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Merge branch release-2019 into release-2020
2019-11-29
Ma
r
k
A
braham
Merge br
a
nch rel
e
ase-2019 into rele
a
se
-
2020
commit
|
commitdiff
|
tree
2019-11-29
A
rtem Zhmu
r
ov
Rename
s
ome
variables in GPU U
p
d
a
te
commit
|
commitdiff
|
tree
2019-11-28
Paul
Bauer
Che
c
k for using correct hwloc headers and runt
i
me
commit
|
commitdiff
|
tree
2019-11-28
Ar
t
em Zhmurov
Clear
d
e
v
ice
f
o
r
ce b
u
ff
e
r
if
i
t was reallocate
d
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmurov
A
dd method for coordi
n
ates scal
i
n
g into GPU update
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Er
i
c Irrgang
Add gmxap
i
_extension
tests to 'tests'
t
arget
.
commit
|
commitdiff
|
tree
2019-11-27
Alan Gray
Event-bas
e
d
Dependency for GPU
F
orce Halo
E
xchange
commit
|
commitdiff
|
tree
2019-11-26
Mark Abr
a
ham
I
m
prove handlin
g
of task-assign
m
ent excepti
o
ns
commit
|
commitdiff
|
tree
2019-11-25
Ala
n
Gra
y
Fix race conditio
n
in GPU X hal
o
exchange
w
ith GPU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
Ch
r
i
s
t
i
an Blau
InM
e
m
o
r
ySerializer wit
h
endianess swap
.
commit
|
commitdiff
|
tree
2019-11-21
Mark Ab
r
aham
N
ew cool quote
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
Add D2H copies for the
c
heckpointing
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
Move the copy of th
e
v
eloc
i
ties for the o
u
tput close
r
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
B
e
r
k
He
s
s
Q
uiet pdb2gmx a
n
d use
g
m
x
_
fatal
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric Irrgang
Remove st
u
b
c
ontent
from
gm
x
api d
o
cs
.
commit
|
commitdiff
|
tree
2019-11-16
Mar
k
Ab
r
aham
Relaxe
d
lis
t
ed forces test tol
e
rances
commit
|
commitdiff
|
tree
2019-11-06
Berk
Hess
Dep
r
ecated sc-r-pow
e
r
=
48
commit
|
commitdiff
|
tree
2019-11-04
Pa
u
l Ba
u
er
Add bui
l
d for clang-
f
ormat
commit
|
commitdiff
|
tree
2019-11-04
P
a
ul Bauer
S
p
l
i
t
u
p
source code formatting scripts
commit
|
commitdiff
|
tree
2019-11-04
T
e
emu Murtola
Upd
a
te cl
a
ng
-
for
m
at config
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eri
c
Irr
g
ang
Improve uniform
i
ty
o
f
O
S
X CMake c
o
nfig
u
ration
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric I
r
rgang
Restore CMake convenience t
a
r
ge
t
s
for
sample
_
restra
i
nt
.
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
R
emove dead code fo
r
nbnx
m
H2D coordin
a
te copy e
v
ent
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
B
u
g
f
ix
f
o
r
event passe
d
to GPU comm featu
r
e
s
commit
|
commitdiff
|
tree
2019-10-31
Pascal Merz
C
h
ec
k
for co
n
tradicting environmen
t
varia
b
les (modu
l
ar
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Mark Abraha
m
Tests for
valid p
e
r
io
d
i
c a
c
t
i
o
n
s
commit
|
commitdiff
|
tree
2019-10-29
M
.
E
ric
Irrgan
g
Disabl
e
i
t
s test
s
w
h
en sample_restrain
t
is not the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
Decrease
t
he
maximum allowed Python versi
o
n
f
or gmxapi
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmurov
Disabl
e
GPU update when coo
r
dinates swappin
g
is enabled
commit
|
commitdiff
|
tree
2019-10-24
Be
r
k Hess
Add bool useDom
a
inDecomposition
in mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Ad
d
gmx_m
t
op_
i
nteraction_count()
commit
|
commitdiff
|
tree
2019-10-23
ejjordan
Ma
k
e t_n
e
xtnb an implementation detail
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Correct f
o
r sk
e
wed box before doma
i
n decom
p
osition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Al
a
n Gray
Enab
l
e GPU Peer Access in GPU Utiliti
e
s
commit
|
commitdiff
|
tree
2019-10-22
ejjord
a
n
Rem
o
v
e u
n
used func
t
ion
s
from
gmxpreprocess
commit
|
commitdiff
|
tree
2019-10-22
Berk Hess
Requ
i
re
-ei for essential dynamics
commit
|
commitdiff
|
tree
2019-10-22
ejj
o
rda
n
Remo
v
e unused fun
c
t
i
on gener
a
t
e
_excls and m
a
k
e
cl
e
an_excls
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
B
e
rk He
s
s
Co
n
st corre
c
tness for genhyd
r
o
commit
|
commitdiff
|
tree
2019-10-15
Paul Bauer
Fix bu
g
in preproc
e
ssing
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eric Irrga
n
g
Fix logic
e
rro
r
in gmxap
i
.
v
ersion
.
api_is_at_le
a
st()
.
commit
|
commitdiff
|
tree
2019-10-13
Mark
A
b
raham
Ensure environm
e
nt variabl
e
use doe
s
not gi
v
e
warnings
commit
|
commitdiff
|
tree
2019-10-12
Berk
Hes
s
A
dd c
l
ass
F
ixedCa
p
a
cityVector
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
Centralize management of coor
d
inates ready on G
P
U
ev
e
nt
commit
|
commitdiff
|
tree
2019-10-08
Pr
a
sha
n
th Kanduri
Fused two if branches with the same c
o
nd
i
tional
commit
|
commitdiff
|
tree
2019-10-02
Ca
r
sten
Kutzner
U
pdate
t
he www link to
t
he Doxyge
n
do
c
umen
t
ation in
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
Berk H
e
ss
Fix harmles
s
OpenMP w
r
ite r
a
ce
commit
|
commitdiff
|
tree
2019-10-02
Mar
k
Abraham
Improve PME testin
g
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Use gm
x
::Range in do
m
de
c
commit
|
commitdiff
|
tree
2019-10-01
Artem Z
h
murov
StatePro
p
agatorDa
t
aGpu
o
bject to manage
G
P
U forces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Mark Abraham
F
ix icc warnings
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Completely
remov
e
ch
a
rge groups
commit
|
commitdiff
|
tree
2019-10-01
Paul Bauer
F
ix chain ID handl
i
ng in make_nd
x
commit
|
commitdiff
|
tree
2019-10-01
Christoph Ju
n
g
h
ans
cma
k
e
: ad
d
missing
he
a
der
t
o
legacy
api
commit
|
commitdiff
|
tree
2019-10-01
Mark Abr
a
ham
Removed dependenc
y
on c
o
mm
r
ec
of m
d
run setu
p
commit
|
commitdiff
|
tree
2019-09-30
C
a
r
st
e
n Kutzner
Mov
e
ForcePr
o
v
i
ders class into the gmx name
s
pace
commit
|
commitdiff
|
tree
2019-09-30
Mark
Abr
a
h
a
m
Make a builder
f
or DD
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
R
e
move charge grou
p
code from forcerec
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Páll
Make t
h
e wa
i
t on PME GPU result
s
condi
t
io
n
al
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Impr
o
v
e
MiMiC test impl
e
m
e
ntatio
n
commit
|
commitdiff
|
tree
2019-09-27
Mark Abr
a
h
a
m
F
ix gr
o
f
i
le
o
utput with in
d
ex groups
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Fix
gro
file outp
u
t with i
n
dex g
r
o
u
ps
commit
|
commitdiff
|
tree
2019-09-27
M
a
r
k
A
br
a
ham
R
emove leftover support for pre-9
.
0 CUDA
commit
|
commitdiff
|
tree
2019-09-24
Paul
Bauer
Add test f
o
r noappe
n
d
commit
|
commitdiff
|
tree
2019-09-24
Mark Abra
h
am
Fix
n
o-MP
I
CUDA build
commit
|
commitdiff
|
tree
2019-09-24
Mar
k
Abraham
Merge "Merge bran
c
h relea
s
e-20
1
9 in
t
o ma
s
te
r
"
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraha
m
Fix clang unused-funct
i
on wa
r
nings
commit
|
commitdiff
|
tree
2019-09-24
Paul Bau
e
r
Add releas
e
note
s
for modular simulator
commit
|
commitdiff
|
tree
2019-09-23
Paul Bauer
Fix issues
when PME rank request
b
e
c
omes
ne
g
ative
commit
|
commitdiff
|
tree
2019-09-23
Paul
Bauer
Cha
n
ge MPI
s
et
u
p to c
o
m
municate T
P
R as buffer
commit
|
commitdiff
|
tree
2019-09-23
Pascal
M
erz
Z
e
r
o
pressure a
n
d viri
a
l
tensors at beginning of step
commit
|
commitdiff
|
tree
2019-09-23
Pascal Mer
z
I
n
t
roduce F
E
P int
o
m
o
dular simul
a
tor
commit
|
commitdiff
|
tree
2019-09-22
Christo
p
h Junghans
workaro
u
n
d
fo
r
rhel bug #1749463
,
cm
a
ke bug
#18
3
4
9
commit
|
commitdiff
|
tree
2019-09-22
Paul
B
auer
Remove update
f
lag again
commit
|
commitdiff
|
tree
2019-09-22
Be
r
k Hess
Remove
cgs_gl from gmx_domd
e
c_co
m
m
_t
commit
|
commitdiff
|
tree
2019-09-20
Mar
k
Abraham
R
efactor to crea
t
e a GpuTa
s
kAssignm
e
nts object
commit
|
commitdiff
|
tree
2019-09-19
Be
r
k Hess
R
e
move bLocalCG fro
m
DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove obsolet
e
m
ake_
e
xclusions_zon
e
_cg()
commit
|
commitdiff
|
tree
2019-09-19
C
h
ristian Bl
a
u
Check input
r
e
cor
d
als
o
i
n tests
commit
|
commitdiff
|
tree
2019-09-19
M
ark Abraham
Use GPU halo exchan
g
e
only when compatible DD
i
s
a
va
i
lable
commit
|
commitdiff
|
tree
2019-09-19
Mark
Abr
a
ham
F
urther improv
e
getDD
G
ridSe
t
up
commit
|
commitdiff
|
tree
2019-09-19
P
aul
Baue
r
A
d
d basic interface to run upd
a
t
e on
GPU
commit
|
commitdiff
|
tree
2019-09-19
B
e
r
k
Hess
Ad
d
haveFreeEner
g
yW
o
rk to DomainL
i
fetime
W
orkloa
d
fl
a
g
s
commit
|
commitdiff
|
tree
2019-09-19
Christian Bla
u
Cons
i
stently ch
a
nge densityfitting spreading
w
eight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Added
free-energy k
e
rnel
perform
a
nce
n
ote
commit
|
commitdiff
|
tree
2019-09-18
B
e
rk Hess
Fi
x
in
c
orre
c
t DD n
d
im
assert
i
on
commit
|
commitdiff
|
tree
2019-09-18
Pascal Merz
v-
r
escale
t
hermostat for mo
d
u
lar
simu
l
at
o
r
commit
|
commitdiff
|
tree
2019-09-18
Paul Bauer
Read TPR file
b
od
y
i
n buffer
commit
|
commitdiff
|
tree
2019-09-18
Alan Gray
GPU Force
H
al
o
Exchan
g
e
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix position pinning for modular sim
u
lator
commit
|
commitdiff
|
tree
2019-09-16
Berk
H
ess
Remove obsole
t
e mdp option ns-type
commit
|
commitdiff
|
tree
2019-09-16
e
j
jordan
Add some
c
ool quotes
commit
|
commitdiff
|
tree
2019-09-16
Paul Bauer
F
o
rma
t
ting
f
i
xes
for r
e
f
erence
manual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Eric Irrgang
A
d
d gmxapi rel
e
a
s
e
note
s
.
commit
|
commitdiff
|
tree
2019-09-16
Ala
n
Gra
y
GPU
h
a
l
o exchange
commit
|
commitdiff
|
tree
2019-09-16
Be
r
k He
s
s
Ad
d
virtual si
t
e
t
ype 2FD
commit
|
commitdiff
|
tree
2019-09-16
Mark Abr
a
ha
m
Avoid short-r
a
ng
e
GPU operat
i
ons
wi
t
h no
w
ork
commit
|
commitdiff
|
tree
2019-09-16
Berk
H
ess
R
e
mo
v
e cu
t
-off s
c
hemes from
m
anual
commit
|
commitdiff
|
tree
2019-09-16
Szilár
d
Páll
E
l
iminate
u
n
necessary GPU stream dependency c
a
l
l
commit
|
commitdiff
|
tree
2019-09-16
Be
r
k Hess
Ad
d
option request 1D DD w
i
th 1
p
u
l
s
e
commit
|
commitdiff
|
tree
2019-09-16
Ke
v
in Boyd
Remove group scheme from deprecat
e
d
release notes
commit
|
commitdiff
|
tree
next