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-- Jason M. Swails Quantum Theory Project University of Florida Ph.D. Candidate 352-392-4032 On Mar 25, 2013, at 1:43 AM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote: > Dear Dr. Jason and Amber people, > Thanks a lot for helping me figure about that small (silly) directory name > error. After fixing that it seems to have worked fine as shown below and > patch level is also 35 and 14 for AmberTools and Amber respectively now. I > hope whatever files patch_amber.py has moved, is what was expected, please > suggest if you find something wrong there. > > About setting mirrors: As we had discussed earlier > here<http://archive.ambermd.org/201301/0451.html>, > I tried many ways but my proxy settings won't let me go online while using > patch_amber.py and gives error "No internet access!". Thus I have to follow > this path. > > The make install & make test steps gave a few warnings, but have completed > successfully as seen in the bottom of this message. > > Out of curiosity: whenever a new patch becomes available for AmberTools, is > it necessary for us to reconfigure/recompile Amber along with AmberTools > and vise-versa? > Thanks a lot. > > linux-rfml:/usr/local/newamber/amber12 # vim patch_amber.py > linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --update-tree > Determining patches to download for AmberTools12 > Downloading bugfix.14 > Downloading bugfix.15 > Downloading bugfix.16 > Downloading bugfix.17 > Downloading bugfix.18 > Downloading bugfix.19 > Downloading bugfix.20 > Downloading bugfix.21 > Downloading bugfix.22 > Downloading bugfix.23 > Downloading bugfix.24 > Downloading bugfix.25 > Downloading bugfix.26 > Downloading bugfix.27 > Downloading bugfix.28 > Downloading bugfix.29 > Downloading bugfix.30 > Downloading bugfix.31 > Downloading bugfix.32 > Downloading bugfix.33 > Downloading bugfix.34 > Downloading bugfix.35 > > Determining patches to download for Amber12 > Amber12 is up to date. Nothing to download > > Applying AmberTools12 patches > Moving bugfix.14 to AmberTools_Applied_Patches > Moving bugfix.15 to AmberTools_Applied_Patches > Creating file > /usr/local/newamber/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.cpp > Creating file > /usr/local/newamber/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.h > Moving bugfix.16 to AmberTools_Applied_Patches > Moving bugfix.17 to AmberTools_Applied_Patches > Moving bugfix.18 to AmberTools_Applied_Patches > Moving bugfix.19 to AmberTools_Applied_Patches > Moving bugfix.20 to AmberTools_Applied_Patches > Moving bugfix.21 to AmberTools_Applied_Patches > This patch patches patch_amber.py. I will quit after this patch so the rest > may be applied with the updated version. > Moving bugfix.22 to AmberTools_Applied_Patches > linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --update-tree > Determining patches to download for AmberTools12 > Downloading bugfix.23 > Downloading bugfix.24 > Downloading bugfix.25 > Downloading bugfix.26 > Downloading bugfix.27 > Downloading bugfix.28 > Downloading bugfix.29 > Downloading bugfix.30 > Downloading bugfix.31 > Downloading bugfix.32 > Downloading bugfix.33 > Downloading bugfix.34 > Downloading bugfix.35 > > Determining patches to download for Amber12 > Downloading bugfix.9.bz2_ > Decompressing .patches/Amber_Unapplied_Patches/bugfix.9.bz2 with > /usr/bin/bunzip2 > Downloading bugfix.10 > Downloading bugfix.11 > Downloading bugfix.12 > Downloading bugfix.13 > Downloading bugfix.14 > > Applying AmberTools12 patches > Moving bugfix.23 to AmberTools_Applied_Patches > Moving bugfix.24 to AmberTools_Applied_Patches > Moving bugfix.25 to AmberTools_Applied_Patches > Moving bugfix.26 to AmberTools_Applied_Patches > Moving bugfix.27 to AmberTools_Applied_Patches > Moving bugfix.28 to AmberTools_Applied_Patches > Moving bugfix.29 to AmberTools_Applied_Patches > Moving bugfix.30 to AmberTools_Applied_Patches > Moving bugfix.31 to AmberTools_Applied_Patches > Moving bugfix.32 to AmberTools_Applied_Patches > Moving bugfix.33 to AmberTools_Applied_Patches > Moving bugfix.34 to AmberTools_Applied_Patches > Moving bugfix.35 to AmberTools_Applied_Patches > Applying Amber12 patches > Creating file /usr/local/newamber/amber12/src/pmemd/src/cuda/kCNF.h > Changing mode to 644 > Creating file /usr/local/newamber/amber12/src/pmemd/src/cuda/ptxmacros.h > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/Run.pme.amd1 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/Run.pme.amd2 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/Run.pme.amd3 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/dhfr.pdb > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/md12.x > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/amd/dhfr_pme/mdout.pme.amd1.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/amd/dhfr_pme/mdout.pme.amd2.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/amd/dhfr_pme/mdout.pme.amd3.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/prmtop > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/Run.ips.amd1 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/Run.ips.amd2 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/Run.ips.amd3 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/inpcrd > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/amd/gact_ips/mdout.ips.amd1.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/amd/gact_ips/mdout.ips.amd2.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/amd/gact_ips/mdout.ips.amd3.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/prmtop > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/Run.gb.amd1 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/Run.gb.amd2 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/Run.gb.amd3 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/md4.x > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/mdout.gb.amd1.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/mdout.gb.amd2.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/mdout.gb.amd3.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/prmtop > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/rna.pdb > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat/mdout.pure_wat.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat/mdout.vrand.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_npt_ntt1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nve.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt2.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt3.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_npt_ntt1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_nve.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt2.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt3.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/Run.pme.amd1 > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/Run.pme.amd2 > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/Run.pme.amd3 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/dhfr.pdb > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/md12.x > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd1.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd1.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd1.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd2.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd2.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd2.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd2.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd3.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd3.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd3.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd3.GPU_SPFP > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/prmtop > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/Run.ips.amd1 > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/Run.ips.amd2 > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/Run.ips.amd3 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/cuda/amd/gact_ips/inpcrd > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd1.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd1.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd1.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd2.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd2.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd2.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd2.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd3.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd3.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd3.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd3.GPU_SPFP > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/cuda/amd/gact_ips/prmtop > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/cuda/amd/rna_gb/Run.gb.amd1 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/cuda/amd/rna_gb/Run.gb.amd2 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/cuda/amd/rna_gb/Run.gb.amd3 > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/cuda/amd/rna_gb/md4.x > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd1.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd1.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd1.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd2.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd2.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd2.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd2.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd3.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd3.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd3.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd3.GPU_SPFP > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/cuda/amd/rna_gb/prmtop > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/cuda/amd/rna_gb/rna.pdb > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr/mdout.dhfr_charmm_md.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr/mdout.dhfr_charmm_min.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap/mdout.dhfr_charmm_md.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap/mdout.dhfr_charmm_min.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_md.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_md_NPT.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_min.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_noshake_md.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_noshake_min.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr_pbc/mdout.dhfr_charmm_pbc_noshake_md.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/chamber/dhfr_pbc/mdout.dhfr_charmm_pbc_noshake_min.GPU_SPFP > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.min.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.noshake.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntb2.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntb2_ntt1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntb2_ntt1_ntr1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntb2_ntt3.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntr1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/igb1_ntc1_min.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest0_ntt0_igb1_ntc1_coldstart.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest0_ntt0_igb1_ntc1_hotstart.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc1.mdcrd.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc1.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc1.rst.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc2.mdcrd.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc2.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc2.rst.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb2_ntc1.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb2_ntc2.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc1.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2_alpb.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2_ntr1.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2_rgbmax.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2_saltcon.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb7_ntc2.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb8_ntc2.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt1_igb1_ntc2.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt2_igb1_ntc2.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt3_igb1_ntc2.out.GPU_SPFP > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/cuda/ips/mdout.ips.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/ips/mdout.ips_ntt3.GPU_SPFP > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/cuda/jac/jac.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/large_solute_count/mdout.ntb2_ntt1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb7.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/Run.nmropt_1angle_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/angle_gb_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/angle_gb_vs_t.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/angle_gb_vs_t.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/angle_gb_vs_t.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/Run.dist_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/dist_gb_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/dist_gb_vs_t.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/dist_gb_vs_t.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/dist_gb_vs_t.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance_COM/Run.distCOM_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance_COM/distCOM_gb.RST > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance_COM/distCOM_gb_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance_COM/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance/Run.jar_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance/dist_gb.RST > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance/dist_gb_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance_COM/Run.jar_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance_COM/distCOM_gb.RST > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance_COM/distCOM_gb_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance_COM/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_torsion/Run.jar_torsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_torsion/jartorsion_gb.RST > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_torsion/jartorsion_gb.dat.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_torsion/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/myoglobin_gb.inpcrd > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/myoglobin_gb.prmtop > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/Run.nmropt_1_torsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.RST > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/Run.nmropt_1tautp_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/Run.nmropt_1temp_gb > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/Run.nmropt_1angle_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/angle_pbc_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/angle_pbc_vs_t.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/angle_pbc_vs_t.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/angle_pbc_vs_t.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/Run.dist_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/dist_pbc_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/dist_pbc_vs_t.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/dist_pbc_vs_t.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/dist_pbc_vs_t.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/Run.distCOM_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/distCOM_pbc.RST > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/distCOM_pbc_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/Run.jar_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/dist_pbc.RST > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/dist_pbc_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/Run.jar_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/distCOM_pbc.RST > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/distCOM_pbc_vs_t.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/distCOM_pbc_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_torsion/Run.jar_torsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_torsion/jartorsion_pbc.RST > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_torsion/jartorsion_pbc.dat.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_torsion/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/myoglobin_pbc.inpcrd > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/myoglobin_pbc.prmtop > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/Run.nmropt_1_torsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/Run.nmropt_1tautp_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/Run.nmropt_1temp_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/mdout.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/mdout.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/mdout.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/mdout.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/npt_ntr_ntt3_oct/mdout.ntp1.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nucleosome/nucleosome_md1_ntt1.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nucleosome/nucleosome_md2_ntt0.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/nucleosome/nucleosome_min.out.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/tip4pew/mdout.tip4pew_box_npt.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/tip4pew/mdout.tip4pew_box_nvt.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/tip4pew/mdout.tip4pew_oct_npt.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/tip4pew/mdout.tip4pew_oct_nvt.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/tip5p/mdout.tip5p_box_npt.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/tip5p/mdout.tip5p_box_nvt.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/tip5p/mdout.tip5p_oct_npt.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/tip5p/mdout.tip5p_oct_nvt.GPU_SPFP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/trpcage/trpcage_md.out.GPU_SPFP > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/Makefile > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/2xangle/2xangle_gb_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/2xangle/Run.nmropt_1_2xangle_gb > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/2xangle/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/angle/Run.nmropt_1angle_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/angle/angle_gb_vs_t.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/angle/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/distance/Run.dist_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/distance/dist_gb_vs_t.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/distance/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/distance_COM/Run.distCOM_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/distance_COM/distCOM_gb_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/distance_COM/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_comtorsion/Run.jar_comtorsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_comtorsion/jartorsion_com_gb.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_comtorsion/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance/Run.jar_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance/dist_gb_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance_COM/Run.jar_gb > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance_COM/distCOM_gb_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance_COM/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod/Run.lcod_jar > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod/lcod_vs_t.dat.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod_dist/Run.jar_lcod > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod_dist/lcod_vs_t.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod_dist/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_torsion/Run.jar_torsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_torsion/jartorsion_gb.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/jar_torsion/mdout.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/lcod/Run.lcod > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/lcod/lcod_vs_t.dat.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/lcod/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/lcod_com/Run.lcod_com > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/lcod_com/lcod_vs_t.dat.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/lcod_com/mdout.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/myoglobin_gb.inpcrd > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/myoglobin_gb.prmtop > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_2xtorsion/2xtorsion_gb.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_2xtorsion/Run.nmropt_1_2xtorsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_2xtorsion/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_torsion/Run.nmropt_1_torsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_torsion/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/tautp/Run.nmropt_1tautp_gb > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/tautp/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/gb/temp/Run.nmropt_1temp_gb > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/nmropt/gb/temp/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/2xangle/2xangle_pbc_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/2xangle/Run.nmropt_1_2xangle_pbc > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/nmropt/pme/2xangle/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/angle/Run.nmropt_1angle_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/angle/angle_pbc_vs_t.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/pme/angle/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/distance/Run.dist_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/distance/dist_pbc_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/distance/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/distance_COM/Run.distCOM_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/distance_COM/distCOM_pbc_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/distance_COM/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_comtorsion/Run.jar_comtorsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_comtorsion/jartorsion_com_pbc.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_comtorsion/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance/Run.jar_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance/dist_pbc_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance_COM/Run.jar_pbc > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance_COM/distCOM_pbc_vs_t.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance_COM/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod/Run.jar_lcod > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod/lcod_vs_t.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod_dist/Run.lcod_dist > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod_dist/lcod_vs_t.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod_dist/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_torsion/Run.jar_torsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_torsion/jartorsion_pbc.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/jar_torsion/mdout.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/pme/lcod/Run.lcod_pme > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/lcod/lcod_vs_t.dat.save > Changing mode to 644 > Creating file /usr/local/newamber/amber12/test/nmropt/pme/lcod/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/lcod_com/Run.lcod_com > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/lcod_com/lcod_vs_t.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/lcod_com/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/myoglobin_pbc.inpcrd > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/myoglobin_pbc.prmtop > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_2xtorsion/2xtorsion_pbc.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_2xtorsion/Run.nmropt_1_2xtorsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_2xtorsion/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_torsion/Run.nmropt_1_torsion > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_torsion/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/tautp/Run.nmropt_1tautp_pbc > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/nmropt/pme/tautp/mdout.save > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/nmropt/pme/temp/Run.nmropt_1temp_pbc > Changing mode to 755 > Creating file /usr/local/newamber/amber12/test/nmropt/pme/temp/mdout.save > Changing mode to 644 > Moving bugfix.9 to Amber_Applied_Patches > Moving bugfix.10 to Amber_Applied_Patches > Moving bugfix.11 to Amber_Applied_Patches > Moving bugfix.12 to Amber_Applied_Patches > Moving bugfix.13 to Amber_Applied_Patches > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/cta_radix_rank.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/cta_radix_sort.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/downsweep/cta.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/downsweep/kernel.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/downsweep/kernel_policy.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/enactor.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/pass_policy.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/problem_instance.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/single/cta.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/single/kernel.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/single/kernel_policy.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/sort_utils.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/spine/cta.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/spine/kernel.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/spine/kernel_policy.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/tex_ref.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/upsweep/cta.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/upsweep/kernel.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/upsweep/kernel_policy.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/allocator.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/basic_utils.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/cta_work_distribution.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/cuda_properties.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/device_intrinsics.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/error_utils.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/io/load_tile.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/io/modified_load.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/io/modified_store.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/io/store_tile.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/kernel_props.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/multi_buffer.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/ns_umbrella.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/numeric_traits.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/operators.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/raking_grid.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/random_bits.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/reduction/cooperative_reduction.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/reduction/serial_reduce.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/reduction/warp_reduce.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/scan/cooperative_scan.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/scan/serial_scan.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/scan/warp_scan.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/spine.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/spinlock.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/srts_details.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/srts_grid.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/tex_vector.cuh > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/vector_types.cuh > Changing mode to 755 > Creating file /usr/local/newamber/amber12/src/pmemd/src/gbsa.F90 > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/myoglobin/Run_md_myoglobin_igb8_gbsa > Changing mode to 755 > Creating file > /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8_gbsa.out.CPU > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8_gbsa.out.GPU_DPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8_gbsa.out.GPU_SPDP > Changing mode to 644 > Creating file > /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8_gbsa.out.GPU_SPFP > Changing mode to 644 > Moving bugfix.14 to Amber_Applied_Patches > linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --update-tree > Determining patches to download for AmberTools12 > AmberTools12 is up to date. Nothing to download > > Determining patches to download for Amber12 > Amber12 is up to date. Nothing to download > > linux-rfml:/usr/local/newamber/amber12 # ./configure gnu > Checking for updates... > AmberTools12 is up to date > Amber12 is up to date > > Searching for python2... Found python2.7: /usr/bin/python2.7 > > Obtaining the gnu suite version: > gcc -v > The version is 4.6.2 > > Testing the gcc compiler: > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c > OK > > Testing the gfortran compiler: > gfortran -O0 -o testp testp.f > OK > > Testing mixed C/Fortran compilation: > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o > testp.c > gfortran -O0 -c -o testp.f.o testp.f > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o > testp.f.o -lgfortran -w > OK > > Testing pointer size: > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size > test_pointer_size.c > Detected 32 bit operating system. > > Testing flex: OK > > Configuring NetCDF (may be time-consuming)... > > NetCDF configure succeeded. > > Checking for zlib: OK > > Checking for libbz2: OK > > Configuring fftw-3.3 (may be time-consuming)... > > fftw-3.3 configure succeeded. > > Configuring XBLAS (may be time-consuming)... > > XBLAS configure succeeded. > > Configuring MTK++ (may be time-consuming)... > > MTK++-0.2.0 configure succeeded. > > The configuration file, config.h, was successfully created. > > The next step is to type 'make install' > > Cleaning the src directories. This may take a few moments. > Configure complete. > linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --patch-level > Latest patch applied to AmberTools12: 35 > Latest patch applied to Amber12: 14 > > linux-rfml:/usr/local/newamber/amber12 # make install > make[3]: Leaving directory > `/usr/local/newamber/amber12/src/pmemd.amoeba/src' > Installation of pmemd.amoeba complete > make[2]: Leaving directory `/usr/local/newamber/amber12/src/pmemd.amoeba' > > Installation of Amber12 (serial) is complete at Mon Mar 25 15:29:40 IST > 2013. > > make[1]: Leaving directory `/usr/local/newamber/amber12/src' > linux-rfml:/usr/local/newamber/amber12 # make test > ........ > make[2]: Leaving directory `/usr/local/newamber/amber12/test' > 524 file comparisons passed > 36 file comparisons failed > 26 tests experienced errors > Test log file saved as > /usr/local/newamber/amber12/logs/test_amber_serial/2013-03-25_15-59-30.log > Test diffs file saved as > /usr/local/newamber/amber12/logs/test_amber_serial/2013-03-25_15-59-30.diff > make[1]: Leaving directory `/usr/local/newamber/amber12/test' > > Summary of AmberTools serial tests: > > 604 file comparisons passed > 6 file comparisons failed > 0 tests experienced errors > Test log file saved as > /usr/local/newamber/amber12/logs/test_at_serial/2013-03-25_15-32-02.log > Test diffs file saved as > /usr/local/newamber/amber12/logs/test_at_serial/2013-03-25_15-32-02.diff > > > > On Mon, Mar 25, 2013 at 5:49 AM, Jason Swails <jason.swails.gmail.com>wrote: > >> Please disregard my last suggestion. I found your problem. >> >> On Sun, Mar 24, 2013 at 8:17 AM, Vaibhav Dixit <vaibhavadixit.gmail.com >>> wrote: >> >>> >>> linux-rfml:/usr/local/newamber/amber12 # ls >>> ../../bugfixes/AmberTools12/12.0/ >> >> You are storing the bug fixes for AmberTools 12 in >> /usr/local/bugfixes/AmberTools12/12.0/ but you are looking for them in >> /usr/local/bugfixes/AmberTools/12.0/ (notice the extra 12 in the first >> version). Therefore, patch_amber.py finds no patches for AmberTools 12 and >> patches nothing. And bugfixes for Amber 9 and above cannot be >> applied/found until bugfix.22 from AmberTools has been applied. >> >> So change the directory name from AmberTools12 to AmberTools and everything >> should work. >> >> The question remains though, why set up mirrors instead of allowing >> patch_amber.py to download the files directly? >> >> All the best, >> Jason >> >> -- >> 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 > > > > -- > With regards > > Vaibhav A. Dixit > Ph.D. > Department of Medicinal Chemistry > Natl. Inst. Pharm. Edu. & Res. (NIPER) > Sector 67, Phase X, S.A.S. Nagar (Mohali) > Punjab -160 062 INDIA > Phone (Mobile): +919915214408, +91-7709129400. > E-mail: vaibhavadixit.gmail.com > www.niper.nic.in > _______________________________________________ > 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 Mon Mar 25 2013 - 03:30:03 PDT