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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 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 - 22:30:04 PST