Applying all bugfixes in /home/amutha/Desktop/amber_patch/bugfix.all.tar.bz2 Patching AMBER installation in /home/amutha/Desktop/amber_patch/amber11 Directory exists warnings can be safely ignored. patching file src/sander/qm_mm.f patching file src/sander/nonbond_list.f patching file src/pmemd/src/mdin_ctrl_dat.fpp patching file src/pmemd/src/cuda/gpu.cpp patching file src/pmemd/src/cuda/gpu.cpp patching file src/sander/makedepend patching file src/sander/Makefile patching file src/sander/mdread.f patching file src/mm_pbsa/mm_pbsa_calceneent.pm patching file src/mm_pbsa/mm_pbsa_readinput.pm patching file src/pmemd/src/Makefile patching file AmberTools/src/configure Hunk #1 FAILED at 19. Hunk #2 FAILED at 370. Hunk #3 FAILED at 504. Hunk #4 FAILED at 633. Hunk #5 FAILED at 643. Hunk #6 FAILED at 657. Hunk #7 FAILED at 989. Hunk #8 FAILED at 1022. Hunk #9 FAILED at 1058. Hunk #10 FAILED at 1310. Hunk #11 FAILED at 1344. Hunk #12 FAILED at 1492. Hunk #13 FAILED at 1546. 13 out of 13 hunks FAILED -- saving rejects to file AmberTools/src/configure.rej patching file benchmarks/jac/bench.jac.cuda patching file src/Makefile patching file src/pmemd/config_data/linux_em64t_cuda_DPDP.gfortran.mpi patching file src/pmemd/config_data/linux_em64t_cuda_SPSP.gfortran.mpi patching file src/pmemd/config_data/linux_em64t_cuda.gfortran.mpi patching file src/pmemd/src/angles.fpp patching file src/pmemd/src/angles_ub.fpp patching file src/pmemd/src/bonds.fpp patching file src/pmemd/src/cmap.fpp patching file src/pmemd/src/cuda/cuda_info.fpp patching file src/pmemd/src/cuda/gpu.cpp patching file src/pmemd/src/cuda/gpu.h patching file src/pmemd/src/cuda/gputypes.cpp patching file src/pmemd/src/cuda/gputypes.h patching file src/pmemd/src/cuda/kCalculateGBBornRadii.cu patching file src/pmemd/src/cuda/kCalculateGBNonbondEnergy1.cu patching file src/pmemd/src/cuda/kCalculateGBNonbondEnergy.cu patching file src/pmemd/src/cuda/kCalculateLocalForces.cu patching file src/pmemd/src/cuda/kCalculatePMENonbondEnergy.cu patching file src/pmemd/src/cuda/kCCF.h patching file src/pmemd/src/cuda/kCPNE.h patching file src/pmemd/src/cuda/kForcesUpdate.cu patching file src/pmemd/src/cuda/kNeighborList.cu patching file src/pmemd/src/cuda/kNTPKernels.h patching file src/pmemd/src/cuda/kPGGW.h patching file src/pmemd/src/cuda/kPGS.h patching file src/pmemd/src/cuda/kPMEInterpolation.cu patching file src/pmemd/src/cuda/kRandom.cu patching file src/pmemd/src/cuda/kRandom.h patching file src/pmemd/src/cuda/kShake.cu patching file src/pmemd/src/cuda/kU.h patching file src/pmemd/src/cuda/kUpdate.cu patching file src/pmemd/src/cuda/Makefile patching file src/pmemd/src/dihedrals.fpp patching file src/pmemd/src/dihedrals_imp.fpp patching file src/pmemd/src/dynamics.fpp patching file src/pmemd/src/extra_pnts_nb14.fpp patching file src/pmemd/src/f90depends patching file src/pmemd/src/gb_force.fpp patching file src/pmemd/src/gb_parallel.fpp patching file src/pmemd/src/Makefile patching file src/pmemd/src/master_setup.fpp patching file src/pmemd/src/mdin_ctrl_dat.fpp patching file src/pmemd/src/mol_list.fpp patching file src/pmemd/src/parallel.fpp patching file src/pmemd/src/pme_force.fpp patching file src/pmemd/src/pmemd.fpp patching file src/pmemd/src/runmd.fpp patching file src/pmemd/src/shake.fpp patching file test/cuda/4096wat/mdout.pure_wat.GPU_DPDP patching file test/cuda/4096wat/mdout.pure_wat.GPU_SPDP patching file test/cuda/4096wat/mdout.pure_wat.GPU_SPSP patching file test/cuda/4096wat/mdout.vrand.GPU_DPDP patching file test/cuda/4096wat/mdout.vrand.GPU_SPDP patching file test/cuda/4096wat/mdout.vrand.GPU_SPSP patching file test/cuda/4096wat/Run.pure_wat patching file test/cuda/4096wat/Run.vrand patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_npt_ntt1.GPU_SPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_npt_ntt1.GPU_SPSP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nve.GPU_SPDP patching file 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patching file test/cuda/gb_ala3/Run.irest1_ntt0_igb5_ntc2_alpb patching file test/cuda/gb_ala3/Run.irest1_ntt0_igb5_ntc2_ntr1 patching file test/cuda/gb_ala3/Run.irest1_ntt0_igb5_ntc2_rgbmax patching file test/cuda/gb_ala3/Run.irest1_ntt0_igb5_ntc2_saltcon patching file test/cuda/gb_ala3/Run.irest1_ntt1_igb1_ntc2 patching file test/cuda/gb_ala3/Run.irest1_ntt2_igb1_ntc2 patching file test/cuda/gb_ala3/Run.irest1_ntt3_igb1_ntc2 patching file test/cuda/jac/jac.out patching file test/cuda/jac/jac.out.GPU_DPDP patching file test/cuda/jac/jac.out.GPU_SPDP patching file test/cuda/jac/jac.out.GPU_SPSP patching file test/cuda/jac/Run.jac patching file test/cuda/Makefile patching file test/cuda/myoglobin/myoglobin_md.out.GPU_DPDP patching file test/cuda/myoglobin/myoglobin_md.out.GPU_SPDP patching file test/cuda/myoglobin/myoglobin_md.out.GPU_SPSP patching file test/cuda/myoglobin/Run_md_myoglobin patching file test/cuda/nucleosome/nucleosome_md1_ntt1.out.GPU_DPDP patching file test/cuda/nucleosome/nucleosome_md1_ntt1.out.GPU_SPDP patching file test/cuda/nucleosome/nucleosome_md1_ntt1.out.GPU_SPSP patching file test/cuda/nucleosome/nucleosome_md2_ntt0.out.GPU_DPDP patching file test/cuda/nucleosome/nucleosome_md2_ntt0.out.GPU_SPDP patching file test/cuda/nucleosome/nucleosome_md2_ntt0.out.GPU_SPSP patching file test/cuda/nucleosome/nucleosome_min.out.GPU_DPDP patching file test/cuda/nucleosome/nucleosome_min.out.GPU_SPDP patching file test/cuda/nucleosome/nucleosome_min.out.GPU_SPSP patching file test/cuda/nucleosome/Run_md.1 patching file test/cuda/nucleosome/Run_md.2 patching file test/cuda/nucleosome/Run_min.1 patching file test/cuda/trpcage/Run_md_trpcage patching file test/cuda/trpcage/trpcage_md.out.GPU_DPDP patching file test/cuda/trpcage/trpcage_md.out.GPU_SPDP patching file test/cuda/trpcage/trpcage_md.out.GPU_SPSP patching file test/Makefile patching file test/test_amber_cuda_parallel.sh patching file src/pmemd/src/cuda/gpu.cpp patching file src/pmemd/src/cuda/kCPNE.h patching file src/pmemd/src/cuda/kCalculatePMENonbondEnergy.cu patching file src/pmemd/Makefile patching file src/pmemd/src/cuda/cuda_info.fpp patching file src/pmemd/src/cuda/kCLF.h patching file test/cuda/Makefile patching file src/pmemd/src/cuda/gpu.cpp patching file src/pmemd/src/cuda/gputypes.cpp patching file src/pmemd/src/cuda/gputypes.h patching file src/pmemd/src/pmemd_clib.c patching file src/sander/mdread.f patching file src/pmemd/src/cuda/gpu.cpp patching file src/pmemd/src/cuda/Makefile.advanced patching file src/pmemd/src/fft1d.fpp patching file src/pmemd/src/mdin_ewald_dat.fpp patching file src/pmemd/src/pmemd.fpp patching file src/pmemd/src/timers.fpp patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_npt_ntt1.GPU_DPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_npt_ntt1.GPU_SPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_npt_ntt1.GPU_SPSP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nve.GPU_DPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nve.GPU_SPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nve.GPU_SPSP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt1.GPU_DPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt1.GPU_SPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt1.GPU_SPSP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt2.GPU_DPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt2.GPU_SPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt2.GPU_SPSP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt3.GPU_DPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt3.GPU_SPDP patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt3.GPU_SPSP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_npt_ntt1.GPU_DPDP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_npt_ntt1.GPU_SPDP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nve.GPU_DPDP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nve.GPU_SPDP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt1.GPU_DPDP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt1.GPU_SPDP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt2.GPU_DPDP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt2.GPU_SPDP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt3.GPU_DPDP patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt3.GPU_SPDP patching file AmberTools/src/configure Reversed (or previously applied) patch detected! Skipping patch. 2 out of 2 hunks ignored -- saving rejects to file AmberTools/src/configure.rej patching file src/pmemd/config_data/linux_em64t_cuda_DPDP.gfortran.mpi patching file src/pmemd/config_data/linux_em64t_cuda_DPDP.gfortran patching file src/pmemd/config_data/linux_em64t_cuda.gfortran.mpi patching file src/pmemd/config_data/linux_em64t_cuda.gfortran patching file src/pmemd/config_data/linux_em64t_cuda_SPDP.gfortran patching file src/pmemd/config_data/linux_em64t_cuda_SPSP.gfortran.mpi patching file src/pmemd/config_data/linux_em64t_cuda_SPSP.gfortran patching file src/pmemd/config_data/linux_p4_cuda_DPDP.gfortran patching file src/pmemd/config_data/linux_p4_cuda.gfortran patching file src/pmemd/config_data/linux_p4_cuda_SPDP.gfortran patching file src/pmemd/config_data/linux_p4_cuda_SPSP.gfortran patching file src/pmemd/src/master_setup.fpp patching file src/pmemd/src/mdin_ctrl_dat.fpp patching file src/pmemd/src/pmemd.fpp patching file src/pmemd/src/runfiles.fpp patching file src/pmemd/src/timers.fpp patching file src/pmemd/src/cuda/cuda_info.fpp patching file src/pmemd/src/cuda/gpu.cpp patching file src/pmemd/src/cuda/gpu.h patching file src/pmemd/src/cuda/gputypes.cpp patching file src/pmemd/src/cuda/gputypes.h patching file src/pmemd/src/cuda/kNeighborList.cu patching file src/pmemd/src/cuda/kPGGW.h patching file src/pmemd/src/cuda/kPGS.h patching file src/pmemd/src/cuda/kPMEInterpolation.cu patching file src/pmemd/src/cuda/Makefile patching file src/pmemd/src/cuda/B40C/radixsort_base.cu patching file src/pmemd/src/cuda/B40C/radixsort_early_exit.cu patching file src/pmemd/src/cuda/B40C/radixsort_multi_cta.cu patching file src/pmemd/src/cuda/B40C/radixsort_single_grid.cu patching file src/pmemd/src/cuda/B40C/README.TXT patching file src/pmemd/src/cuda/B40C/kernel/radixsort_kernel_common.cu patching file src/pmemd/src/cuda/B40C/kernel/radixsort_key_conversion.cu patching file src/pmemd/src/cuda/B40C/kernel/radixsort_reduction_kernel.cu patching file src/pmemd/src/cuda/B40C/kernel/radixsort_scanscatter_kernel.cu patching file src/pmemd/src/cuda/B40C/kernel/radixsort_singlegrid_kernel.cu patching file src/pmemd/src/cuda/B40C/kernel/radixsort_spine_kernel.cu patching file src/pmemd/src/cuda/B40C/KernelCommon/b40c_error_synchronize.cu patching file src/pmemd/src/cuda/B40C/KernelCommon/b40c_kernel_utils.cu patching file src/pmemd/src/cuda/B40C/KernelCommon/b40c_vector_types.cu patching file src/sander/mdread.f patching file src/sander/softcore.f patching file test/softcore/dynlmb/out.0.save patching file src/sander/ew_directe3.h patching file src/sander/ew_directe4.h patching file src/sander/runmin.f Applied patches 1 to 16. Now applying bugfix.17 Applied patch 17. CUDA upgrade complete. Applying patches after 17... patching file src/pmemd/src/extra_pnts_nb14.fpp patching file src/pmemd/src/gb_ene.fpp patching file src/pmemd/src/pairs_calc_novec.i patching file src/pmemd/src/pairs_calc_vec.i patching file src/sander/egb.f patching file src/sander/extra_pts.f patching file src/sander/ifdefs patching file src/sander/nonbond_list.f Hunk #2 succeeded at 1662 with fuzz 1. Hunk #3 succeeded at 1739 (offset -2 lines). patching file src/sander/short_ene.f patching file src/pmemd/src/cuda/gpu.cpp patching file src/pmemd/src/cuda/gputypes.h patching file src/pmemd/src/cuda/kBNL.h patching file src/pmemd/src/cuda/gputypes.h patching file src/pmemd/src/cuda/cuda_info.fpp patching file src/pmemd/src/cuda/gpu.cpp patching file src/pmemd/src/cuda/gputypes.h patching file src/pmemd/src/cuda/kBNL.h patching file src/pmemd/src/cuda/kNeighborList.cu patching file src/pmemd/src/cuda/gpu.cpp patching file src/pmemd/src/cuda/gputypes.cpp patching file src/pmemd/src/cuda/gputypes.h patching file src/pmemd/src/cuda/kCCF.h patching file src/pmemd/src/cuda/kNeighborList.cu patching file src/pmemd/src/cuda/kShake.cu patching file src/pmemd/src/master_setup.fpp patching file src/pmemd/src/runfiles.fpp patching file src/pmemd/src/extra_pnts_nb14.fpp Reversed (or previously applied) patch detected! Skipping patch. 2 out of 2 hunks ignored -- saving rejects to file src/pmemd/src/extra_pnts_nb14.fpp.rej patching file src/pmemd/src/gb_ene.fpp Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/gb_ene.fpp.rej patching file src/pmemd/src/pairs_calc_novec.i Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/pairs_calc_novec.i.rej patching file src/pmemd/src/pairs_calc_vec.i Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/pairs_calc_vec.i.rej patching file src/sander/egb.f Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/sander/egb.f.rej patching file src/sander/extra_pts.f Reversed (or previously applied) patch detected! Skipping patch. 6 out of 6 hunks ignored -- saving rejects to file src/sander/extra_pts.f.rej The next patch would delete the file src/sander/ifdefs, which does not exist! Skipping patch. 1 out of 1 hunk ignored patching file src/sander/nonbond_list.f Reversed (or previously applied) patch detected! Skipping patch. 3 out of 3 hunks ignored -- saving rejects to file src/sander/nonbond_list.f.rej patching file src/sander/short_ene.f Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/sander/short_ene.f.rej patching file src/pmemd/src/cuda/gpu.cpp Hunk #1 FAILED at 442. Hunk #2 FAILED at 3033. Hunk #3 FAILED at 3068. Hunk #4 FAILED at 3859. 4 out of 4 hunks FAILED -- saving rejects to file src/pmemd/src/cuda/gpu.cpp.rej patching file src/pmemd/src/cuda/gputypes.h Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/cuda/gputypes.h.rej patching file src/pmemd/src/cuda/kBNL.h Hunk #1 FAILED at 42. Hunk #2 FAILED at 58. Hunk #3 FAILED at 115. Hunk #4 FAILED at 372. Hunk #5 FAILED at 429. 5 out of 5 hunks FAILED -- saving rejects to file src/pmemd/src/cuda/kBNL.h.rej patching file src/pmemd/src/cuda/gputypes.h Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/cuda/gputypes.h.rej patching file src/pmemd/src/cuda/cuda_info.fpp Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/cuda/cuda_info.fpp.rej patching file src/pmemd/src/cuda/gpu.cpp Hunk #1 FAILED at 441. Hunk #2 FAILED at 2511. Hunk #3 FAILED at 3070. Hunk #4 FAILED at 3765. Hunk #5 FAILED at 3821. Hunk #6 FAILED at 5372. Hunk #7 FAILED at 5618. Hunk #8 FAILED at 6774. 8 out of 8 hunks FAILED -- saving rejects to file src/pmemd/src/cuda/gpu.cpp.rej patching file src/pmemd/src/cuda/gputypes.h Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/cuda/gputypes.h.rej patching file src/pmemd/src/cuda/kBNL.h Reversed (or previously applied) patch detected! Skipping patch. 12 out of 12 hunks ignored -- saving rejects to file src/pmemd/src/cuda/kBNL.h.rej patching file src/pmemd/src/cuda/kNeighborList.cu Reversed (or previously applied) patch detected! Skipping patch. 4 out of 4 hunks ignored -- saving rejects to file src/pmemd/src/cuda/kNeighborList.cu.rej patching file src/pmemd/src/cuda/gpu.cpp Reversed (or previously applied) patch detected! Skipping patch. 18 out of 18 hunks ignored -- saving rejects to file src/pmemd/src/cuda/gpu.cpp.rej patching file src/pmemd/src/cuda/gputypes.cpp Reversed (or previously applied) patch detected! Skipping patch. 5 out of 5 hunks ignored -- saving rejects to file src/pmemd/src/cuda/gputypes.cpp.rej patching file src/pmemd/src/cuda/gputypes.h Reversed (or previously applied) patch detected! Skipping patch. 5 out of 5 hunks ignored -- saving rejects to file src/pmemd/src/cuda/gputypes.h.rej patching file src/pmemd/src/cuda/kCCF.h Reversed (or previously applied) patch detected! Skipping patch. 5 out of 5 hunks ignored -- saving rejects to file src/pmemd/src/cuda/kCCF.h.rej patching file src/pmemd/src/cuda/kNeighborList.cu Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/cuda/kNeighborList.cu.rej patching file src/pmemd/src/cuda/kShake.cu Reversed (or previously applied) patch detected! Skipping patch. 3 out of 3 hunks ignored -- saving rejects to file src/pmemd/src/cuda/kShake.cu.rej patching file src/pmemd/src/master_setup.fpp Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/master_setup.fpp.rej patching file src/pmemd/src/runfiles.fpp Reversed (or previously applied) patch detected! Skipping patch. 1 out of 1 hunk ignored -- saving rejects to file src/pmemd/src/runfiles.fpp.rej patching file src/pmemd/src/master_setup.fpp patching file src/pmemd/src/runfiles.fpp !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! !!! !!! IMPORTANT IMPORTANT IMPORTANT IMPORTANT IMPORTANT !!! !!! !!! !!! BE SURE TO APPLY ALL BUG FIXES FOR AMBERTOOLS 1.5 !!! !!! BEFORE ATTEMPTING TO BUILD PMEMD.CUDA. YOU MUST !!! !!! HAVE AT LEAST UP TO BUGFIX.13 IN ORDER TO BUILD !!! !!! THE UPDATED PMEMD.CUDA SUCCESSFULLY !!! !!! !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!