Re: [AMBER] AmberTools 1.5 + Amber 11 installation - bugfixes conflicts?

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 23 Jun 2011 14:02:53 -0600

Your ordering is fine. You just have to make sure bugfixes are applied before that package is installed, and that AT15_Amber11.py is run AFTER the bugfixes and configure, but before the amber 11 install process. The errors to configure patching are expected and benign. They happen because configure is part of AmberTools, and the amber11 bugfix.all tries to patch the 1.4 version of configure.

HTH,
Jason 

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Jun 23, 2011, at 8:17 AM, Richard Owczarzy <rowczarzy.idtdna.com> wrote:
> 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
> 
> -------------------------------------------------------------------------------------------------------
> ./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
> 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 369.
> Hunk #3 FAILED at 495.
> Hunk #4 FAILED at 629.
> Hunk #5 FAILED at 642.
> Hunk #6 FAILED at 654.
> Hunk #7 FAILED at 986.
> Hunk #8 FAILED at 1018.
> 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
> 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
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> patching file test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nve.GPU_SPDP
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> 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.CPU
> patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_npt_ntt1.GPU_DPDP
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> patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nve.GPU_DPDP
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> patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nve.GPU_SPSP
> patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt1.CPU
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> patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt2.CPU
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> patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt2.GPU_SPSP
> patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt3.CPU
> 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 test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt3.GPU_SPSP
> patching file test/cuda/4096wat_oct/Run.pure_wat_oct_NPT_NTT1
> patching file test/cuda/4096wat_oct/Run.pure_wat_oct_NVE
> patching file test/cuda/4096wat_oct/Run.pure_wat_oct_NVT_NTT1
> patching file test/cuda/4096wat_oct/Run.pure_wat_oct_NVT_NTT2
> patching file test/cuda/4096wat_oct/Run.pure_wat_oct_NVT_NTT3
> patching file test/cuda/chamber/dhfr/mdout.dhfr_charmm_md.GPU_DPDP
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> patching file test/cuda/chamber/dhfr/mdout.dhfr_charmm_md.GPU_SPSP
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> patching file test/cuda/chamber/dhfr/mdout.dhfr_charmm_min.GPU_SPDP
> patching file test/cuda/chamber/dhfr/mdout.dhfr_charmm_min.GPU_SPSP
> patching file test/cuda/chamber/dhfr/Run.dhfr_charmm.md
> patching file test/cuda/chamber/dhfr/Run.dhfr_charmm.min
> patching file test/cuda/chamber/dhfr_cmap/mdout.dhfr_charmm_md.GPU_DPDP
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> patching file test/cuda/chamber/dhfr_cmap/Run.dhfr_charmm.md
> patching file test/cuda/chamber/dhfr_cmap/Run.dhfr_charmm.min
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> patching file test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_md.GPU_SPDP
> patching file test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_md.GPU_SPSP
> patching file test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_min.GPU_DPDP
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> patching file test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_min.GPU_SPSP
> patching file test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_noshake_md.GPU_DPDP
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> patching file test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_noshake_md.GPU_SPSP
> patching file test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_noshake_min.GPU_SPDP
> patching file test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_noshake_min.GPU_SPSP
> patching file test/cuda/chamber/dhfr_cmap_pbc/Run.dhfr_cmap_pbc_charmm.md
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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.j
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Received on Thu Jun 23 2011 - 13:30:03 PDT
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