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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 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-developersReceived on Tue Feb 16 2016 - 23:00:03 PST