-j8 works fine for serial build (I am testing openmp build now). I used
-j24 since my node has 24 cores.
Hai
On Sat, Mar 5, 2016 at 3:34 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Sat, Mar 5, 2016 at 12:36 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> > FYI: I've just tried "*make install -j24"* in another machine and got
> error
>
> I wonder if "make" with 24 threads is simply testing the limits of the
> already complex and fragile network of dependencies that sander
> has...does the problem happen at lower "make" thread counts?
>
> -Dan
>
> >
> > "Fatal Error: Can't rename module file 'pbtimer_module.mod0' to
> > 'pbtimer_module.mod': No such file or directory
> > make[2]: *** [timer.o] Error 1
> > make[2]: *** Waiting for unfinished jobs....
> > make[2]: Leaving directory
> > `/gpfs/gpfs/project1/dacase-001/haichit/amber/amber/AmberTools/src/pbsa'
> > make[1]: *** [serial] Error 2
> > make[1]: Leaving directory
> > `/gpfs/gpfs/project1/dacase-001/haichit/amber/amber/AmberTools/src'
> > make: *** [install] Error 2
> > "
> >
> > info: gcc 4.4.7, Linux, 24 cores/node; use "*git clean -fdx .*" then
> > "*./configure
> > -noX11 gnu*" then "*make install -j24*"; git
> > commit: 570e427eaf02a99d81e6bf1c36d7d3a51a27c529 (today)
> >
> > *However*, this error seems happened randomly, sometimes the install
> > finished without any errors.
> >
> > Hai
> >
> > On Thu, Feb 18, 2016 at 3:54 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> >> 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
> >>>
> >>> _______________________________________________
> >>> 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
>
>
>
> --
> -------------------------
> 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
>
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Received on Sat Mar 05 2016 - 13:00:05 PST
