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Centralize management of coordinates ready on GPU event
2019-10-12
Ar
t
em Zhmurov
Ce
n
tral
i
ze managemen
t
of coo
r
di
n
a
t
es ready o
n
G
P
U
e
vent
commit
|
commitdiff
|
tree
2019-10-08
P
r
a
shanth Kanduri
F
u
s
ed t
w
o if bra
n
ches
w
ith
the
same conditional
commit
|
commitdiff
|
tree
2019-10-02
Berk Hess
Fix harmless OpenMP wri
t
e race
commit
|
commitdiff
|
tree
2019-10-02
Mark Abraham
I
m
prov
e
PME testing
commit
|
commitdiff
|
tree
2019-10-01
Berk
H
ess
Use gmx::Range in domdec
commit
|
commitdiff
|
tree
2019-10-01
Artem Zhmurov
State
P
r
opag
a
torDataG
p
u obje
c
t to manage GPU forces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Mark Abra
h
am
Fix icc warnings
commit
|
commitdiff
|
tree
2019-10-01
Berk
Hess
Completely remove
c
h
arg
e
group
s
commit
|
commitdiff
|
tree
2019-10-01
Christoph Junghans
cmake:
a
d
d
miss
i
ng header to legacy api
commit
|
commitdiff
|
tree
2019-10-01
M
a
rk Abraham
Removed dependency
o
n commrec of
m
drun se
t
u
p
commit
|
commitdiff
|
tree
2019-09-30
Carsten
Kutzn
e
r
Move ForceP
r
oviders class into the gmx na
m
espace
commit
|
commitdiff
|
tree
2019-09-30
Mark
A
braham
Make
a
b
u
il
d
er for DD
commit
|
commitdiff
|
tree
2019-09-30
Be
r
k Hes
s
Remove charge
g
roup code f
r
om forcerec
commit
|
commitdiff
|
tree
2019-09-30
Szilárd
P
áll
Ma
k
e the wait on PME GPU
r
esults conditional
commit
|
commitdiff
|
tree
2019-09-27
M
a
rk A
b
raham
Improv
e
MiMiC test implementat
i
on
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Fix gro file
output
with index
g
roups
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Remove l
e
ftover support for
p
re
-
9
.
0 CUDA
commit
|
commitdiff
|
tree
2019-09-24
Paul B
a
u
er
Add
test
f
o
r noap
p
e
n
d
commit
|
commitdiff
|
tree
2019-09-24
Mark Ab
r
aham
Fix n
o
-MPI CUDA b
u
ild
commit
|
commitdiff
|
tree
2019-09-24
Mar
k
Abra
h
a
m
Merge "Merge b
r
a
n
ch release-201
9
into master"
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraha
m
F
ix clang
unused-function w
a
rnings
commit
|
commitdiff
|
tree
2019-09-24
Paul Bauer
Add release note
s
for mo
d
ular simulator
commit
|
commitdiff
|
tree
2019-09-23
Paul B
a
uer
F
i
x issues wh
e
n
P
M
E rank request becomes negative
commit
|
commitdiff
|
tree
2019-09-23
P
aul Ba
u
e
r
Change MPI setup to co
m
mun
i
cate TPR as buffe
r
commit
|
commitdiff
|
tree
2019-09-23
Pascal
M
e
rz
Zero pres
s
ure
a
nd virial tensors a
t
beginning of step
commit
|
commitdiff
|
tree
2019-09-23
Pascal Mer
z
Introduce FEP into m
o
du
l
ar simul
a
tor
commit
|
commitdiff
|
tree
2019-09-22
C
h
ri
s
toph
J
ungha
n
s
w
o
rkar
o
und for
r
h
e
l
bu
g
#1
7
49463,
cmak
e
bug #18
3
49
commit
|
commitdiff
|
tree
2019-09-22
P
aul Ba
u
er
R
emov
e
updat
e
flag again
commit
|
commitdiff
|
tree
2019-09-22
B
e
rk H
e
ss
Re
m
o
ve cg
s
_gl
fr
o
m gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-20
M
ark Abraham
Refactor to
create a GpuTaskAssignments
object
commit
|
commitdiff
|
tree
2019-09-19
B
e
rk Hess
R
e
move bL
o
c
a
l
CG from
DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk H
e
ss
Remo
v
e obsolete mak
e
_exclusion
s
_zone_
c
g()
commit
|
commitdiff
|
tree
2019-09-19
C
hristian Blau
Chec
k
input record al
s
o in test
s
commit
|
commitdiff
|
tree
2019-09-19
Mark Abraha
m
Use GP
U
halo exchange o
n
l
y when compatibl
e
DD
is
available
commit
|
commitdiff
|
tree
2019-09-19
Mark
A
braham
Further improve get
D
DGr
i
dSetup
commit
|
commitdiff
|
tree
2019-09-19
P
aul Bauer
Add
b
asic interface to run
update on
G
PU
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Add haveFre
e
En
e
rgyW
o
r
k
t
o DomainLifetimeWorkload flags
commit
|
commitdiff
|
tree
2019-09-19
C
h
ristian Blau
Consistently cha
n
g
e
de
n
s
ity
f
itting
spreading
weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Be
r
k H
e
ss
Added free
-
ener
g
y ke
r
n
e
l
p
e
r
formance note
commit
|
commitdiff
|
tree
2019-09-18
Berk H
e
ss
Fix incor
r
e
c
t DD ndim
as
s
ertion
commit
|
commitdiff
|
tree
2019-09-18
P
ascal Merz
v-r
e
sc
a
le thermostat fo
r
modular s
i
mulator
commit
|
commitdiff
|
tree
2019-09-18
Pau
l
Bauer
Read TPR file b
o
dy in buff
e
r
commit
|
commitdiff
|
tree
2019-09-18
Alan Gray
GPU
For
c
e Halo Exc
h
a
nge
commit
|
commitdiff
|
tree
2019-09-17
Pascal
Merz
Fix p
o
siti
o
n
pin
n
ing for
modular
simulator
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Re
m
ove obs
o
lete
m
dp option
ns-ty
p
e
commit
|
commitdiff
|
tree
2019-09-16
ejjor
d
a
n
Add so
m
e
cool q
u
o
t
es
commit
|
commitdiff
|
tree
2019-09-16
Pa
u
l Bauer
Forma
t
t
i
ng
f
ixes for
r
e
ference manual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Er
i
c Irrgang
A
dd gmxapi releas
e
n
otes
.
commit
|
commitdiff
|
tree
2019-09-16
Alan Gray
GPU ha
l
o e
x
c
hange
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
A
d
d
v
irtual site ty
p
e 2FD
commit
|
commitdiff
|
tree
2019-09-16
M
a
rk
Abraham
Avoi
d
short-r
a
nge G
P
U ope
r
ations wi
t
h no w
o
r
k
commit
|
commitdiff
|
tree
2019-09-16
Berk
Hess
R
emo
v
e c
u
t-off schemes from manual
commit
|
commitdiff
|
tree
2019-09-16
Szi
l
árd Páll
Eliminate unnecessary GPU stre
a
m dependency ca
l
l
commit
|
commitdiff
|
tree
2019-09-16
Berk H
e
ss
Add o
p
tion
r
equest
1
D
DD with 1 pulse
commit
|
commitdiff
|
tree
2019-09-16
K
evin Boyd
Remove group scheme from de
p
recated release n
o
tes
commit
|
commitdiff
|
tree
2019-09-15
P
a
s
cal
M
erz
I
n
t
roduce the modular
s
i
mulat
o
r
commit
|
commitdiff
|
tree
2019-09-15
P
e
ter Ka
s
son
Pat
c
h gmxa
p
i
f
or Python
3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric
Irrgang
Normalize u
s
age of
GMXTOOLCHAIND
I
R in gmxapi
s
etup
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
D
o
n
o
t
use
g
r
o
macs
-
t
o
olchain in darwin gmxap
i
builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric I
r
rgang
Up
d
ate
gmxapi setup
.
py
commit
|
commitdiff
|
tree
2019-09-12
Mark Abraham
D
i
sab
l
e
repor
t
-methods end-to-end test
commit
|
commitdiff
|
tree
2019-09-12
Szilárd Páll
Re
o
rganize on-GPU
P
ME force reduction flag
h
a
ndling
commit
|
commitdiff
|
tree
2019-09-12
Artem Zhmur
o
v
Change
P
adde
d
Vector to PaddedHostVe
c
tor for fo
r
c
e
CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Christi
a
n Bl
a
u
Ad
d
release note f
o
r densit
y
f
it
t
ing
.
commit
|
commitdiff
|
tree
2019-09-12
P
ascal
Merz
Update
modul
a
r
simula
t
or
tests
commit
|
commitdiff
|
tree
2019-09-12
Erik L
i
ndahl
A
dded SIMD
log2
and pow math functi
o
ns
commit
|
commitdiff
|
tree
2019-09-12
Eri
k
Lind
a
hl
Update SIMD
math tes
t
s
a
nd
im
p
rove a
c
curacy
commit
|
commitdiff
|
tree
2019-09-11
P
a
u
l Bauer
Rem
o
v
e -sub optio
n
f
r
om trj
c
onv
commit
|
commitdiff
|
tree
2019-09-11
Ar
t
em Zhmurov
Fix
f
or the post
-
submit fai
l
ure
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Decou
p
le GPU force buff
e
r ma
n
agement from buf
f
er ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrg
a
ng
U
s
e GR
O
MACS C
M
ake toolchai
n
file for gmxapi Pyth
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
P
aul Ba
u
er
Bas
i
c toolchain to faci
l
it
a
te GMXAPI b
u
i
l
d
commit
|
commitdiff
|
tree
2019-09-11
M
.
Er
i
c Irrgan
g
Add
gmx
a
pi
.
mod
i
fy_input o
p
era
t
ion
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
P
r
ovide a gmxap
i
.
read_tpr oper
a
tion
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Upda
t
e gmx
a
pi
.
simulation
.
c
o
nt
e
xt details
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Upda
t
e
gmxapi Py
t
ho
n
p
ackage infras
t
ructure for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
ric Irrgang
Normalize some testing resources for the P
y
t
h
o
n
p
ackages
.
commit
|
commitdiff
|
tree
2019-09-11
Magnu
s
Lundborg
Tidy
u
p
the FE kernel
commit
|
commitdiff
|
tree
2019-09-10
Paul
B
auer
Fix ni
g
htly buil
d
commit
|
commitdiff
|
tree
2019-09-10
Szilárd Páll
Use t
h
rea
d
-MP
I
in the gpucomm
m
atrix
commit
|
commitdiff
|
tree
2019-09-10
Pascal Me
r
z
Co
o
rdi
n
a
te Propagator
s
commit
|
commitdiff
|
tree
2019-09-10
Pascal M
e
rz
St
a
tePropagatorData
:
Intro
d
u
c
ed const box accessor
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal Me
r
z
A
dd trivial
c
onst qualifiers to shellfc and
EnergyOutput
commit
|
commitdiff
|
tree
2019-09-10
Pa
s
cal Me
r
z
Co
n
straint element for the modular
s
i
mulator
commit
|
commitdiff
|
tree
2019-09-09
S
zilárd Páll
Pass gmx::
F
o
r
ceF
l
ags
to CPU nbnxm dispatch code
commit
|
commitdiff
|
tree
2019-09-09
Szilárd
P
á
ll
Pass
t
he new gmx::ForceFlags to
the
n
bnxm modu
l
e
commit
|
commitdiff
|
tree
2019-09-09
Berk
He
s
s
Re
m
ove incorrect c
h
eck with rf-zero
commit
|
commitdiff
|
tree
2019-09-09
Pas
c
al Merz
Domain
decomposition and PME load ba
l
ancing
f
or modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Relative entropy
a
s d
e
n
sity similari
t
y measur
e
commit
|
commitdiff
|
tree
2019-09-09
Paul
Bauer
Add gmx c
o
n
v
ert-trj
commit
|
commitdiff
|
tree
2019-09-09
Berk Hes
s
Rename DDSetup to DDGridSet
u
p
commit
|
commitdiff
|
tree
2019-09-09
Berk Hes
s
C
l
ean up PME rank
v
ariables
commit
|
commitdiff
|
tree
2019-09-09
B
erk
Hess
Re
f
act
o
r init_domain_decom
p
osit
i
o
n
(
)
commit
|
commitdiff
|
tree
2019-09-07
Pascal Merz
Ma
k
e pme_loadbal_do(
)
independent of t_sta
t
e
commit
|
commitdiff
|
tree
2019-09-07
Pascal Merz
ForceEl
e
ment an
d
ShellFCElement
for the mo
d
ul
a
r
s
imulator
commit
|
commitdiff
|
tree
2019-09-06
Szilár
d
Páll
Add gpu
u
pdate and gp
u
comm OnDem
a
nd tokens
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Ex
t
ract gettin
g
of DDRank
S
et
u
p
commit
|
commitdiff
|
tree
2019-09-06
Berk
Hess
Add PP grid info
t
o DDRankSetup
commit
|
commitdiff
|
tree
2019-09-05
Mark Abraham
Update mdrun t
e
st comp
a
rison
i
nfrastru
c
tur
e
commit
|
commitdiff
|
tree
2019-09-05
Pascal Mer
z
R
ename
MicroState to Stat
e
PropagatorD
a
ta for modular
.
.
.
commit
|
commitdiff
|
tree
next