Re: [AMBER] Amber updates brings duplicate patch

From: viktor drobot <linux776.gmail.com>
Date: Thu, 21 Nov 2019 15:03:52 +0300

My patch version is 2.7.6. Re-checked on pure tarball:
[viktor.desolve-lab /tmp]$ md5sum AmberTools19.tar.bz2
afffe8a5473a0bd143b98f0396f52f0f  AmberTools19.tar.bz2

[viktor.desolve-lab /tmp]$ tar -xjf AmberTools19.tar.bz2

[viktor.desolve-lab /tmp]$ cd amber18

[viktor.desolve-lab /tmp/amber18]$ ./update_amber --update
Preparing to apply updates... please wait.
Downloading updates for AmberTools 19
Downloading AmberTools 19/update.1 (4.48 KB)
Applying AmberTools 19/update.1
Downloading AmberTools 19/update.2 (1.24 KB)
Applying AmberTools 19/update.2
Downloading AmberTools 19/update.3 (2.46 KB)
Applying AmberTools 19/update.3
Downloading AmberTools 19/update.4 (28.16 MB)
Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
Done.
Applying AmberTools 19/update.4
Downloading AmberTools 19/update.5 (1.36 KB)
Applying AmberTools 19/update.5
Downloading AmberTools 19/update.6 (16.04 KB)
Applying AmberTools 19/update.6
Downloading AmberTools 19/update.7 (1.05 KB)
Applying AmberTools 19/update.7
Downloading AmberTools 19/update.8 (13.97 MB)
Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
Done.
Applying AmberTools 19/update.8
/tmp/amber18/updateutils/patch.py:313: PatchingWarning: Previously
applied patch detected. Skipping.
   warnings.warn('Previously applied patch detected. Skipping.',
Downloading AmberTools 19/update.9 (319.49 KB)
Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
Done.
Applying AmberTools 19/update.9

NOTE: update_amber only updates the raw source code! You must recompile
if you want
       any changes to take effect!

I also manually downloaded all updates and applied them by hand. Here
are the results (and the cause of the problem):
[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.1
patching file test/Makefile
[viktor.desolve-lab /tmp/amber18]$ echo $?
0

[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.2
patching file AmberTools/src/packmol_memgen/packmol_memgen/main.py
[14:56 viktor.desolve-lab /tmp/amber18]$ echo $?
0

[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.3
patching file AmberTools/src/rism/rism3d.snglpnt.c
patching file AmberTools/src/rism/rism_options.l
[viktor.desolve-lab /tmp/amber18]$ echo $?
0

[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.4
patching file AmberTools/src/rism/amber_rism_interface.F90
patching file AmberTools/src/rism/rism3d.snglpnt.c
patching file AmberTools/src/rism/rism3d_c.F90
patching file AmberTools/src/rism/rism3d_fft.F90
patching file AmberTools/src/rism/rism3d_solvent_c.F90
patching file AmberTools/src/rism/rism_options.l
patching file AmberTools/src/rism/rism_report_c.F90
patching file AmberTools/src/rism/rism_util.F90
patching file AmberTools/src/rism/safemem.F90
patching file AmberTools/src/sff/mm_options.l
patching file AmberTools/src/sff/sff.c
patching file AmberTools/src/sff/sff.h
patching file AmberTools/test/nab/Run.rism_dist
patching file AmberTools/test/nab/checkrism3d
patching file AmberTools/test/nab/chgdist.4.dx.check
patching file AmberTools/test/nab/cuv.H1.4.dx.check
patching file AmberTools/test/nab/cuv.O.4.dx.check
patching file AmberTools/test/nab/cuv_dT.H1.4.dx.check
patching file AmberTools/test/nab/cuv_dT.O.4.dx.check
patching file AmberTools/test/nab/entropy.4.dx.check
patching file AmberTools/test/nab/entropy.H1.4.dx.check
patching file AmberTools/test/nab/entropy.O.4.dx.check
patching file AmberTools/test/nab/entropy.mol.4.dx.check
patching file AmberTools/test/nab/entropyGF.4.dx.check
patching file AmberTools/test/nab/entropyGF.H1.4.dx.check
patching file AmberTools/test/nab/entropyGF.O.4.dx.check
patching file AmberTools/test/nab/entropyPCPLUS.4.dx.check
patching file AmberTools/test/nab/entropyUC.4.dx.check
patching file AmberTools/test/nab/exchem.4.dx.check
patching file AmberTools/test/nab/exchem.H1.4.dx.check
patching file AmberTools/test/nab/exchem.O.4.dx.check
patching file AmberTools/test/nab/exchem.mol.4.dx.check
patching file AmberTools/test/nab/exchemGF.4.dx.check
patching file AmberTools/test/nab/exchemGF.H1.4.dx.check
patching file AmberTools/test/nab/exchemGF.O.4.dx.check
patching file AmberTools/test/nab/exchemPCPLUS.4.dx.check
patching file AmberTools/test/nab/exchemUC.4.dx.check
patching file AmberTools/test/nab/g.xmin.O.0.dx.check
patching file AmberTools/test/nab/guv.2.H1.2.dx.check
patching file AmberTools/test/nab/guv.2.O.1.dx.check
patching file AmberTools/test/nab/guv.2.O.3.dx.check
patching file AmberTools/test/nab/guv.H1.4.dx.check
patching file AmberTools/test/nab/guv.O.4.dx.check
patching file AmberTools/test/nab/guv_dT.H1.4.dx.check
patching file AmberTools/test/nab/guv_dT.O.4.dx.check
patching file AmberTools/test/nab/huv.H1.4.dx.check
patching file AmberTools/test/nab/huv.O.4.dx.check
patching file AmberTools/test/nab/potUV.4.dx.check
patching file AmberTools/test/nab/potUV.H1.4.dx.check
patching file AmberTools/test/nab/potUV.O.4.dx.check
patching file AmberTools/test/nab/potUV.mol.4.dx.check
patching file AmberTools/test/nab/quv.1.xyzv.trunc.check
patching file AmberTools/test/nab/quv.2.xyzv.trunc.check
patching file AmberTools/test/nab/quv.3.xyzv.trunc.check
patching file AmberTools/test/nab/quv.4.dx.check
patching file AmberTools/test/nab/rism3d.selftest.hnc.out.check
patching file AmberTools/test/nab/rism3d.selftest.kh.out.check
patching file AmberTools/test/nab/rism3d.selftest.pse3.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.2.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.list.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.ljfit.boxset.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.ljfit.bufferset.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.ljset.bufferfit.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.ljset.bufferset.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.ljtol.bufferfit.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.nacl.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.nacl.tree.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.np0.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.np1.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.np16.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.np2.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.np32.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.np4.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.np8.out.check
patching file AmberTools/test/nab/rism3d.snglpnt.tree.out.check
patching file AmberTools/test/nab/rismdist.nab
patching file AmberTools/test/nab/rismdist.out.check
patching file AmberTools/test/nab/solvene.4.dx.check
patching file AmberTools/test/nab/solvene.H1.4.dx.check
patching file AmberTools/test/nab/solvene.O.4.dx.check
patching file AmberTools/test/nab/solvene.mol.4.dx.check
patching file AmberTools/test/nab/solveneGF.4.dx.check
patching file AmberTools/test/nab/solveneGF.H1.4.dx.check
patching file AmberTools/test/nab/solveneGF.O.4.dx.check
patching file AmberTools/test/nab/solvenePCPLUS.4.dx.check
patching file AmberTools/test/nab/solveneUC.4.dx.check
patching file test/rism3d/ala/Run.ala.dist
patching file test/rism3d/ala/ala.dist.out.save
patching file test/rism3d/ala/ala.hnc.out.save
patching file test/rism3d/ala/ala.imin5.out.save
patching file test/rism3d/ala/ala.list.out.save
patching file test/rism3d/ala/ala.mdiis0.out.save
patching file test/rism3d/ala/ala.mdiis1.out.save
patching file test/rism3d/ala/ala.min.out.save
patching file test/rism3d/ala/ala.nacl.out.save
patching file test/rism3d/ala/ala.np0.out.save
patching file test/rism3d/ala/ala.np1.out.save
patching file test/rism3d/ala/ala.np2.out.save
patching file test/rism3d/ala/ala.pse1.out.save
patching file test/rism3d/ala/ala.resize.out.save
patching file test/rism3d/ala/ala.tree.out.save
patching file test/rism3d/ala/asympcr.5.dx.save
patching file test/rism3d/ala/chgdist.5.dx.save
patching file test/rism3d/ala/cuv_dT.H1.5.dx.save
patching file test/rism3d/ala/cuv_dT.O.5.dx.save
patching file test/rism3d/ala/entropy.5.dx.save
patching file test/rism3d/ala/entropy.H1.5.dx.save
patching file test/rism3d/ala/entropy.O.5.dx.save
patching file test/rism3d/ala/entropy.mol.5.dx.save
patching file test/rism3d/ala/entropyGF.5.dx.save
patching file test/rism3d/ala/entropyGF.H1.5.dx.save
patching file test/rism3d/ala/entropyGF.O.5.dx.save
patching file test/rism3d/ala/exchem.5.dx.save
patching file test/rism3d/ala/exchem.H1.5.dx.save
patching file test/rism3d/ala/exchem.O.5.dx.save
patching file test/rism3d/ala/exchem.mol.5.dx.save
patching file test/rism3d/ala/exchemGF.5.dx.save
patching file test/rism3d/ala/exchemGF.H1.5.dx.save
patching file test/rism3d/ala/exchemGF.O.5.dx.save
patching file test/rism3d/ala/guv.O.5.dx.save
patching file test/rism3d/ala/guv_dT.H1.5.dx.save
patching file test/rism3d/ala/guv_dT.O.5.dx.save
patching file test/rism3d/ala/huv.H1.5.dx.save
patching file test/rism3d/ala/potUV.5.dx.save
patching file test/rism3d/ala/potUV.H1.5.dx.save
patching file test/rism3d/ala/potUV.O.5.dx.save
patching file test/rism3d/ala/potUV.mol.5.dx.save
patching file test/rism3d/ala/quv.5.dx.save
patching file test/rism3d/ala/quv.5.xyzv.trunc.save
patching file test/rism3d/ala/solvene.5.dx.save
patching file test/rism3d/ala/solvene.H1.5.dx.save
patching file test/rism3d/ala/solvene.O.5.dx.save
patching file test/rism3d/ala/solvene.mol.5.dx.save
patching file test/rism3d/ala/solveneGF.5.dx.save
patching file test/rism3d/ala/solveneGF.H1.5.dx.save
patching file test/rism3d/ala/solveneGF.O.5.dx.save
patching file test/rism3d/ala/uuv.H1.5.dx.save
patching file test/rism3d/ala/uuv.O.5.dx.save
patching file test/rism3d/phosphate/ph1-nacl.out.save
patching file test/rism3d/phosphate/ph1-nacl.pse1.out.save
patching file test/rism3d/phosphate/ph1-nacl.pse3.out.save
patching file test/rism3d/phosphate/ph1.out.save
patching file test/rism3d/phosphate/ph1.pse1.out.save
patching file test/rism3d/phosphate/ph1.pse3.out.save
patching file test/rism3d/phosphate/ph10-nacl.out.save
patching file test/rism3d/phosphate/ph10.out.save
patching file test/rism3d/phosphate/ph2.out.save
patching file test/rism3d/phosphate/ph20.out.save
patching file test/sander_rism3d_asfe_oin/ala.out.save
[viktor.desolve-lab /tmp/amber18]$ echo $?
0

[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.5
patching file AmberTools/src/configure_python
patching file cmake/PythonInterpreterConfig.cmake
[viktor.desolve-lab /tmp/amber18]$ echo $?
0

[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.6
patching file
AmberTools/src/packmol_memgen/packmol_memgen/lib/pdbremix/data.py
patching file AmberTools/test/packmol_memgen/Run.packmol-memgen
patching file test/cnste_remd/EREM/Run.Eremd
patching file test/cnste_remd/EREMrst/Run.Eremdrst
patching file test/cnste_remd/Explicit_EREM/Run.Eremd
patching file test/cnstph_remd/Explicit_pHREM/Run.pHremd
patching file test/cnstph_remd/pHREM/Run.pHremd
patching file test/cnstph_remd/pHREMrst/Run.pHremdrst
patching file test/nfe/common.sh
patching file test/test_amber_cuda_serial.sh
[viktor.desolve-lab /tmp/amber18]$ echo $?
0

[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.7
patching file AmberTools/src/rism/rism_options.l
[viktor.desolve-lab /tmp/amber18]$ echo $?
0

[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.8
patching file AmberTools/src/sander/extra_pts.F90
patching file test/cnste_remd/Explicit_EREM/Run.Eremd
patching file test/cnstph_remd/Explicit_pHREM/Run.pHremd
patching file test/middle-scheme/QMMM_Constr_ALA_Methol/Run.qmmm
patching file test/middle-scheme/QMMM_Constr_ALA_Methol/Run.qmmm.MPI
patching file test/middle-scheme/QMMM_Constr_ALA_Methol/qmmm.rst
*Not deleting file test/middle-scheme/QMMM_Constr_ALA_Methol/qmmm.rst as
content differs from patch*
patching file test/pmemdTI/softcore/complex/out.save
patching file test/pmemdTI/softcore/complex/restrt.save
patching file test/qmmm2/adqmmm_na+28water/Run.adqmmm
patching file test/softcore/complex/out.0.save
patching file test/softcore/complex/out.1.save
patching file test/softcore/complex/restrt.0.save
patching file test/softcore/complex/restrt.1.save
patching file test/ti_decomp/ti_sc_decomp_1.out.save
patching file test/ti_decomp/ti_sc_decomp_2.out.save
[viktor.desolve-lab /tmp/amber18]$ echo $?
*1*

[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.9
patching file dat/leap/cmd/leaprc.protein.ff19SB
patching file dat/leap/lib/amino19.lib
patching file dat/leap/parm/frcmod.ff19SB
patching file dat/leap/parm/frcmod.ff19SB_XXX
patching file dat/leap/parm/parm19.dat
patching file test/Makefile
patching file test/ff19SB/Run.pmemd (renamed from test/ff18SB/Run.ff18SB)
patching file test/ff19SB/Run.sander
patching file test/ff19SB/inpcrd (renamed from test/ff18SB/inpcrd)
patching file test/ff19SB/mdout.save.pmemd (renamed from
test/ff18SB/mdout.ff18SB.save)
patching file test/ff19SB/mdout.save.sander
patching file test/ff19SB/prmtop (renamed from test/ff18SB/prmtop)
[14:57 viktor.desolve-lab /tmp/amber18]$ echo $?
0

It complains about differences in
*test/middle-scheme/QMMM_Constr_ALA_Methol/qmmm.rst* and patch so
returns code 1 and Python script thinks that there was a problem. Seems
like that file should be deleted but patch is not applying clearly...

-------- Original message --------
> On Wed, Nov 20, 2019, viktor drobot wrote:
>
>> Yes, it's pure tarball downloaded from ambermd.org
> Does the system always complain about the same update?
>
> The update_amber script is just running "patch", so you can download
> update.8 from the web site, and try applying it "by hand" to your final source
> code. The script uses "patch -p0 -N -s < update.8". Try leaving out
> the "-N" when you do this by hand, which should give extra info.
>
> I'm using patch version 2.5.8. I suppose it's possible that there could
> be differences with different versions....but seems unlikely for a
> program that dates to 1988 and is universally used throughout the
> internet.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Nov 21 2019 - 04:30:02 PST
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