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Merge branch 'origin/release-2020' into merge-2020-into-2021
2020-09-20
Artem Zhmurov
Set
acti
v
e
d
e
v
ice when
the
d
evice s
t
re
a
m m
a
nager i
s
.
.
.
commit
|
commitdiff
|
tree
2020-09-20
Arte
m
Zhmur
o
v
Allow
u
s
i
ng old environment
v
a
ria
b
les, bu
t
pr
i
nt
deprec
a
tion
.
.
.
commit
|
commitdiff
|
tree
2020-09-18
Berk H
e
ss
Remove
c
utoff_sch
e
me from
t
_for
c
erec and i
n
teraction_
c
o
n
st_t
commit
|
commitdiff
|
tree
2020-09-17
Artem Zhmurov
R
e
move the CPU hardware conte
x
t fro
m
the general
l
ist
.
.
.
commit
|
commitdiff
|
tree
2020-09-16
Mar
k
Abraham
A
c
tivate AMD OpenCL build in
r
ele
a
se matrix
commit
|
commitdiff
|
tree
2020-09-16
Paul
Bauer
Break
o
ff
s
ome te
s
ts from mdrun tests
commit
|
commitdiff
|
tree
2020-09-16
Christian Blau
Extend user docs on affine transformation
s
for
den
s
i
t
i
es
commit
|
commitdiff
|
tree
2020-09-16
P
ascal Merz
Implement modular
check
p
oin
t
ing
commit
|
commitdiff
|
tree
2020-09-15
Ar
t
em Zh
m
urov
U
s
e commo
n
devic
e
context header fo
r
Ope
n
CL
commit
|
commitdiff
|
tree
2020-09-15
Paul Ba
u
e
r
Br
e
a
k
off so
m
e tests from mdrun
t
ests
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Irrgang
Remove
o
utdated
work
a
round
.
commit
|
commitdiff
|
tree
2020-09-15
Berk Hess
Only exte
n
d Ewald table when necessary
commit
|
commitdiff
|
tree
2020-09-15
Erik Lind
a
hl
E
n
a
ble GMX_GPU=SYCL compil
e
s
commit
|
commitdiff
|
tree
2020-09-15
Paul B
a
uer
Fix missing
includ
e
for MSVC b
u
ild
commit
|
commitdiff
|
tree
2020-09-15
Alan Gray
P
ass devFlags in
t
o c
r
e
a
te
S
imulationWorkload replacing
.
.
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irr
g
ang
Refi
n
e the CMakeLists
.
txt fo
r
MPI
gm
x
a
pi tests
.
commit
|
commitdiff
|
tree
2020-09-13
B
erk H
e
ss
Decouple nsttcouple a
n
d
n
s
tpcouple fr
o
m ns
t
l
ist
commit
|
commitdiff
|
tree
2020-09-11
Artem Zhmurov
Define stubs for GPU data st
r
u
ctu
r
e
s in
SY
C
L to
m
ake
.
.
.
commit
|
commitdiff
|
tree
2020-09-10
Rola
n
d Sch
u
lz
Fix Visual
S
tudio build
commit
|
commitdiff
|
tree
2020-09-10
Roland Schulz
Simpif
y
Checkp
o
intData
commit
|
commitdiff
|
tree
2020-09-08
Alan Gr
a
y
B
u
g fix
i
n
call
to d
e
viceStreamManager c
o
nstructor
commit
|
commitdiff
|
tree
2020-09-08
Pascal Mer
z
M
a
ke legac
y
en
e
rgy el
e
m
e
n
t
s
use Checkpoin
t
Data
commit
|
commitdiff
|
tree
2020-09-07
A
r
t
em Zhmurov
Access th
e
d
e
v
i
c
e status directly, remove the getter
commit
|
commitdiff
|
tree
2020-09-06
Pas
c
al Merz
Pre
p
a
r
e
legacy ch
e
ckpoint for modular simulator
checkpointing
commit
|
commitdiff
|
tree
2020-09-03
Mag
n
us Lu
n
dborg
Print lambd
a
s
tate t
o
log file
i
f usin
g
A
W
H
for FEP
.
commit
|
commitdiff
|
tree
2020-09-02
B
e
rk He
s
s
Enable
s
p
lit
t
ing of listed
interaction calcu
l
ation
commit
|
commitdiff
|
tree
2020-09-02
G
illes Gouail
l
ardet
Fix improved
S
I
MD angles()
commit
|
commitdiff
|
tree
2020-08-31
Paul Bauer
Merge branch 'release-2020' int
o
mast
e
r
commit
|
commitdiff
|
tree
2020-08-26
Mark
Abr
a
h
am
Permit build wi
t
h
C
U
DA 11
.
0
commit
|
commitdiff
|
tree
2020-08-26
Gilles Gouaillardet
fix ch
e
c
k
_as
s
ign_in
t
era
c
tions_atom()
commit
|
commitdiff
|
tree
2020-08-20
Er
i
k Lindah
l
Ena
b
le
C
I testing of
O
penAPI / Op
e
nCL
commit
|
commitdiff
|
tree
2020-08-17
Mar
k
Abraham
Restore
u
se of CUDA 11
.
0 in CI
commit
|
commitdiff
|
tree
2020-08-17
Paul Bauer
Fix clang-
f
o
r
mat
commit
|
commitdiff
|
tree
2020-08-17
Mark A
b
rah
a
m
Bui
l
d f
e
w
er un
n
ecessary SIM
D
kernels
i
n CI
commit
|
commitdiff
|
tree
2020-08-16
Pascal Merz
Modular simulator: Don'
t
wra
p
std
:
:function in uniqu
e
_ptr
commit
|
commitdiff
|
tree
2020-08-14
A
r
tem Z
h
murov
Fix D
e
viceStream
M
anager tes
t
s
commit
|
commitdiff
|
tree
2020-08-12
Jeff Ha
m
mond
im
p
l
ement
A
VX-51
2
second
F
MA detection
commit
|
commitdiff
|
tree
2020-08-07
Mark Abr
a
ham
Fix release build wa
r
ning
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Ir
r
gang
Fix some minor typesetting
i
ssue
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
ric
Ir
r
gang
Imp
r
ove instal
l
docs links
.
commit
|
commitdiff
|
tree
2020-07-31
Berk
H
ess
Move foreign
p
otential
e
nergy a
c
cumulation
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Irr
g
ang
Use GMXAPI CMake opti
o
n
guard fo
r
gmxapi target d
e
claration
.
commit
|
commitdiff
|
tree
2020-07-29
Kevin Boy
d
Fi
x
undef
i
ned b
e
havior flag
g
ed
b
y
U
B
SAN
commit
|
commitdiff
|
tree
2020-07-29
Artem Zhmurov
R
evert c++
-
17 features th
a
t are not s
u
pported by CUDA
.
.
.
commit
|
commitdiff
|
tree
2020-07-27
Paul Bauer
Revert "Cha
n
ge
builds that
use f
a
iling docker contain
e
rs"
commit
|
commitdiff
|
tree
2020-07-09
Paul Bauer
Prepare for GROMACS 2020
.
4
commit
|
commitdiff
|
tree
2020-07-09
Paul Ba
u
er
GR
O
MACS version
2
020
.
3
commit
|
commitdiff
|
tree
2020-07-01
Rol
a
nd Schulz
Simplify Iterators
commit
|
commitdiff
|
tree
2020-07-01
Paul B
a
uer
Dis
a
ble failing bu
i
lds fo
r
master branch
commit
|
commitdiff
|
tree
2020-06-26
Paul B
a
uer
Mak
e
DSSP de
f
ault path
configur
a
ble
commit
|
commitdiff
|
tree
2020-06-26
Roland Schulz
MKL NULL
-
>nu
l
lptr a
n
d remov
e
dead c
o
de
commit
|
commitdiff
|
tree
2020-06-25
Ma
r
k Abr
a
ham
Re
s
tored the co
m
m
ent
commit
|
commitdiff
|
tree
2020-06-25
A
rtem Zhmuro
v
M
ake cl_nbparam into a
stru
c
t
commit
|
commitdiff
|
tree
2020-06-24
Berk Hess
Add c
l
a
ss ListedForces
commit
|
commitdiff
|
tree
2020-06-24
B
e
r
k
Hess
C
han
g
e grompp
disres cos
t
to li
n
ear
commit
|
commitdiff
|
tree
2020-06-24
R
o
land Sc
h
ulz
F
i
x
c
l
F
F
T
bu
i
ld witho
u
t GMX_LOAD_PLUGIN
S
commit
|
commitdiff
|
tree
2020-06-23
Berk
H
ess
Add virtual site wit
h
o
n
e constructing a
t
om
commit
|
commitdiff
|
tree
2020-06-23
Kevin Boyd
[WIP] R
u
n r
e
g
ress
i
on
tests
u
nd
e
r ASA
N
commit
|
commitdiff
|
tree
2020-06-22
M
.
Er
i
c
Irrgang
Refo
r
mat pai
r
s
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
r
i
c Ir
r
gang
Use Gromac
s
::g
m
x
target to hint gmxapi tests
.
commit
|
commitdiff
|
tree
2020-06-17
Er
i
k
L
ind
a
hl
Simplified unifor
m
GPU
se
l
e
c
tion
i
n CMake
commit
|
commitdiff
|
tree
2020-06-15
Erik
L
indahl
Replace tri
v
alue option
s
with pl
a
in boo
l
eans
commit
|
commitdiff
|
tree
2020-06-12
A
r
te
m
Zhmurov
Replace compil
e
_cpp_a
s
_cuda
(
.
.
.
) with
CUDA runtime
.
.
.
commit
|
commitdiff
|
tree
2020-06-11
P
au
l
Bauer
F
ix false initiali
z
ation valu
e
s in gmx hbo
n
d
commit
|
commitdiff
|
tree
2020-06-10
Paul Bauer
Proper fix for gm
x
do_dss
p
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
r
ic Irrgan
g
Compartmenta
l
ize jo
b
r
ules
.
commit
|
commitdiff
|
tree
2020-06-09
Artem Zh
m
u
r
o
v
Make SD
s
t
u
ff
private for upda
t
e
.
cp
p
commit
|
commitdiff
|
tree
2020-06-09
A
rtem Z
h
murov
Make SD stuff private for update
.
c
pp
commit
|
commitdiff
|
tree
2020-06-05
Paul Ba
u
er
Fix s
e
gment
a
t
ion fault when reading en
e
r
g
y
terms
commit
|
commitdiff
|
tree
2020-06-05
Berk Hess
Remo
v
e COM from SETT
L
E
commit
|
commitdiff
|
tree
2020-06-05
Art
e
m
Zhmurov
Make a err
o
r
m
e
ssage less confusing
commit
|
commitdiff
|
tree
2020-06-05
Paul Bauer
Use moltype directly for
o
bta
i
ni
n
g res
i
dueAtomRang
e
s
commit
|
commitdiff
|
tree
2020-06-04
Paul
Bauer
Ad
d
a
bil
i
ty to
c
hose
r
egressiont
e
st commit and b
r
anc
h
commit
|
commitdiff
|
tree
2020-06-04
Terry Mahaff
e
y
Remove
t
he c++14 fla
g
for CUDA builds on Windows
.
This
.
.
.
commit
|
commitdiff
|
tree
2020-06-04
A
r
t
em Z
h
murov
Cool quot
e
commit
|
commitdiff
|
tree
2020-06-03
E
rik Lindah
l
Remove 'register' storage cl
a
ss
in
c
lFFT
commit
|
commitdiff
|
tree
2020-06-03
Gilles Gouailla
r
de
t
n
o
nbonded-benchmark: run combrule=none when the -all
.
.
.
commit
|
commitdiff
|
tree
2020-06-02
Paul Bauer
A
d
d
fun
c
t
i
o
n
to
g
et resid
u
e start
a
n
d end
commit
|
commitdiff
|
tree
2020-06-01
Ma
r
k Ab
r
ah
a
m
Fix atomics configure test
commit
|
commitdiff
|
tree
2020-05-29
Mark Abr
a
h
a
m
M
ake Cygwin build work
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irr
g
ang
Remove unu
s
e
d (and
b
r
oken) image from D
o
c
ker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
Artem
Zhmurov
Remove t
h
e depende
n
c
e on C
o
nstraints object on t_mdatoms
commit
|
commitdiff
|
tree
2020-05-25
Paul B
a
ue
r
F
i
x c
l
ang-tidy warnings
commit
|
commitdiff
|
tree
2020-05-23
Pa
u
l Bauer
Mod
e
rnize
convert-
t
pr
commit
|
commitdiff
|
tree
2020-05-23
Paul
Bauer
Add tes
t
s for tool help output writing
commit
|
commitdiff
|
tree
2020-05-22
P
a
ul Bauer
Avo
i
d parsing
o
f fatalerror
.
c
pp as lint f
a
ilu
r
e
commit
|
commitdiff
|
tree
2020-05-15
Ar
t
em Zhmurov
Un
i
fy CUDA an
d
OpenCL lookup-table
creation
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
rgan
g
Reduce consol
e
l
o
g out
p
ut from sample_
r
estraint tests
.
commit
|
commitdiff
|
tree
2020-05-14
Berk He
s
s
E
x
t
ract
p
ostP
r
ocessForceWithShiftForces
(
)
commit
|
commitdiff
|
tree
2020-05-14
Paul Bauer
Avoid CI errors from overlo
a
ding r
e
so
u
rc
e
s
commit
|
commitdiff
|
tree
2020-05-12
Berk Hess
Ex
t
r
a
ct helper force buffer
s
to a separ
a
t
e
class
commit
|
commitdiff
|
tree
2020-05-12
Ber
k
H
ess
R
e
fac
t
o
r vir
t
ual site interface
commit
|
commitdiff
|
tree
2020-05-12
Paul Bauer
Fix arc
h
ive build
commit
|
commitdiff
|
tree
2020-05-07
Berk Hess
Avoid warning during PME tunin
g
commit
|
commitdiff
|
tree
2020-05-06
Paul Bauer
Merge branch 'or
i
gin
/
release-2
0
20' into ma
s
te
r
commit
|
commitdiff
|
tree
2020-05-05
Paul
B
auer
F
ix cop
y
rig
h
t
commit
|
commitdiff
|
tree
2020-05-04
Paul
Bau
e
r
Use
t
est conve
r
sio
n
script from
s
ource
commit
|
commitdiff
|
tree
2020-05-04
Paul Bauer
Fix incorrect
h
eader and linter scripts
commit
|
commitdiff
|
tree
2020-05-04
Pascal Merz
C
a
tc
h
errors in v-re
s
cal
e
and Parrinello-
R
ah
m
an ch
e
ckpointing
commit
|
commitdiff
|
tree
2020-05-01
Paul Bauer
Prepare for 2020
.
3
commit
|
commitdiff
|
tree
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