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Merge branch release-2019 into release-2020
2019-11-29
Mark
A
b
r
aham
Merg
e
branch releas
e
-2019 into
r
el
e
ase-20
2
0
commit
|
commitdiff
|
tree
2019-11-29
Art
e
m Zhmurov
Rename
s
ome variables
i
n G
P
U Update
commit
|
commitdiff
|
tree
2019-11-28
Paul Bauer
Check for usi
n
g correct hwloc headers a
n
d runtime
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Clea
r
dev
i
c
e force
b
uffe
r
i
f
it
was reallocated
commit
|
commitdiff
|
tree
2019-11-27
Artem Zh
m
urov
Add method for coordina
t
es s
c
aling into GPU updat
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric I
r
r
g
ang
Add gm
x
api_extension tests
to 'tests'
t
arget
.
commit
|
commitdiff
|
tree
2019-11-27
Alan Gray
Ev
e
nt
-
bas
e
d Dependen
c
y f
o
r GP
U
For
c
e H
a
lo E
x
change
commit
|
commitdiff
|
tree
2019-11-26
Mark Abraha
m
Imp
r
ove
handling of task-assi
g
nment
exce
p
tio
n
s
commit
|
commitdiff
|
tree
2019-11-25
Al
a
n
Gray
Fix race cond
i
t
ion in
GPU X halo excha
n
g
e
w
ith GPU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
Chri
s
ti
a
n Blau
InMemorySerializer w
i
t
h
en
d
ian
e
ss swap
.
commit
|
commitdiff
|
tree
2019-11-21
Mark Ab
r
aham
New c
o
ol q
u
ote
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
Ad
d
D2
H
copie
s
for the chec
k
pointing
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
M
o
ve the c
o
py of the
velo
c
ities for
t
h
e
outpu
t
closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
B
e
r
k Hess
Quiet pdb2gmx and use gmx_fata
l
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric Irrg
a
ng
R
e
move
stub content from gmxa
p
i
d
ocs
.
commit
|
commitdiff
|
tree
2019-11-16
Mar
k
Abraham
Relaxed list
e
d
forces test tolerances
commit
|
commitdiff
|
tree
2019-11-06
Berk Hess
Deprecated sc-r
-
power=48
commit
|
commitdiff
|
tree
2019-11-04
Paul Bauer
Add build for
c
l
a
ng-for
m
at
commit
|
commitdiff
|
tree
2019-11-04
Paul
Bauer
Split up sourc
e
code f
o
rmatting scri
p
t
s
commit
|
commitdiff
|
tree
2019-11-04
T
e
emu Murt
o
la
Upda
t
e cl
a
ng-
f
o
r
mat config
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
I
m
prove unif
o
rmity
of OS
X
C
Make con
f
iguration
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
R
estore
C
M
a
k
e
c
o
nvenience t
a
rgets
f
o
r
samp
l
e_restr
a
int
.
commit
|
commitdiff
|
tree
2019-10-31
Al
a
n Gray
Remove dead code
for nbnxm H2D coordinat
e
copy eve
n
t
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
Bug fix
for
event p
a
ssed
t
o GP
U
co
m
m
featu
r
e
s
commit
|
commitdiff
|
tree
2019-10-31
Pa
s
c
a
l Merz
C
hec
k
for contradic
t
ing enviro
n
ment
v
aria
b
l
es (modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
M
ark Abraham
Tests for
valid p
e
riod
i
c
actions
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
Disable
its t
e
st
s
when sample_restraint is not the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Er
i
c Irrga
n
g
Decreas
e
the ma
x
imum
allowed Py
t
hon
v
e
rsio
n
for gmxapi
.
commit
|
commitdiff
|
tree
2019-10-29
Arte
m
Zhmurov
Disable GPU update when c
o
o
rdinates swapping is en
a
bled
commit
|
commitdiff
|
tree
2019-10-24
B
e
rk Hess
Add bool
useDom
a
inDecomposition in mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Ad
d
g
m
x_mtop_intera
c
ti
o
n_count()
commit
|
commitdiff
|
tree
2019-10-23
e
j
jor
d
an
Ma
k
e t
_
ne
x
t
n
b
an
implementation det
a
i
l
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Correct for skewed box be
f
ore do
m
ain decomposition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
A
l
an Gray
Enable GPU Peer
Acce
s
s in GPU Utilities
commit
|
commitdiff
|
tree
2019-10-22
ejjorda
n
Remove unused functio
n
s from gmxprep
r
ocess
commit
|
commitdiff
|
tree
2019-10-22
Berk He
s
s
Require -ei for essentia
l
dynamics
commit
|
commitdiff
|
tree
2019-10-22
ejjordan
Remove unu
s
ed function generate_excls and make
c
l
e
a
n
_excls
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Berk H
e
ss
Co
n
st correctness for ge
n
hydr
o
commit
|
commitdiff
|
tree
2019-10-15
Paul Bauer
Fix bug in preproces
s
ing
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eric Irrgang
Fix logic err
o
r in gm
x
api
.
v
ersi
o
n
.
api_is_at_lea
s
t
(
)
.
commit
|
commitdiff
|
tree
2019-10-13
Mark Abraham
Ensu
r
e environ
m
en
t
v
a
riabl
e
use do
e
s not
give warnings
commit
|
commitdiff
|
tree
2019-10-12
Berk
H
es
s
Add class FixedCapacityVector
commit
|
commitdiff
|
tree
2019-10-12
A
rtem
Z
hm
u
rov
Centr
a
l
i
ze management of coordinat
e
s
r
ead
y
on GPU event
commit
|
commitdiff
|
tree
2019-10-08
Prashan
t
h Kan
d
u
ri
F
u
se
d
two if br
a
nc
h
es with the s
a
me
c
ond
i
tion
a
l
commit
|
commitdiff
|
tree
2019-10-02
Carsten
K
utzner
Update the www li
n
k to t
h
e Dox
y
gen d
o
cu
m
entation in
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
Berk Hess
F
i
x
harml
e
s
s
O
p
enMP
w
r
i
te race
commit
|
commitdiff
|
tree
2019-10-02
Mark A
b
raha
m
I
m
prove
PME testin
g
commit
|
commitdiff
|
tree
2019-10-01
Berk
H
e
s
s
Use gmx::Range in domdec
commit
|
commitdiff
|
tree
2019-10-01
A
rtem Zhmurov
St
a
t
ePropagat
o
rDataGp
u
o
b
j
e
ct to manage GP
U
forc
e
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
M
a
r
k Abraham
Fix icc warnings
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Completely r
e
move charge group
s
commit
|
commitdiff
|
tree
2019-10-01
Paul
Bauer
Fix chain ID ha
n
dlin
g
in make_ndx
commit
|
commitdiff
|
tree
2019-10-01
Christoph
J
unghans
cmake:
a
d
d
m
issing header to
le
g
acy api
commit
|
commitdiff
|
tree
2019-10-01
Mark
A
brah
a
m
Removed depend
e
nc
y
on commrec of mdrun setup
commit
|
commitdiff
|
tree
2019-09-30
C
arsten
K
utzner
Mo
v
e ForceProv
i
ders cl
a
ss
i
nto t
h
e
gmx namespac
e
commit
|
commitdiff
|
tree
2019-09-30
Mark Abraham
M
a
ke a builder for DD
commit
|
commitdiff
|
tree
2019-09-30
B
e
rk Hess
R
emove charge group code fro
m
for
c
erec
commit
|
commitdiff
|
tree
2019-09-30
Szilárd
Páll
Make the wait on PME GPU results condit
i
onal
commit
|
commitdiff
|
tree
2019-09-27
Mark
Abraham
Improve MiMiC te
s
t
i
m
plementation
commit
|
commitdiff
|
tree
2019-09-27
M
ark Abrah
a
m
Fix
gro file output wit
h
in
d
ex g
r
oups
commit
|
commitdiff
|
tree
2019-09-27
Mark
Ab
r
aha
m
Fix gro file output with index groups
commit
|
commitdiff
|
tree
2019-09-27
Mark Abr
a
ham
Remove left
o
ver support for pre-9
.
0 CUD
A
commit
|
commitdiff
|
tree
2019-09-24
Paul
Bauer
A
d
d te
s
t for
n
oappend
commit
|
commitdiff
|
tree
2019-09-24
Mark
A
braham
Fi
x
no-MP
I
CUDA
b
uild
commit
|
commitdiff
|
tree
2019-09-24
Mark Abr
a
ham
Merge "
M
e
r
ge
br
a
nch release-
2
0
1
9 into master"
commit
|
commitdiff
|
tree
2019-09-24
M
ark Ab
r
aham
Fix clang unused-f
u
nc
t
ion warnings
commit
|
commitdiff
|
tree
2019-09-24
Paul Bauer
Add relea
s
e notes for
m
odular si
m
ulator
commit
|
commitdiff
|
tree
2019-09-23
Paul Baue
r
Fix issues when
P
ME rank reque
s
t be
c
omes negat
i
ve
commit
|
commitdiff
|
tree
2019-09-23
P
a
ul Bauer
Change MPI
s
etup to co
m
m
u
nicate TPR a
s
b
u
ffer
commit
|
commitdiff
|
tree
2019-09-23
Pasca
l
Merz
Zero
p
ressure and vir
i
a
l tensors at
b
eginni
n
g of step
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Intr
o
duce FEP into modular s
i
mulator
commit
|
commitdiff
|
tree
2019-09-22
Chri
s
top
h
Jungha
n
s
w
o
rkarou
n
d for rhe
l
b
u
g
#
1749463, cmake bug #1834
9
commit
|
commitdiff
|
tree
2019-09-22
P
a
u
l Bauer
R
e
m
ove upda
t
e f
l
a
g again
commit
|
commitdiff
|
tree
2019-09-22
Berk He
s
s
Remove c
g
s
_gl from g
m
x_
d
omdec_co
m
m_t
commit
|
commitdiff
|
tree
2019-09-20
Mark Abraha
m
Refactor to create
a GpuTaskAs
s
ignme
n
t
s object
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove bLocal
C
G f
r
om DD co
d
e
commit
|
commitdiff
|
tree
2019-09-19
B
erk
Hess
Remove obsole
t
e make_exclusions_zone_
c
g()
commit
|
commitdiff
|
tree
2019-09-19
Chri
s
ti
a
n Blau
Check input r
e
cord
a
l
so
i
n
tests
commit
|
commitdiff
|
tree
2019-09-19
Ma
r
k Abraham
U
s
e GPU halo exchange o
n
ly w
h
en
c
ompatible DD is a
v
ailabl
e
commit
|
commitdiff
|
tree
2019-09-19
Mark A
b
raham
F
u
rt
h
er improve getDDGridSetup
commit
|
commitdiff
|
tree
2019-09-19
Pa
u
l
B
a
uer
A
d
d
ba
s
ic interface
to ru
n
update on GPU
commit
|
commitdiff
|
tree
2019-09-19
Berk
Hess
Add haveFr
e
eEnergyWo
r
k
to
D
omainLifetimeWorkload fl
a
gs
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Consiste
n
tly c
h
ange densityfi
t
ti
n
g spreading we
i
ght
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Added free-e
n
ergy
k
ernel p
e
rfo
r
mance note
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Fi
x
incorrect DD n
d
i
m assertion
commit
|
commitdiff
|
tree
2019-09-18
Pasca
l
M
e
rz
v
-
re
s
c
ale the
r
m
o
stat for modular simul
a
tor
commit
|
commitdiff
|
tree
2019-09-18
Paul Bauer
Read TPR file bod
y
in b
u
ffer
commit
|
commitdiff
|
tree
2019-09-18
Al
a
n Gray
GPU Force H
a
lo
E
xchange
commit
|
commitdiff
|
tree
2019-09-17
Pascal M
e
rz
Fix position pinning for m
o
dula
r
s
imulato
r
commit
|
commitdiff
|
tree
2019-09-16
B
erk Hess
Remove obsolete mdp option ns-type
commit
|
commitdiff
|
tree
2019-09-16
ejj
o
rda
n
Add some
c
oo
l
quotes
commit
|
commitdiff
|
tree
2019-09-16
Paul Bauer
Formatting fix
e
s f
o
r reference manua
l
commit
|
commitdiff
|
tree
2019-09-16
M
.
E
r
ic Irrgang
Add gmxapi re
l
ease not
e
s
.
commit
|
commitdiff
|
tree
2019-09-16
Alan Gray
GPU halo exchange
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add
virtual site
type 2FD
commit
|
commitdiff
|
tree
2019-09-16
Mark Ab
r
aha
m
Avoid s
h
ort-r
a
nge G
P
U operations with no work
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
Hes
s
Remove cut-off s
c
hemes
f
rom manual
commit
|
commitdiff
|
tree
2019-09-16
Sz
i
lárd Páll
Eliminate unnecessary GPU stream dependency call
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add option r
e
q
u
est 1D DD with 1 p
u
lse
commit
|
commitdiff
|
tree
2019-09-16
Kevin Boyd
Remove group sche
m
e
from deprecated release n
o
tes
commit
|
commitdiff
|
tree
next