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update plumed support to include version 2.6.0. Fix bug in API check

This commit is contained in:
Axel Kohlmeyer 2020-02-13 15:57:26 +01:00
parent 5d467bcc74
commit 4cacc4701d
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GPG Key ID: D9B44E93BF0C375A
7 changed files with 64 additions and 53 deletions
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4
cmake/Modules/Packages/USER-PLUMED.cmake
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@ -49,8 +49,8 @@ if(PKG_USER-PLUMED)
message(STATUS "PLUMED download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz
URL_MD5 de30d6e7c2dcc0973298e24a6da24286
URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
URL_MD5 204d2edae58d9b10ba3ad460cad64191
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}

3
doc/src/Build_extras.rst
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@ -880,6 +880,9 @@ USER-PLUMED package
Before building LAMMPS with this package, you must first build PLUMED.
PLUMED can be built as part of the LAMMPS build or installed separately
from LAMMPS using the generic `plumed installation instructions <plumedinstall_>`_.
The USER-PLUMED package has been tested to work with Plumed versions
2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
with a different version of the Plumed kernel.
PLUMED can be linked into MD codes in three different modes: static,

34
examples/USER/plumed/log.27Nov18.peptide-plumed.g++.1 → examples/USER/plumed/log.4Feb20.peptide-plumed.g++.1
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@ -1,5 +1,4 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
LAMMPS (4 Feb 2020)
# Solvated 5-mer peptide
units real
@ -39,6 +38,8 @@ read_data data.peptide
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.000809431 secs
read_data CPU = 0.0102327 secs
neighbor 2.0 bin
neigh_modify delay 5
@ -66,6 +67,7 @@ fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000631809 secs
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
@ -77,13 +79,13 @@ variable pe equal pe
run 101
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
using double precision FFTW3
3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
@ -106,7 +108,7 @@ SHAKE stats (type/ave/delta) on step 0
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 18.74 | 18.74 | 18.74 Mbytes
Per MPI rank memory allocation (min/avg/max) = 19.07 | 19.07 | 19.07 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
@ -129,22 +131,22 @@ SHAKE stats (type/ave/delta) on step 100
31 104.52 0.000760401
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
Loop time of 2.73445 on 1 procs for 101 steps with 2004 atoms
Loop time of 2.69839 on 1 procs for 101 steps with 2004 atoms
Performance: 6.383 ns/day, 3.760 hours/ns, 36.936 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 6.468 ns/day, 3.711 hours/ns, 37.430 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2617 | 2.2617 | 2.2617 | 0.0 | 82.71
Bond | 0.0044148 | 0.0044148 | 0.0044148 | 0.0 | 0.16
Kspace | 0.17883 | 0.17883 | 0.17883 | 0.0 | 6.54
Neigh | 0.23945 | 0.23945 | 0.23945 | 0.0 | 8.76
Comm | 0.011672 | 0.011672 | 0.011672 | 0.0 | 0.43
Output | 0.00028348 | 0.00028348 | 0.00028348 | 0.0 | 0.01
Modify | 0.0365 | 0.0365 | 0.0365 | 0.0 | 1.33
Other | | 0.001611 | | | 0.06
Pair | 2.2853 | 2.2853 | 2.2853 | 0.0 | 84.69
Bond | 0.0065637 | 0.0065637 | 0.0065637 | 0.0 | 0.24
Kspace | 0.14949 | 0.14949 | 0.14949 | 0.0 | 5.54
Neigh | 0.1938 | 0.1938 | 0.1938 | 0.0 | 7.18
Comm | 0.0096588 | 0.0096588 | 0.0096588 | 0.0 | 0.36
Output | 0.00039172 | 0.00039172 | 0.00039172 | 0.0 | 0.01
Modify | 0.050643 | 0.050643 | 0.050643 | 0.0 | 1.88
Other | | 0.00258 | | | 0.10
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0

34
examples/USER/plumed/log.27Nov18.peptide-plumed.g++.4 → examples/USER/plumed/log.4Feb20.peptide-plumed.g++.4
View File

@ -1,5 +1,4 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
LAMMPS (4 Feb 2020)
# Solvated 5-mer peptide
units real
@ -39,6 +38,8 @@ read_data data.peptide
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.00095129 secs
read_data CPU = 0.0199838 secs
neighbor 2.0 bin
neigh_modify delay 5
@ -66,6 +67,7 @@ fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000829935 secs
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
@ -77,13 +79,13 @@ variable pe equal pe
run 101
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
using double precision FFTW3
3d grid and FFT values/proc = 4312 960
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
@ -106,7 +108,7 @@ SHAKE stats (type/ave/delta) on step 0
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.87 | 16.06 Mbytes
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.23 | 16.42 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
@ -129,22 +131,22 @@ SHAKE stats (type/ave/delta) on step 100
31 104.52 0.000760401
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
Loop time of 0.812799 on 4 procs for 101 steps with 2004 atoms
Loop time of 0.873215 on 4 procs for 101 steps with 2004 atoms
Performance: 21.472 ns/day, 1.118 hours/ns, 124.262 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 19.987 ns/day, 1.201 hours/ns, 115.664 timesteps/s
92.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.57957 | 0.59988 | 0.62504 | 2.6 | 73.80
Bond | 0.00080013 | 0.0017412 | 0.0028315 | 2.1 | 0.21
Kspace | 0.075724 | 0.10008 | 0.12023 | 6.4 | 12.31
Neigh | 0.067733 | 0.067947 | 0.068168 | 0.1 | 8.36
Comm | 0.01375 | 0.014175 | 0.014681 | 0.3 | 1.74
Output | 0.00025511 | 0.00051183 | 0.001277 | 0.0 | 0.06
Modify | 0.026406 | 0.026436 | 0.026462 | 0.0 | 3.25
Other | | 0.002027 | | | 0.25
Pair | 0.58191 | 0.61681 | 0.66371 | 3.8 | 70.64
Bond | 0.00099587 | 0.0023546 | 0.0041356 | 2.8 | 0.27
Kspace | 0.096162 | 0.14486 | 0.18119 | 8.1 | 16.59
Neigh | 0.059843 | 0.059864 | 0.059876 | 0.0 | 6.86
Comm | 0.013623 | 0.01368 | 0.013723 | 0.0 | 1.57
Output | 0.00031137 | 0.0010193 | 0.0024326 | 2.6 | 0.12
Modify | 0.031552 | 0.031697 | 0.032087 | 0.1 | 3.63
Other | | 0.002938 | | | 0.34
Nlocal: 501 ave 512 max 492 min
Histogram: 1 0 0 1 0 1 0 0 0 1

33
examples/USER/plumed/reference/p.log
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@ -1,12 +1,12 @@
PLUMED: PLUMED is starting
PLUMED: Version: 2.4.2 (git: Unknown) compiled on Jul 11 2018 at 19:09:03
PLUMED: Please cite this paper when using PLUMED [1]
PLUMED: Version: 2.6.0 (git: Unknown) compiled on Feb 13 2020 at 15:49:44
PLUMED: Please cite these papers when using PLUMED [1][2]
PLUMED: For further information see the PLUMED web page at http://www.plumed.org
PLUMED: Root: /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2/
PLUMED: For installed feature, see /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2//src/config/config.txt
PLUMED: Root: /home/akohlmey/compile/lammps/build-gcc/plumed_build-prefix/lib/plumed
PLUMED: For installed feature, see /home/akohlmey/compile/lammps/build-gcc/plumed_build-prefix/lib/plumed/src/config/config.txt
PLUMED: Molecular dynamics engine: LAMMPS
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Running over 4 nodes
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 2004
@ -14,13 +14,13 @@ PLUMED: File suffix:
PLUMED: FILE: plumed.dat
PLUMED: Action UNITS
PLUMED: with label @0
PLUMED: length: A
PLUMED: energy: kcal/mol
PLUMED: length: A = 0.1 nm
PLUMED: energy: kcal/mol = 4.184 kj/mol
PLUMED: time: ps
PLUMED: charge: e
PLUMED: mass: amu
PLUMED: using physical units
PLUMED: inside PLUMED, Boltzmann constant is 0.001987
PLUMED: inside PLUMED, Boltzmann constant is 0.0019872
PLUMED: Action DISTANCE
PLUMED: with label dd
PLUMED: between atoms 45 48
@ -44,14 +44,15 @@ PLUMED: Timestep: 0.002000
PLUMED: KbT has not been set by the MD engine
PLUMED: It should be set by hand where needed
PLUMED: Relevant bibliography:
PLUMED: [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
PLUMED: [1] The PLUMED consortium, Nat. Methods 16, 670 (2019)
PLUMED: [2] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
PLUMED: Cycles Total Average Minumum Maximum
PLUMED: 1 0.020354 0.020354 0.020354 0.020354
PLUMED: 1 Prepare dependencies 102 0.000256 0.000003 0.000001 0.000006
PLUMED: 2 Sharing data 102 0.010002 0.000098 0.000078 0.000546
PLUMED: 3 Waiting for data 102 0.001398 0.000014 0.000011 0.000072
PLUMED: 4 Calculating (forward loop) 102 0.001797 0.000018 0.000013 0.000058
PLUMED: 5 Applying (backward loop) 102 0.002666 0.000026 0.000022 0.000062
PLUMED: 6 Update 102 0.001126 0.000011 0.000007 0.000055
PLUMED: 1 0.010018 0.010018 0.010018 0.010018
PLUMED: 1 Prepare dependencies 102 0.000241 0.000002 0.000001 0.000003
PLUMED: 2 Sharing data 102 0.002132 0.000021 0.000006 0.000151
PLUMED: 3 Waiting for data 102 0.001640 0.000016 0.000008 0.000067
PLUMED: 4 Calculating (forward loop) 102 0.000825 0.000008 0.000005 0.000013
PLUMED: 5 Applying (backward loop) 102 0.000522 0.000005 0.000002 0.000015
PLUMED: 6 Update 102 0.001755 0.000017 0.000011 0.000067

4
lib/plumed/Install.py
View File

@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py',
# settings
version = "2.5.3"
version = "2.6.0"
mode = "static"
# help message
@ -46,6 +46,8 @@ checksums = { \
'2.5.1' : 'c2a7b519e32197a120cdf47e0f194f81', \
'2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \
'2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \
'2.5.4' : 'f31b7d16a4be2e30aa7d5c19c3d37853', \
'2.6.0' : '204d2edae58d9b10ba3ad460cad64191', \
}
# parse and process arguments

5
src/USER-PLUMED/fix_plumed.cpp
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@ -78,8 +78,9 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
int api_version;
p->cmd("getApiVersion",&api_version);
if (api_version > 6)
error->all(FLERR,"Incompatible API version for PLUMED in fix plumed");
if ((api_version < 5) || (api_version > 7))
error->all(FLERR,"Incompatible API version for PLUMED in fix plumed. "
"Only Plumed 2.4.x, 2.5.x, and 2.6.x are tested and supported.");
// If the -partition option is activated then enable
// inter-partition communication