I am trying to install AmberTools 1.5 + Amber 11 into empty amber11 directory.
The priority of steps is not clear to me.
I assumed that the order is the following:
1) unpack AmberTools 1.5
2) apply bugfixes for AmberTools 1.5
3) compile using gcc and test AmberTools 1.5
4) unpack Amber 11
Should I first apply Amber 11 bugfixes and then run AT15_Amber11.py?
If I try to do that, I get patching errors for the current Amber11 bugfixes.
The errors seem to be for AmberTools/src/configure file.
What is the correct procedure for the fresh installation?
Sincerely,
Richard Owczarzy
Integrated DNA Technologies
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./apply_bugfix.x bugfix.all
Applying all bugfixes in bugfix.all
Patching AMBER installation in /usr/local/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
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patching file src/sander/makedepend
patching file src/sander/Makefile
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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 369.
Hunk #3 FAILED at 495.
Hunk #4 FAILED at 629.
Hunk #5 FAILED at 642.
Hunk #6 FAILED at 654.
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Hunk #9 FAILED at 1055.
Hunk #10 FAILED at 1309.
Hunk #11 FAILED at 1343.
Hunk #12 FAILED at 1497.
Hunk #13 FAILED at 1551.
13 out of 13 hunks FAILED -- saving rejects to file AmberTools/src/configure.rej
patching file benchmarks/jac/bench.jac.cuda
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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
Done
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Received on Thu Jun 23 2011 - 07:30:03 PDT
