Re: [AMBER] patching unsuccessful even after modifying patch_amber.py

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Mon, 25 Mar 2013 11:34:02 +0530

Dear Dr. Jason, Dr. Daniel Roe and Amber people,
Even after patching AmberTools12 and Amber12 as shown in the email below,
the cpptraj is showing V12.1 and not V12.5 as Daniel had mentioned
here<http://archive.ambermd.org/201303/0397.html>.
Can you please help me troubleshoot as to why cpptraj is not the expected
version? Is there any newer tar file for AmberTools12 now?
Thank you.

linux-rfml:/usr/local/newamber/amber12 # cpptraj

CPPTRAJ: Trajectory Analysis. V12.1
    ___ ___ ___ ___
     | \/ | \/ | \/ |
    _|_/\_|_/\_|_/\_|_

INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> quit

linux-rfml:/usr/local/newamber/amber12 #


On Mon, Mar 25, 2013 at 11:13 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
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
> Creating file
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance_COM/mdout.CPU
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> Changing mode to 644
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> Changing mode to 755
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 755
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 755
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/Run.nmropt_1angle_pbc
> Changing mode to 755
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/dist_pbc_vs_t.CPU
> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/mdout.GPU_DPDP
> Changing mode to 644
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> Changing mode to 644
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> Changing mode to 644
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> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/Run.distCOM_pbc
> Changing mode to 755
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> Changing mode to 644
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> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/distCOM_pbc_vs_t.CPU
> Changing mode to 644
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> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/Run.jar_pbc
> Changing mode to 755
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> /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
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> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/mdout.CPU
> Changing mode to 644
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> /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
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> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/distCOM_pbc_vs_t.CPU
> Changing mode to 644
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> /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
>

-- 
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
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Received on Sun Mar 24 2013 - 23:30:03 PDT