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-- Paul Rigor http://www.ics.uci.edu/~prigor On Wed, May 25, 2011 at 7:25 PM, Jason Swails <jason.swails.gmail.com>wrote: > On Wed, May 25, 2011 at 10:19 PM, Paul Rigor <paul.rigor.uci.edu> wrote: > > > Hi all, > > > > So this is the error message I get after running configure with the > > following parameters: > > ./configure -cuda_DPDP -mpi > > > > Compiler? > > > > > > There's an unreferenced fortran function called mexit(). I know it's > under > > pmemd_lib.f90 and its object file is actually getting linked to the > > master_setup.o. So why does this error persist? > > > > It's always helpful to print the exact commands you used along with the > exact error messages copied and pasted from the terminal -- it removes a > lot > of the guesswork from troubleshooting. > > Try running a "make clean" and recompiling. If you still get those kinds > of > complaints, try doing > > cd $AMBERHOME/src/pmemd/src && make depends > cd $AMBERHOME/src/ && make cuda_parallel > > The important step being the first one that updates the dependencies > (perhaps an extra mexit got hacked in somewhere?) > > HTH, > Jason > > > > However, compiling just -cuda_DPDP and the tests pass with flying colors: > > 54 file comparisons passed > > 0 file comparisons failed > > 0 tests experienced errors > > Test log file saved as logs/test_amber_cuda/2011-05-25_19-11-35.log > > No test diffs to save! > > > > > > Thanks, > > Paul > > > > ==Tail of build log with -cuda_DPDP -mpi== > > make[3]: Entering directory > > > > > `/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src/pmemd/src/cuda' > > make[3]: `cuda.a' is up to date. > > make[3]: Leaving directory > > > > > `/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src/pmemd/src/cuda' > > mpif90 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -Duse_DPDP -o pmemd.cuda > > gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o > mdin_ctrl_dat.o > > mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o > dynamics_dat.o > > img.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o > pme_recip_dat.o > > pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o > pme_fft_dat.o > > fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o > > dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o > loadbal.o > > shake.o prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o > > veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o > > pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o > > get_cmdline.o master_setup.o pme_alltasks_setup.o pme_setup.o > > ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o angles_ub.o > > dihedrals_imp.o cmap.o charmm.o charmm_gold.o -L/usr/local/cuda/lib64 > > -L/usr/local/cuda/lib -lcufft -lcudart ./cuda/cuda.a > > /extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/lib/libnetcdf.a > > master_setup.o: In function `__master_setup_mod__printdefines': > > master_setup.f90:(.text+0xaa2): undefined reference to `mexit_' > > collect2: ld returned 1 exit status > > make[2]: *** [pmemd.cuda] Error 1 > > make[2]: Leaving directory > > `/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src/pmemd/src' > > make[1]: *** [cuda] Error 2 > > make[1]: Leaving directory > > `/extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src/pmemd' > > make: *** [cuda] Error 2 > > 07:01 PM 28580 prigor.nimbus > > /extra/dock2/VirtualDrugScreening/tools/amber/md/11-1.5.0/src > > > > Thanks, > > Paul > > -- > > Paul Rigor > > http://www.ics.uci.edu/~prigor > > > > > > > > On Wed, May 25, 2011 at 6:51 PM, Paul Rigor <paul.rigor.uci.edu> wrote: > > > > > Here's the log after recompiling, applying the patches, etc (but still > no > > > cuda_parallel target) and without having to mess with the netCDF > library. > > > > > > 42 file comparisons passed > > > 12 file comparisons failed > > > 0 tests experienced errors > > > Test log file saved as logs/test_amber_cuda/2011-05-25_18-22-30.log > > > Test diffs file saved as logs/test_amber_cuda/2011-05-25_18-22-30.diff > > > > > > Thanks, > > > Paul > > > > > > > > > -- > > > Paul Rigor > > > http://www.ics.uci.edu/~prigor > > > > > > > > > > > > On Wed, May 25, 2011 at 5:53 PM, Paul Rigor <paul.rigor.uci.edu> > wrote: > > > > > >> Hi gang, > > >> > > >> So I'm still checking with our system admin, I still do not see the > > >> cuda_parallel target, just serial, parallel and cuda. So we probably > > don't > > >> have the latest sources? In any case, here are the logs for the serial > > and > > >> mpi versions of amber. I've made sure to patch and also clean up > before > > >> running their respective make target. > > >> > > >> I'll keep you posted on the cuda and cuda_parallel builds for SDK 4.0 > > (and > > >> 3.2). > > >> > > >> Thanks, > > >> Paul > > >> > > >> > > >> > > >> -- > > >> Paul Rigor > > >> http://www.ics.uci.edu/~prigor > > >> > > >> > > >> > > >> On Wed, May 25, 2011 at 4:18 PM, Ross Walker <ross.rosswalker.co.uk > > >wrote: > > >> > > >>> > > Yes it does. Line 45 of $AMBERHOME/src/Makefile > > >>> > > > > >>> > > cuda_parallel: configured_cuda configured_parallel clean > > $(NETCDFLIB) > > >>> > > .echo "Starting installation of ${AMBER} (cuda parallel) > at > > >>> > `date`". > > >>> > > cd pmemd && $(MAKE) cuda_parallel > > >>> > > > > >>> > > Something smells fishy with your copy of AMBER 11 to me if it is > > >>> > missing > > >>> > > this. > > >>> > > > > >>> > > > >>> > Could be unpatched. I don't think we had cuda_parallel at Amber11 > > >>> > release, right? > > >>> > > >>> But how would he get any parallel version compiled??? - Or maybe it > is > > >>> just > > >>> the serial version linked with MPI. Ugh... > > >>> > > >>> > > >>> _______________________________________________ > > >>> AMBER mailing list > > >>> AMBER.ambermd.org > > >>> http://lists.ambermd.org/mailman/listinfo/amber > > >>> > > >> > > >> > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > -- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Candidate > 352-392-4032 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed May 25 2011 - 20:00:02 PDT