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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 Fri, Mar 4, 2016 at 11:36 PM, Hai Nguyen <nhai.qn.gmail.com> wrote: > FYI: I've just tried "*make install -j24"* in another machine and got error > > "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 _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Sat Mar 05 2016 - 11:30:03 PST