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Fixes for Intel and container build fixes
2020-11-23
Paul Bauer
Fixes
for I
n
t
e
l and cont
a
iner build fixes
commit
|
commitdiff
|
tree
2020-10-05
Paul Bauer
Fi
x
d
e
bug messag
e
locatio
n
commit
|
commitdiff
|
tree
2020-09-10
Gi
l
les
G
ouaillardet
f
i
x check_as
s
ign_interac
t
ions_atom()
commit
|
commitdiff
|
tree
2020-06-16
Art
e
m Zhmurov
Add mis
s
ing end-of-line in
t
he GPU upd
a
te assignment
.
.
.
commit
|
commitdiff
|
tree
2020-06-04
Artem Zhmuro
v
Upd
a
te t
h
e
r
elease notes
commit
|
commitdiff
|
tree
2020-04-29
Artem Zhmurov
Fix
the number of st
e
ps
c
heck when
c
heckpoint is loaded
commit
|
commitdiff
|
tree
2020-04-01
Mark Abraham
Fix
m
i
nor
bug with
t
ools t
i
m
e
-unit conversions
commit
|
commitdiff
|
tree
2020-03-19
Sz
i
lárd Pá
l
l
Fix DLB ini
t
ial state re
p
orting
commit
|
commitdiff
|
tree
2020-03-07
Paul Bau
e
r
Add clang-tidy script
commit
|
commitdiff
|
tree
2020-03-02
Paul Bauer
Ad
d
Cuda build to g
i
tlab
C
I
commit
|
commitdiff
|
tree
2020-02-22
David van der Spoel
Fixed
b
ug in gm
x
disre due to i
n
c
o
ns
i
stency in inpu
t
.
commit
|
commitdiff
|
tree
2020-02-15
Sz
i
lá
r
d Páll
Fix
g
puud
p
ate and g
p
u
comm matrix docs
commit
|
commitdiff
|
tree
2020-01-24
Szilárd
Pá
l
l
Fix deadlock in PP-
P
ME
balancing startup delay
commit
|
commitdiff
|
tree
2020-01-22
Ber
k
Hess
C
l
arify COMM/posres gromp
p
n
o
te
commit
|
commitdiff
|
tree
2019-12-30
Mark Abraham
Remove us
e
of
t
uple in LI
N
CS
cod
e
for GPU
i
m
plementation
commit
|
commitdiff
|
tree
2019-12-20
P
a
ul
B
aue
r
Fix wrong header in release notes
commit
|
commitdiff
|
tree
2019-12-18
A
l
an Gray
Fix conditional on a
s
serti
o
n for combining GPU Upd
a
te
.
.
.
commit
|
commitdiff
|
tree
2019-12-17
Ber
k
H
ess
A
dd note for COM removal with position restra
i
nts
commit
|
commitdiff
|
tree
2019-12-17
A
r
tem Zhmuro
v
Clean-up buffer-op
s
CUDA kernels
commit
|
commitdiff
|
tree
2019-12-17
Sz
i
lárd Páll
Comment t
h
e use
of
w
aitCoo
r
di
n
a
t
esCopiedToD
e
v
ice
commit
|
commitdiff
|
tree
2019-12-17
P
a
u
l
Bauer
Se
t
c
orrect depen
d
ency
for doc build
o
n gmxapi
commit
|
commitdiff
|
tree
2019-12-17
Paul Baue
r
F
ix compiler warning about
e
xtra ;
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Páll
Add wallcycle co
u
nting t
o
StatePropagat
o
rDataGpu
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
Enable mo
s
t of the pulling
f
lavor
s
with GPU
update
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmurov
Set GPU updat
e
to f
a
l
se in
c
ase of a reru
n
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
M
a
ke Leap-Frog CU
D
A
k
er
n
el selection safer
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhm
u
rov
F
i
x pr
e
s
sure coupl
i
ng with GPU
update
commit
|
commitdiff
|
tree
2019-11-27
Artem
Zhmur
o
v
Combine two booleans
in m
d
loop
commit
|
commitdiff
|
tree
2019-11-27
Mark
A
braham
Disable GPU PME
-
PP communication
w
i
t
h
m
drun -
p
mefft cpu
commit
|
commitdiff
|
tree
2019-11-26
Alan
G
ray
Bug fi
x
for nonlocal D
2
H
c
o
o
r
d
inat
e
t
rans
f
er synchroniz
a
tion
commit
|
commitdiff
|
tree
2019-11-23
Artem Zhmu
r
ov
N
e
w
cool quote
commit
|
commitdiff
|
tree
2019-11-20
A
lan Gray
Move pmeP
p
Co
m
mGpu reset
o
utside do_md
commit
|
commitdiff
|
tree
2019-11-19
Mar
k
Abraha
m
Upd
a
ted rel
e
a
se notes f
o
r
CODATA updat
e
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmurov
F
ix
i
c
c
-19 warning in ni
g
htly
matrix
commit
|
commitdiff
|
tree
2019-11-13
Pa
u
l Bauer
Add build
t
o run c
l
ang-format u
p
date on Jenk
i
ns
commit
|
commitdiff
|
tree
2019-11-03
Sz
i
l
á
rd P
á
ll
Imp
r
ove
Simul
a
t
ionWorkload doxygen
commit
|
commitdiff
|
tree
2019-10-30
Berk H
e
ss
Fix walls with GPU u
p
date
commit
|
commitdiff
|
tree
2019-10-29
Ber
k
Hess
D
i
sable press
u
re
coup
l
ing
with GPU upd
a
t
e
commit
|
commitdiff
|
tree
2019-10-28
S
z
ilárd Páll
Extend SimulationWor
k
l
o
ad with CPU fla
g
s
commit
|
commitdiff
|
tree
2019-10-21
Szilár
d
Páll
O
verride
G
M
X_GPU_DD_COMMS if
n
on
b
ondeds are
off
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmurov
Remove excessive H2D and
D2H coordinates copies
when
.
.
.
commit
|
commitdiff
|
tree
2019-10-17
Sz
i
l
á
rd Pá
l
l
Disa
b
le
G
MX
_
GPU_PME_PP_COMMS if PME is
n
o
t off
l
oad
e
d
commit
|
commitdiff
|
tree
2019-10-16
Szilárd Páll
Fix initializati
o
n of
f
ield in P
M
E data s
t
ructure
commit
|
commitdiff
|
tree
2019-10-16
Artem Zhmur
o
v
Link GPU force producer and
c
o
nsume
r
t
a
sks
commit
|
commitdiff
|
tree
2019-10-15
A
lan Gray
PM
E
/
P
P G
P
U Pimpl
C
lass
a
nd GPU->C
P
U Com
m
unication fo
r
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Sz
i
lárd Páll
L
i
n
k
GPU
coordinat
e
pro
d
ucer and consum
e
r tasks
commit
|
commitdiff
|
tree
2019-10-14
Ar
t
em Zhmurov
A
d
d
s
e
parate construc
t
or to StatePropagatorDataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-13
Szil
á
rd Páll
Ena
b
l
e
StatePropagatorGpuData fo
r
force
t
ransfers
commit
|
commitdiff
|
tree
2019-10-13
Szilárd Páll
Move bu
f
fer o
p
s / PME F reducti
o
n
flags into Ste
p
Wo
r
klo
a
d
commit
|
commitdiff
|
tree
2019-10-12
Artem
Z
hmu
r
ov
Ce
n
tralize management of forces ready on
G
P
U
ev
e
nt
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
Change c
o
py mode to Async in PME only
rank
commit
|
commitdiff
|
tree
2019-10-11
Artem Zh
m
urov
Wrong locality
w
as used wh
e
n
ignoring the PME f
o
rce
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Páll
M
igrate
code to us
i
ng SimulationWorkl
o
ad
f
lags
commit
|
commitdiff
|
tree
2019-10-10
S
z
i
lárd
Páll
Remove incorrect GPU task depende
n
cy
commit
|
commitdiff
|
tree
2019-10-10
S
z
ilár
d
Páll
Pass list of EventSy
n
chronizers t
o
GPU reductio
n
commit
|
commitdiff
|
tree
2019-10-10
Paul Baue
r
Basic
p
opulatio
n
of
s
imulation
workloa
d
commit
|
commitdiff
|
tree
2019-10-10
Artem Zhmurov
Add managemen
t
for
v
elocities and f
o
rces copy eve
n
t
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
S
zilárd Páll
A
dd
m
anagemen
t
for
c
oordinates copy
e
vents into Sta
t
eP
r
opaga
.
.
.
commit
|
commitdiff
|
tree
2019-10-07
Arte
m
Zhmurov
Pass t
h
e GPU streams to
StatePropagatorDataGpu
c
onstructor
commit
|
commitdiff
|
tree
2019-10-07
Mark
Abra
h
am
Ex
t
end G
P
U trai
t
s class
commit
|
commitdiff
|
tree
2019-10-07
Artem
Z
hmurov
Clean up t
h
e c
o
m
ments sections in Update-C
o
nst
r
ai
n
commit
|
commitdiff
|
tree
2019-10-07
Artem
Zhmurov
Fix a bug in GP
U
halo exchange initiali
z
at
i
o
n
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Use gmx::Range for iZones i
n
pair
search
commit
|
commitdiff
|
tree
2019-10-02
Carsten Kutzner
Update
t
h
e
www
l
ink to the Doxyge
n
documentation in
.
.
.
commit
|
commitdiff
|
tree
2019-09-30
Szilá
r
d Páll
M
ove PME GPU program building later
commit
|
commitdiff
|
tree
2019-09-27
A
rtem Zhm
u
rov
Sligh
t
imp
r
ovements to GPU update/
c
onstr
a
int
s
init
i
alization
commit
|
commitdiff
|
tree
2019-09-27
Szilárd
Páll
S
witch GPU
update off by default
commit
|
commitdiff
|
tree
2019-09-27
Artem
Zhmu
r
o
v
Introduce stream
m
anage
m
ent
t
o GPU Update-Constra
i
nts
commit
|
commitdiff
|
tree
2019-09-27
Be
r
k Hess
E
x
t
r
act gmx::Ra
n
ge
commit
|
commitdiff
|
tree
2019-09-27
Mark Abra
h
am
S
t
op checking CUDA
version reported by nvcc
commit
|
commitdiff
|
tree
2019-09-22
A
rte
m
Zhmurov
Disab
l
e GPU update/constrain
t
s
when neither PME nor
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Ma
r
k Abraham
Make gmx
_
m
u
lti
s
im_t
a
C++ o
b
je
c
t
commit
|
commitdiff
|
tree
2019-09-10
Mar
k
Abra
h
am
A
v
oi
d
warning in no-mpi build
commit
|
commitdiff
|
tree
2019-09-10
A
rtem Zhmu
r
ov
Maki
n
g De
v
iceBuffer a
v
ailib
l
e in non-GPU
b
uilds
commit
|
commitdiff
|
tree
2019-09-10
Paul
B
auer
A
d
d
indication on how to enable ImageMagick
conv
e
r
t
commit
|
commitdiff
|
tree
2019-09-09
S
z
i
l
árd Páll
Assert the types of Ope
n
C
L
kernels argument
s
commit
|
commitdiff
|
tree
2019-08-25
Artem Z
h
murov
Make use of re
c
ent changes t
o
prepa
r
e
K
e
r
n
elAr
g
u
m
e
n
ts
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Art
e
m
Z
hmurov
Mi
s
celeneou
s
improveme
n
ts to t
h
e
L
e
a
p
Fr
o
g tests
commit
|
commitdiff
|
tree
2019-08-20
Mark
A
brah
a
m
Appl
y
cl
a
ng-tidy-8 r
e
adabil
i
ty-uppercase
-
lit
e
ral-
s
uffix
commit
|
commitdiff
|
tree
2019-08-20
Mark Ab
r
aham
Use potential-shift as default modi
f
i
er
commit
|
commitdiff
|
tree
2019-08-09
Be
r
k
H
ess
Move bonded function tabl
e
i
n
t
o bo
n
ded
.
cpp
commit
|
commitdiff
|
tree
2019-08-08
M
a
rk Abraha
m
I
nitia
l
i
ze
gmx_ekindata_t and
t
_vcm pro
p
erly
commit
|
commitdiff
|
tree
2019-08-06
Artem Zhmurov
Fix for cma
k
e lists in mdlib tests
commit
|
commitdiff
|
tree
2019-07-31
Arte
m
Zhmurov
Change the file str
u
cture
in constraints tests
commit
|
commitdiff
|
tree
2019-07-31
Szilárd
P
á
l
l
S
t
ore wcycle poi
n
ter in nonbond
e
d_ver
l
et_t
commit
|
commitdiff
|
tree
2019-07-26
A
r
tem Zh
m
urov
Remov
e
P
I
mpl scaffoldi
n
g from CUDA version of SETTLE
commit
|
commitdiff
|
tree
2019-07-05
K
e
v
i
n Boyd
Change
error message w
h
en
a
ttem
p
ting to offl
o
a
d
to
.
.
.
commit
|
commitdiff
|
tree
2019-07-05
Ar
t
em
Zhmurov
Remove PI
m
pl s
c
affolding
f
rom
C
UDA version o
f
LIN
C
S
commit
|
commitdiff
|
tree
2019-07-04
A
rtem Zhm
u
ro
v
Use realloc
a
teDeviceBuffer(
.
.
.
)
in
C
UDA version of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Ar
t
em Zhmurov
Early exit
f
or CUDA versions of SETTLE and LINCS
commit
|
commitdiff
|
tree
2019-07-03
Ar
t
em Z
h
m
u
rov
Memory ma
n
agement
f
ixes
i
n
CU
D
A version of LINCS
commit
|
commitdiff
|
tree
2019-06-28
Szilárd Páll
Separate CPU NB kernel and buffer
c
learing
s
ub
c
ounters
commit
|
commitdiff
|
tree
2019-06-28
Ma
g
nus L
u
n
dbo
r
g
Fuse
d
GPU
bo
n
ded kerne
l
s
commit
|
commitdiff
|
tree
2019-06-18
Arte
m
Z
hmu
r
ov
Com
b
ine CUDA Leap-Frog, LINCS and S
E
TTLE
.
I
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Zh
m
urov
Clarify which o
f
the
main ener
g
y ter
m
s
are p
r
inted
.
commit
|
commitdiff
|
tree
2019-05-13
Pau
l
Bauer
Fix math f
o
rmatti
n
g in reference ma
n
ual
commit
|
commitdiff
|
tree
2019-05-12
Artem Zhmu
r
ov
CU
D
A version of
L
e
ap-
F
r
o
g integrator with
bas
i
c tes
t
s
commit
|
commitdiff
|
tree
2019-05-06
Mark Abraham
Improve how mdrun -noappend na
m
es output files
commit
|
commitdiff
|
tree
2019-05-02
Artem Zhmur
o
v
Use test with parameters for EnergyOutput
commit
|
commitdiff
|
tree
2019-04-30
Art
e
m Zhmurov
CU
D
A version of SETTLE algorithm with b
a
sic tests
commit
|
commitdiff
|
tree
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