17, 2016 at 12:59 PM, Ray Luo, Ph.D. <ray.luo.uci.edu>
> wrote:
> >>>>>> Okay, I think I've fixed it. Don't know why the same makefile works
> in
> >>>>>> amber15 but doesn't work in amber16. I'm testing all the
> >>>>>> sander/pbsa/nab combs to make sure all can build without
> interruption
> >>>>>> and also pass the tests.
> >>>>>>
> >>>>>> Ray
> >>>>>> --
> >>>>>> Ray Luo, Ph.D.
> >>>>>> Professor
> >>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
> >>>>>> Chemical and Biomedical Engineering
> >>>>>> University of California, Irvine, CA 92697-3900
> >>>>>>
> >>>>>>
> >>>>>> On Tue, Feb 16, 2016 at 10:34 PM, Ray Luo, Ph.D. <ray.luo.uci.edu>
> wrote:
> >>>>>>> Finally I can reproduce your problem in building the MPI sander ...
> >>>>>>>
> >>>>>>> Will get it fixed tomorrow morning ...
> >>>>>>>
> >>>>>>> Ray
> >>>>>>> --
> >>>>>>> Ray Luo, Ph.D.
> >>>>>>> Professor
> >>>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
> >>>>>>> Chemical and Biomedical Engineering
> >>>>>>> University of California, Irvine, CA 92697-3900
> >>>>>>>
> >>>>>>>
> >>>>>>> On Tue, Feb 16, 2016 at 10:17 PM, Ray Luo, Ph.D. <ray.luo.uci.edu>
> wrote:
> >>>>>>>> Hi Ross,
> >>>>>>>>
> >>>>>>>> Looks like that there is no extra untracked file at least in all
> the
> >>>>>>>> src folders, though there were indeed two .swp files in the test
> >>>>>>>> cases. So I think lack of "git clean -fdx" is not the problem.
> I've
> >>>>>>>> finished the serial build and is running "test.sander.BASIC".
> Looking
> >>>>>>>> good, so far.
> >>>>>>>>
> >>>>>>>> I'll do the MPI build next after another "git clean -fdx" ...
> >>>>>>>>
> >>>>>>>> However, I think one possible reason could be the use of
> multi-thread
> >>>>>>>> in make. There may be inter-dependent issues involved.
> >>>>>>>>
> >>>>>>>> I'll do some experiment with the MPI build to see whether this is
> the cause.
> >>>>>>>>
> >>>>>>>> Ray
> >>>>>>>> --
> >>>>>>>> Ray Luo, Ph.D.
> >>>>>>>> Professor
> >>>>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
> >>>>>>>> Chemical and Biomedical Engineering
> >>>>>>>> University of California, Irvine, CA 92697-3900
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Tue, Feb 16, 2016 at 8:24 PM, Ross Walker <
> ross.rosswalker.co.uk> wrote:
> >>>>>>>>> Hi Ray,
> >>>>>>>>>
> >>>>>>>>> It's not about whether you compiled in that folder - it is
> whether you maybe edited files in that folder that you never committed /
> pushed. Try doing:
> >>>>>>>>>
> >>>>>>>>> git clean -f -d -x
> >>>>>>>>> git status
> >>>>>>>>>
> >>>>>>>>> And see what it reports.
> >>>>>>>>>
> >>>>>>>>> All the best
> >>>>>>>>> Ross
> >>>>>>>>>
> >>>>>>>>>> On Feb 16, 2016, at 23:04, Ray Luo <rluo.uci.edu> wrote:
> >>>>>>>>>>
> >>>>>>>>>> Hi Ross,
> >>>>>>>>>>
> >>>>>>>>>> Yes, I think my folder is clean since I have never compiled
> anything
> >>>>>>>>>> in my amber git folder. Every time after syncing with the master
> >>>>>>>>>> branch, I copy the whole master branch to a new folder for
> compiling
> >>>>>>>>>> and testing.
> >>>>>>>>>>
> >>>>>>>>>> I'm about to test this evening's synced version, but will do
> "git
> >>>>>>>>>> clean -fxd" before configuring/compiling. Maybe this is why.
> >>>>>>>>>>
> >>>>>>>>>> By the way, could you add my uci email to the mailing list as
> well,
> >>>>>>>>>> i.e. "ray.luo.uci.edu"?
> >>>>>>>>>>
> >>>>>>>>>> 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 Tue, Feb 16, 2016 at 7:51 PM, Ross Walker <
> ross.rosswalker.co.uk> wrote:
> >>>>>>>>>>> Hi Ray,
> >>>>>>>>>>>
> >>>>>>>>>>> If I do this - on my OSX laptop (GCC 4.9.3), MPICH version
> 3.1.4
> >>>>>>>>>>>
> >>>>>>>>>>> git pull
> >>>>>>>>>>> git clean -f -d -x
> >>>>>>>>>>> git status
> >>>>>>>>>>> On branch master
> >>>>>>>>>>> Your branch is up-to-date with 'origin/master'.
> >>>>>>>>>>> nothing to commit, working directory clean
> >>>>>>>>>>>
> >>>>>>>>>>> ./configure -mpi gnu
> >>>>>>>>>>> make install
> >>>>>>>>>>>
> >>>>>>>>>>> ...
> >>>>>>>>>>> ...
> >>>>>>>>>>> dnrm2.F90:113.24:
> >>>>>>>>>>>
> >>>>>>>>>>> ASSIGN 110 TO NEXT
> >>>>>>>>>>> 1
> >>>>>>>>>>> Warning: Deleted feature: ASSIGN statement at (1)
> >>>>>>>>>>> mpif90 -DBINTRAJ -DEMIL -DMPI -c -O3 -mtune=native -fPIC
> -ffree-form -I/Users/rcw/amber/amber/include
> -I/Users/rcw/amber/amber/include -o dcopy.o dcopy.F90
> >>>>>>>>>>> mpif90 -DBINTRAJ -DEMIL -DMPI -c -O3 -mtune=native -fPIC
> -ffree-form -I/Users/rcw/amber/amber/include
> -I/Users/rcw/amber/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'
> >>>>>>>>>>> make[3]: *** [pb_force.o] Error 1
> >>>>>>>>>>> make[2]: *** [libpbsa] Error 2
> >>>>>>>>>>> make[1]: *** [parallel] Error 2
> >>>>>>>>>>> make: *** [install] Error 2
> >>>>>>>>>>>
> >>>>>>>>>>> Same problem. Are you sure you have the latest tree and it is
> clean and doesn't have any modified files locally or files you forgot to
> add?
> >>>>>>>>>>>
> >>>>>>>>>>> All the best
> >>>>>>>>>>> Ross
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>> On Feb 16, 2016, at 15:56, Ray Luo, Ph.D. <ray.luo.uci.edu>
> wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>> Hi Ross,
> >>>>>>>>>>>>
> >>>>>>>>>>>> So far I can "configure -mpi gnu", "make install", and can
> also pass
> >>>>>>>>>>>> "make sander.BASIC.MPI". I'm running "make test.parallel.MM".
> I'm
> >>>>>>>>>>>> using "mpirun -np 4" for the mpi jobs. This is on Rocks
> 6.1/Centos
> >>>>>>>>>>>> 6.1. Which step was the problem?
> >>>>>>>>>>>>
> >>>>>>>>>>>> However I disabled "pbsa_mbfocus" in AmberTools/test/ since
> I'm in the
> >>>>>>>>>>>> process of removing this feature to accommodate incoming
> CUDA. I also
> >>>>>>>>>>>> need to update the test cases for sander/nab/mmpbsa ... which
> will be
> >>>>>>>>>>>> partially in today for sander/nab. I'm trying to get
> mmpbsa.py to work
> >>>>>>>>>>>> with the new python environment.
> >>>>>>>>>>>>
> >>>>>>>>>>>> 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 Tue, Feb 16, 2016 at 10:21 AM, Ray Luo, Ph.D. <
> ray.luo.uci.edu> wrote:
> >>>>>>>>>>>>> Hi Ross,
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I'm looking into this ... There was a major overhaul of the
> code in
> >>>>>>>>>>>>> addition to new features in the last check in.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> 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
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER-Developers mailing list
> >>>>> AMBER-Developers.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> -------------------------
> >>>> 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
>
> _______________________________________________
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>
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Received on Thu Feb 18 2016 - 13:00:07 PST
