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StatePropagatorDataGpu object to manage GPU forces, positions and velocities buffers
2019-10-01
Artem Zh
m
u
r
o
v
StatePr
o
pagat
o
r
D
ataGpu object to mana
g
e GPU
fo
r
ces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Mark
A
brah
a
m
Fix icc
w
arnings
commit
|
commitdiff
|
tree
2019-10-01
B
e
r
k
Hess
Compl
e
tel
y
r
emov
e
char
g
e groups
commit
|
commitdiff
|
tree
2019-10-01
C
h
r
is
t
oph Junghans
cmake: add missing header to legacy api
commit
|
commitdiff
|
tree
2019-10-01
Mark Abraham
Removed dependency
o
n com
m
rec of mdrun setup
commit
|
commitdiff
|
tree
2019-09-30
Carsten Kutzner
Mov
e
Force
P
r
o
viders class
i
nto
t
he g
m
x name
s
pace
commit
|
commitdiff
|
tree
2019-09-30
M
ark Abraham
M
ake a build
e
r for
D
D
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Remove charge
g
rou
p
code from forcerec
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Páll
Make the wai
t
on PME GPU r
e
sults cond
i
tional
commit
|
commitdiff
|
tree
2019-09-27
M
a
rk Abra
h
am
Improv
e
MiMiC tes
t
impl
e
m
ent
a
tion
commit
|
commitdiff
|
tree
2019-09-27
M
ark Abraham
F
i
x gr
o
f
ile o
u
tput with
index gro
u
ps
commit
|
commitdiff
|
tree
2019-09-27
Mark Abrah
a
m
Rem
o
ve left
o
ver support for p
r
e-9
.
0 CUDA
commit
|
commitdiff
|
tree
2019-09-24
P
aul Ba
u
e
r
Add t
e
st for noappe
n
d
commit
|
commitdiff
|
tree
2019-09-24
Mark Ab
r
aham
Fix
no-MPI CUDA build
commit
|
commitdiff
|
tree
2019-09-24
Mark A
b
raham
Merge
"
M
erge bra
n
c
h rele
a
se-2019 into mas
t
er"
commit
|
commitdiff
|
tree
2019-09-24
Mark Ab
r
aham
Fix clang unused-function warn
i
ngs
commit
|
commitdiff
|
tree
2019-09-24
Paul B
a
uer
Add release not
e
s
for modular simulator
commit
|
commitdiff
|
tree
2019-09-23
Paul Bauer
Fix
i
s
sues when PME rank request becomes
negati
v
e
commit
|
commitdiff
|
tree
2019-09-23
Paul
Ba
u
er
Change MPI setup
to co
m
municate TP
R
as buffer
commit
|
commitdiff
|
tree
2019-09-23
Pascal
M
er
z
Zero
pressur
e
and virial tensors at beginni
n
g of s
t
ep
commit
|
commitdiff
|
tree
2019-09-23
Pascal Mer
z
Introduce FEP into modular simulator
commit
|
commitdiff
|
tree
2019-09-22
Chr
i
s
t
op
h
Junghans
workarou
n
d for rhel bug #
1
749463, cmake bug #18349
commit
|
commitdiff
|
tree
2019-09-22
Paul B
a
ue
r
Remo
v
e
u
pdate flag again
commit
|
commitdiff
|
tree
2019-09-22
Berk He
s
s
Remov
e
cgs_gl
from gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-20
Mark Abraham
Ref
a
ct
o
r
to crea
t
e a G
p
uT
a
skAssign
m
ents object
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remov
e
bLocalCG fr
o
m DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
R
e
move
o
bsolete make_exclusions_
z
one_cg()
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Check input re
c
ord
a
lso in tests
commit
|
commitdiff
|
tree
2019-09-19
Mark Abraha
m
Use GPU halo exchange
only when c
o
mpatibl
e
D
D is availa
b
l
e
commit
|
commitdiff
|
tree
2019-09-19
Mark Abraham
Furt
h
er
i
m
prove getDDGri
d
Setu
p
commit
|
commitdiff
|
tree
2019-09-19
Paul Bauer
Ad
d
basic interf
a
ce
t
o run
u
pdate
o
n GPU
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Add h
a
veFre
e
EnergyWork to DomainLifetimeWor
k
load flags
commit
|
commitdiff
|
tree
2019-09-19
Ch
r
i
s
tia
n
Blau
Consist
e
ntly change densityfittin
g
s
p
re
a
ding weig
h
t
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Added fr
e
e-energy ke
r
nel performanc
e
note
commit
|
commitdiff
|
tree
2019-09-18
Berk H
e
ss
Fix incor
r
e
c
t DD ndim assertion
commit
|
commitdiff
|
tree
2019-09-18
P
ascal Merz
v-rescale thermo
s
tat for modular
simulator
commit
|
commitdiff
|
tree
2019-09-18
Paul B
a
u
e
r
Read TPR file b
o
dy in buffer
commit
|
commitdiff
|
tree
2019-09-18
Alan Gray
GPU Forc
e
Halo Excha
n
ge
commit
|
commitdiff
|
tree
2019-09-17
P
a
s
cal Merz
Fix positio
n
pinning for
m
o
d
ular simu
l
a
t
or
commit
|
commitdiff
|
tree
2019-09-16
Be
r
k
H
ess
Remove obsolete mdp option ns-type
commit
|
commitdiff
|
tree
2019-09-16
e
j
j
o
rdan
Add some cool quotes
commit
|
commitdiff
|
tree
2019-09-16
P
a
ul
Baue
r
F
o
rmatting
fixes
f
o
r
reference manual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Eric
I
r
r
gan
g
Add gmx
a
pi r
e
l
ease notes
.
commit
|
commitdiff
|
tree
2019-09-16
Alan Gray
GPU halo exchange
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
Hess
Add virtu
a
l site type 2FD
commit
|
commitdiff
|
tree
2019-09-16
Mark Abraha
m
Avoid sh
o
rt-range GPU
operations with
no work
commit
|
commitdiff
|
tree
2019-09-16
Be
r
k Hess
Re
m
ove cut-off sch
e
m
es from manual
commit
|
commitdiff
|
tree
2019-09-16
Szilá
r
d Páll
Elim
i
n
a
te
unne
c
essary GPU stream depen
d
ency call
commit
|
commitdiff
|
tree
2019-09-16
Berk H
e
s
s
Add option r
e
q
u
est
1D DD with 1 puls
e
commit
|
commitdiff
|
tree
2019-09-16
Kevin Boyd
Remove group scheme from d
e
pre
c
a
t
ed release notes
commit
|
commitdiff
|
tree
2019-09-15
Pasca
l
Merz
Introduce the
m
odular s
i
mulator
commit
|
commitdiff
|
tree
2019-09-15
Peter Kasson
Patch gmxapi for
P
yth
o
n
3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eri
c
Irrga
n
g
Normalize usage of
GMXTOOLCHAINDIR in gmx
a
pi
s
e
t
up
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric I
r
r
g
ang
Do
not use gromacs-toolchain in darwin gm
x
api builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric
Irrga
n
g
U
p
d
at
e
g
mx
a
pi setup
.
py
commit
|
commitdiff
|
tree
2019-09-12
M
a
rk Abra
h
am
Di
s
able report-me
t
hods end-to-end
t
est
commit
|
commitdiff
|
tree
2019-09-12
S
zilárd
Páll
Reorganize on-GPU PME force
r
ed
u
ctio
n
flag h
a
n
dl
i
ng
commit
|
commitdiff
|
tree
2019-09-12
Artem Zhmurov
Change Pa
d
dedVector to
PaddedHostVector for fo
r
ce
CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Ch
r
istian Blau
Add
rele
a
se
n
o
te for density fitting
.
commit
|
commitdiff
|
tree
2019-09-12
Pascal
Merz
Update modular
simu
l
ator tests
commit
|
commitdiff
|
tree
2019-09-12
E
r
ik Lind
a
h
l
Added SIMD log2 and pow math functions
commit
|
commitdiff
|
tree
2019-09-12
Er
i
k Lindahl
Update SIMD math tests
and improve accuracy
commit
|
commitdiff
|
tree
2019-09-11
Paul Bauer
Re
m
o
ve -sub option f
r
om trjc
o
nv
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Fix for t
h
e p
o
st-submit failure
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Decou
p
le GP
U
force buffe
r
management
fr
o
m buffer
ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgan
g
Use GROMAC
S
C
M
ake t
o
o
lchain file
f
o
r gmxap
i
P
y
thon
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Paul Bauer
Basic t
o
olchain
t
o facil
i
tate GMX
A
PI bu
i
l
d
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eri
c
Irrgang
Add gm
x
api
.
m
o
dify_i
n
put
o
peratio
n
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Provide a gmxapi
.
rea
d
_tpr ope
r
ati
o
n
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eri
c
Irrg
a
n
g
U
p
date gmxapi
.
simulation
.
context de
t
ails
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
U
p
date gmxapi
P
ython package in
f
rastructure for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eri
c
Ir
r
gang
Normalize some testing
resources for
t
h
e Pyt
h
on packages
.
commit
|
commitdiff
|
tree
2019-09-11
Mag
n
us Lundborg
Tid
y
up the
F
E k
e
rnel
commit
|
commitdiff
|
tree
2019-09-10
Paul Bauer
Fi
x
nig
h
tly build
commit
|
commitdiff
|
tree
2019-09-10
Szilárd Pá
l
l
Use
t
hread-
M
PI
i
n
t
he gp
u
comm ma
t
rix
commit
|
commitdiff
|
tree
2019-09-10
Pascal Me
r
z
Coo
r
dinate Pr
o
pagators
commit
|
commitdiff
|
tree
2019-09-10
Pascal
Merz
S
t
a
tePr
o
paga
t
orData: Introduced const box a
c
cessor
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal Me
r
z
Add tri
v
ial const qualifiers to shel
l
fc
a
nd EnergyOutput
commit
|
commitdiff
|
tree
2019-09-10
Pa
s
cal Merz
Co
n
straint element
f
or
t
h
e
modular simulator
commit
|
commitdiff
|
tree
2019-09-09
S
z
il
á
rd Páll
Pass gm
x
:
:ForceFlags to CPU nbnxm
di
s
patch c
o
de
commit
|
commitdiff
|
tree
2019-09-09
Szil
á
rd Pá
l
l
Pass the
new gm
x
::Forc
e
Flags
to the nbnxm module
commit
|
commitdiff
|
tree
2019-09-09
Berk
H
ess
Remove
i
ncorrect check
w
ith
r
f
-zero
commit
|
commitdiff
|
tree
2019-09-09
Pascal Merz
Domain decompos
i
t
i
on and PME load balanc
i
ng for
modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Relat
i
ve entropy as density similarity measure
commit
|
commitdiff
|
tree
2019-09-09
Paul
Bauer
A
dd gmx convert-trj
commit
|
commitdiff
|
tree
2019-09-09
Be
r
k Hess
Rename DDSetup to DDGridSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk
H
e
ss
Clean
u
p PME
rank v
a
r
iables
commit
|
commitdiff
|
tree
2019-09-09
Berk
H
ess
Refacto
r
init_domain_d
e
c
ompositio
n
()
commit
|
commitdiff
|
tree
2019-09-07
Pa
s
c
a
l
Mer
z
Make pme_loadbal_
d
o() independe
n
t of
t
_state
commit
|
commitdiff
|
tree
2019-09-07
P
ascal Mer
z
ForceEleme
n
t an
d
ShellFCElement for the modular simulator
commit
|
commitdiff
|
tree
2019-09-06
Szilárd
P
ál
l
A
d
d
g
puupdate an
d
gpucomm On
D
emand t
o
kens
commit
|
commitdiff
|
tree
2019-09-06
Be
r
k Hess
Ex
t
ract getting of DDRankSetup
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Ad
d
PP grid info t
o
DDRankSetup
commit
|
commitdiff
|
tree
2019-09-05
Mark Abraham
Up
d
ate mdrun test com
p
arison infrast
r
uctur
e
commit
|
commitdiff
|
tree
2019-09-05
Pascal
M
erz
Rena
m
e MicroSta
t
e to S
t
ate
P
r
opagatorData for modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
Christian Blau
Add r
e
fe
r
ence density file op
t
ion to densityfitting
commit
|
commitdiff
|
tree
2019-09-05
Berk
Hess
Spli
t
off get
t
ing of
t
h
e
DD set
u
p
commit
|
commitdiff
|
tree
2019-09-04
Szil
á
rd Páll
Bump A
R
M HP
C
too
l
chain in
post-submit
to v19
.
3
commit
|
commitdiff
|
tree
2019-09-04
Szilárd Páll
Add back a clan
g
-tidy ex
c
eption
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
Read mrc file using
file na
m
e
commit
|
commitdiff
|
tree
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