I'm attempting to update a new install of Amber18/AmberTools19 under CentOS7.
The configure step fails to apply patch update.8 (and successive patches are skipped).
The package builds and 'make test' succeeds with patches 1-7 applied.
Please see below for details:
---------------------------------------------
[bergman.cubic-login2 18]$ patch -p0 -N --verbose --debug 2 --dry-run < .patches/AmberTools19_Unapplied_Patches/update.8
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|*******> update.8
|
|Author: David Case
|
|Date: August 30, 2019
|
|Programs: sander.MPI
|
|Description: Changes the way that softcore 14 interactions are handled.
| See
http://ambermd.org/SC14_explanation.php
|
|--------------------------------------------------------------------------------
| AmberTools/src/sander/extra_pts.F90 | 8 +-
| test/cnste_remd/Explicit_EREM/Run.Eremd | 2 +-
| test/cnstph_remd/Explicit_pHREM/Run.pHremd | 2 +-
| test/middle-scheme/QMMM_Constr_ALA_Methol/Run.qmmm | 2 +-
| .../QMMM_Constr_ALA_Methol/Run.qmmm.MPI | 2 +-
| test/middle-scheme/QMMM_Constr_ALA_Methol/qmmm.rst | Bin 117616 -> 0 bytes
| test/pmemdTI/softcore/complex/out.save | 355 +-
| test/pmemdTI/softcore/complex/restrt.save | 55220 +++++------
| test/qmmm2/adqmmm_na+28water/Run.adqmmm | 2 +-
| test/softcore/complex/out.0.save | 259 +-
| test/softcore/complex/out.1.save | 257 +-
| test/softcore/complex/restrt.0.save | 55602 +++++------
| test/softcore/complex/restrt.1.save | 55648 +++++------
| test/ti_decomp/ti_sc_decomp_1.out.save | 25226 ++---
| test/ti_decomp/ti_sc_decomp_2.out.save | 278 +-
| 15 files changed, 404289 insertions(+), 98404 deletions(-)
|
|diff --git AmberTools/src/sander/extra_pts.F90 AmberTools/src/sander/extra_pts.F90
|index df46bcf611..eef2bf4894 100644
|--- AmberTools/src/sander/extra_pts.F90
|+++ AmberTools/src/sander/extra_pts.F90
--------------------------
checking file AmberTools/src/sander/extra_pts.F90
Using Plan A...
0 * 1587,9
1 |#ifdef MPI /* SOFT CORE */
2 | ! For dual-topology softcore runs, 1-4 interactions involving sc atoms are modified here
3 | if (ifsc /= 0) then
4 - | ! Check if a softcore atom is involved in this interaction
5 - | if ((nsc(i) == 1 .or. nsc(j) == 1) .and. emil_sc .eq. 0) then
6 - | ! This interactions need to
7 | ! a) get their energies removed from the 1-4 energies
8 | ! b) get their force scaled up by 1/weight
9 | ! This means reversing the work done above, but keeps the code simple
10 = 1587,9
11 |#ifdef MPI /* SOFT CORE */
12 | ! For dual-topology softcore runs, 1-4 interactions involving sc atoms are modified here
13 | if (ifsc /= 0) then
14 + | ! Check if both i and j are softcore atoms
15 + | if ((nsc(i) == 1 .and. nsc(j) == 1) .and. emil_sc .eq. 0) then
16 + | ! These interactions need to
17 | ! a) get their energies removed from the 1-4 energies
18 | ! b) get their force scaled up by 1/weight
19 | ! This means reversing the work done above, but keeps the code simple
20 ^
Hunk #1 succeeded at 1587.
0 * 1614,7
1 | call decpair(2,i,j,scee0*g/(nstlim/ntpr))
2 | call decpair(3,i,j,scnb0*(f12 - f6)/(nstlim/ntpr))
3 | endif
4 - | else if( nsc(i) /= 1 .and. nsc(j) /= 1 ) then
5 | if(decpr .and. idecomp == 1) then
6 | call decpair(4,i,j,scee0*g/(nstlim/ntpr))
7 | call decpair(4,i,j,scnb0*(f12 - f6)/(nstlim/ntpr))
8 = 1614,7
9 | call decpair(2,i,j,scee0*g/(nstlim/ntpr))
10 | call decpair(3,i,j,scnb0*(f12 - f6)/(nstlim/ntpr))
11 | endif
12 + | else if( nsc(i) /= 1 .or. nsc(j) /= 1 ) then
13 | if(decpr .and. idecomp == 1) then
14 | call decpair(4,i,j,scee0*g/(nstlim/ntpr))
15 | call decpair(4,i,j,scnb0*(f12 - f6)/(nstlim/ntpr))
16 ^
Hunk #2 succeeded at 1614.
Hmm... The next patch looks like a unified diff to me...
The text leading up to this was:
--------------------------
|diff --git test/cnste_remd/Explicit_EREM/Run.Eremd test/cnste_remd/Explicit_EREM/Run.Eremd
|index d81c29b2a9..800735ac80 100755
|--- test/cnste_remd/Explicit_EREM/Run.Eremd
|+++ test/cnste_remd/Explicit_EREM/Run.Eremd
--------------------------
checking file test/cnste_remd/Explicit_EREM/Run.Eremd
Using Plan A...
0 * 17,7
1 |
2 |numprocs=`$DO_PARALLEL ../../numprocs`
3 |
4 - |if [ -z `which python` || ! -x `which python` ]; then
5 | python=`which python3`
6 |else
7 | python=`which python`
8 = 17,7
9 |
10 |numprocs=`$DO_PARALLEL ../../numprocs`
11 |
12 + |if [ -z "`which python`" -o ! -x "`which python`" ]; then
13 | python=`which python3`
14 |else
15 | python=`which python`
16 ^
Hunk #1 FAILED at 17.
1 out of 1 hunk FAILED
Hmm... The next patch looks like a unified diff to me...
The text leading up to this was:
--------------------------
|diff --git test/cnstph_remd/Explicit_pHREM/Run.pHremd test/cnstph_remd/Explicit_pHREM/Run.pHremd
|index 3c9b1ed10f..11347bfb41 100755
|--- test/cnstph_remd/Explicit_pHREM/Run.pHremd
|+++ test/cnstph_remd/Explicit_pHREM/Run.pHremd
--------------------------
checking file test/cnstph_remd/Explicit_pHREM/Run.pHremd
Using Plan A...
0 * 17,7
1 |
2 |numprocs=`$DO_PARALLEL ../../numprocs`
3 |
4 - |if [ -z `which python` || ! -x `which python` ]; then
5 | python=`which python3`
6 |else
7 | python=`which python`
8 = 17,7
9 |
10 |numprocs=`$DO_PARALLEL ../../numprocs`
11 |
12 + |if [ -z "`which python`" -o ! -x "`which python`" ]; then
13 | python=`which python3`
14 |else
15 | python=`which python`
16 ^
Hunk #1 FAILED at 17.
1 out of 1 hunk FAILED
Hmm... The next patch looks like a unified diff to me...
The text leading up to this was:
--------------------------
|diff --git test/middle-scheme/QMMM_Constr_ALA_Methol/Run.qmmm test/middle-scheme/QMMM_Constr_ALA_Methol/Run.qmmm
|index 415bd0d4e1..e4dd6166aa 100755
|--- test/middle-scheme/QMMM_Constr_ALA_Methol/Run.qmmm
|+++ test/middle-scheme/QMMM_Constr_ALA_Methol/Run.qmmm
--------------------------
checking file test/middle-scheme/QMMM_Constr_ALA_Methol/Run.qmmm
Using Plan A...
0 * 31,7
1 | -inf qmmm.info \
2 | || goto error
3 | $AMBERHOME/bin/dacdif qmmm.out.save qmmm.out
4 - | rm qmmm.mdcrd qmmm.info
5 |
6 |exit 0
7 |
8 = 31,7
9 | -inf qmmm.info \
10 | || goto error
11 | $AMBERHOME/bin/dacdif qmmm.out.save qmmm.out
12 + | rm qmmm.mdcrd qmmm.info qmmm.rst
13 |
14 |exit 0
15 |
16 ^
Hunk #1 succeeded at 31.
-----------------------------------------------------------------------------
All other hunks in update.8 pass.
Here's info about the file that seems to cause the patch to fail:
bergman.cubic-login2 18]$ md5sum test/cnste_remd/Explicit_EREM/Run.Eremd
b7441d8d3eecec87eaa2a05041e20095 test/cnste_remd/Explicit_EREM/Run.Eremd
[bergman.cubic-login2 18]$ ls -l !$
ls -l test/cnste_remd/Explicit_EREM/Run.Eremd
-rwxr-xr-x. 1 bergman user 1780 Dec 5 2018 test/cnste_remd/Explicit_EREM/Run.Eremd*
--
Mark Bergman voice: 215-746-4061
mark.bergman.pennmedicine.upenn.edu fax: 215-614-0266
http://www.med.upenn.edu/cbica/
IT Technical Director, Center for Biomedical Image Computing and Analytics
Department of Radiology University of Pennsylvania
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Received on Fri Mar 27 2020 - 15:00:02 PDT
