Make sure that you really have compiled "everything" and that you are
actually using the new executable.
To that end, have a look in your build tree's bin directory (e.g.
/path/to/amber12/bin) and check the file creation times. If the creation
time of cpptraj corresponds to the compilation time, you can be sure
that it has been rebuilt.
Then, make sure that the environment variable AMBERHOME corresponds to
your new build tree:
export AMBERHOME=/path/to/amber12
Then, prepend ${AMBERHOME}/bin to your PATH:
export PATH=${AMBERHOME}/bin\:${PATH}
Verify that the freshly built executables are in your PATH. Regarding
cpptraj, you could check once again:
$ ls -ahl $(command -v cpptraj)
2.7M -rwxr-x--- 1 user group 2.7M Mar 11 11:57 /path/to/amber12/bin/cpptraj*
HTH,
Jan-Philip
On 03/25/2013 11:17 AM, Vaibhav Dixit wrote:
> I have recompiled everything, but why the cpptraj version is not the latest?
> Will it affect the analysis I am going to perform (combining trajectories,
> clustering, H-bond, SASA and some other analysis)?
> Thank you.
>
> On Mon, Mar 25, 2013 at 3:33 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> Yes, you need to recompile everything.
>>
>> --
>> 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/amber
>>
>
>
>
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Received on Mon Mar 25 2013 - 04:00:02 PDT
