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Use GPU halo exchange only when compatible DD is available
2019-09-19
Ma
r
k Ab
r
aham
Use GPU ha
l
o
e
xc
h
a
nge onl
y
when compatible DD
is avail
a
ble
commit
|
commitdiff
|
tree
2019-09-19
Mark Abraha
m
F
urthe
r
improve getDDGr
i
dSetup
commit
|
commitdiff
|
tree
2019-09-19
Pa
u
l Ba
u
er
Add bas
i
c
interface
t
o run u
p
dat
e
on GPU
commit
|
commitdiff
|
tree
2019-09-19
Berk H
e
ss
Add haveFree
E
nergyWork to Dom
a
inLif
e
t
imeWorkload flags
commit
|
commitdiff
|
tree
2019-09-19
Chr
i
s
tian Blau
C
o
nsistently change densityfitting spreading wei
g
ht
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Added free-energy
k
ernel performanc
e
n
ote
commit
|
commitdiff
|
tree
2019-09-18
Berk Hes
s
Fix incorrect DD ndim
a
sserti
o
n
commit
|
commitdiff
|
tree
2019-09-18
Pascal Me
r
z
v-rescale the
r
mostat for modula
r
simulator
commit
|
commitdiff
|
tree
2019-09-18
Pa
u
l B
a
uer
Read
TPR file body
i
n
b
u
ffer
commit
|
commitdiff
|
tree
2019-09-18
Alan Gray
G
P
U Force Ha
l
o Exchange
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
F
ix p
o
s
iti
o
n p
i
nning
f
o
r
modula
r
si
m
ulator
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remo
v
e obsolete
mdp op
t
ion
ns-type
commit
|
commitdiff
|
tree
2019-09-16
ejjordan
A
d
d some cool quotes
commit
|
commitdiff
|
tree
2019-09-16
Paul Bauer
F
orma
t
ting fixes for refere
n
ce ma
n
ual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Er
i
c
I
r
r
gan
g
Add gmxapi
r
elease notes
.
commit
|
commitdiff
|
tree
2019-09-16
Alan Gray
GPU halo exchange
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
Hess
Add virtual site type 2FD
commit
|
commitdiff
|
tree
2019-09-16
Mark Abraham
Avoid shor
t
-range GPU operations with
no work
commit
|
commitdiff
|
tree
2019-09-16
B
e
rk Hess
Remove c
u
t-off
schemes f
r
om manual
commit
|
commitdiff
|
tree
2019-09-16
Szi
l
á
rd Páll
Elim
i
na
t
e
u
nnecessary GPU stream
dep
e
ndency c
a
ll
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add option request 1D DD with 1 pulse
commit
|
commitdiff
|
tree
2019-09-16
Kevin B
o
yd
Remove group sch
e
me from depre
c
ated
r
elease notes
commit
|
commitdiff
|
tree
2019-09-15
Pascal Merz
Introduce the modular simu
l
ator
commit
|
commitdiff
|
tree
2019-09-15
Peter Kasson
Patch
g
m
x
api for P
y
tho
n
3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgan
g
Normalize usage of GM
X
TOOLCHAINDIR in gmxapi setup
.
p
y
commit
|
commitdiff
|
tree
2019-09-13
M
.
Er
i
c Irrgang
Do not use gromacs-toolchain in
d
arw
i
n
g
mxa
p
i buil
d
s
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric
I
rrg
a
ng
Update gmxapi setup
.
py
commit
|
commitdiff
|
tree
2019-09-12
Ma
r
k Abraham
Disab
l
e
r
e
p
ort-me
t
hods
end-to-
e
nd test
commit
|
commitdiff
|
tree
2019-09-12
Szilárd Páll
Reorganize on-GPU PME force reduction flag
handling
commit
|
commitdiff
|
tree
2019-09-12
A
r
tem Z
h
m
u
rov
Change Pa
d
ded
V
ector to Pad
d
e
d
H
ostVe
c
t
or for force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
C
hristian Blau
Add relea
s
e n
o
te
f
o
r density fitti
n
g
.
commit
|
commitdiff
|
tree
2019-09-12
Pascal Merz
Updat
e
modu
l
ar simulator tests
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindahl
Added SIMD log2 an
d
pow math
functions
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindahl
U
p
date SIMD math tests
and improve a
c
curacy
commit
|
commitdiff
|
tree
2019-09-11
Paul Bauer
Remove -sub option f
r
om
t
rjconv
commit
|
commitdiff
|
tree
2019-09-11
Ar
t
em Zhm
u
ro
v
F
i
x for the
p
o
st-submit failure
commit
|
commitdiff
|
tree
2019-09-11
Artem
Zhmurov
Deco
u
ple GPU force buff
e
r manag
e
m
e
nt
f
rom buff
e
r ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Use GROMACS C
M
ake toolchain file for g
m
xapi P
y
t
h
on
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Paul Bauer
Basic toolcha
i
n to fa
c
il
i
tate GM
X
A
P
I
buil
d
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric I
r
rgang
Add gmxapi
.
mod
i
f
y
_i
n
put ope
r
ation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eri
c
Irrga
n
g
Prov
i
d
e
a gmxapi
.
read_tpr operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric I
r
rgang
Upda
t
e gmxa
p
i
.
simul
a
t
io
n
.
conte
x
t details
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
U
p
date gmxapi
P
ython package infrastruct
u
r
e
for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Er
i
c Irrgang
Nor
m
alize som
e
t
e
sting
r
esources for the Python
p
a
c
kages
.
commit
|
commitdiff
|
tree
2019-09-11
Ma
g
nus L
u
n
d
borg
Ti
d
y up t
h
e FE kernel
commit
|
commitdiff
|
tree
2019-09-10
Paul Baue
r
F
ix
n
ightly build
commit
|
commitdiff
|
tree
2019-09-10
Szilárd Páll
Use thread-MPI in
the gpucomm ma
t
rix
commit
|
commitdiff
|
tree
2019-09-10
Pascal
M
erz
Coordin
a
te Propaga
t
ors
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
S
tateP
r
opagatorData: Introduced const
b
o
x
ac
c
essor
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
Add trivi
a
l const
q
u
a
li
f
iers to shellfc and Energy
O
utput
commit
|
commitdiff
|
tree
2019-09-10
Pasca
l
Me
r
z
Constraint
elem
e
nt
for the modular simulator
commit
|
commitdiff
|
tree
2019-09-09
Szilárd Páll
Pass
g
mx::ForceFla
g
s to CPU n
b
nxm
d
ispatch co
d
e
commit
|
commitdiff
|
tree
2019-09-09
Szilárd Páll
Pass the new
g
m
x::ForceF
l
a
g
s to the nb
n
x
m
mod
u
l
e
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Re
m
ove
i
ncorre
c
t chec
k
wit
h
rf-zero
commit
|
commitdiff
|
tree
2019-09-09
P
a
scal Merz
Domain decomposition
and PME load balancing for modul
a
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
C
h
ristian Blau
Rel
a
tive entro
p
y as densit
y
similarity m
e
asure
commit
|
commitdiff
|
tree
2019-09-09
Paul Bauer
A
dd g
m
x
convert-trj
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Rena
m
e DDSetup to DD
G
r
idSetup
commit
|
commitdiff
|
tree
2019-09-09
B
e
rk He
s
s
Clea
n
u
p
PME rank v
a
r
i
a
bles
commit
|
commitdiff
|
tree
2019-09-09
B
e
r
k H
e
ss
Refactor
i
nit_doma
i
n
_decomposition()
commit
|
commitdiff
|
tree
2019-09-07
Pascal
Merz
Make pme_l
o
a
d
bal_d
o
() independent of t_stat
e
commit
|
commitdiff
|
tree
2019-09-07
Pascal
M
e
r
z
Force
E
lement and She
l
lFCE
l
eme
n
t
for the modular simulator
commit
|
commitdiff
|
tree
2019-09-06
Sz
i
lárd Páll
Add
gpuupdate and gp
u
c
omm
OnDemand tokens
commit
|
commitdiff
|
tree
2019-09-06
Berk H
e
ss
Extract getting of D
D
RankSe
t
up
commit
|
commitdiff
|
tree
2019-09-06
B
erk H
e
ss
Add PP grid
i
nfo to DDRankSet
u
p
commit
|
commitdiff
|
tree
2019-09-05
Mark
A
braham
Update mdrun test compa
r
ison i
n
frastruct
u
re
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
Rename MicroState
t
o
StatePropagatorData for mo
d
ular
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
Christian Blau
Add refere
n
c
e den
s
ity file option to densityf
i
t
t
ing
commit
|
commitdiff
|
tree
2019-09-05
Berk
H
ess
Spli
t
off gett
i
ng of the DD se
t
up
commit
|
commitdiff
|
tree
2019-09-04
Szilárd Páll
Bu
m
p ARM HPC to
o
lch
a
i
n
in post-s
u
bmit to v19
.
3
commit
|
commitdiff
|
tree
2019-09-04
Sz
i
lár
d
P
áll
A
d
d b
a
ck
a c
l
ang-tidy
e
x
c
ep
t
ion
commit
|
commitdiff
|
tree
2019-09-04
Chr
i
st
i
an Bla
u
Read mrc file usi
n
g file n
a
me
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Mov
e
u
pdate grouping to
D
DSys
t
emInfo
commit
|
commitdiff
|
tree
2019-09-04
M
agnu
s
L
u
n
dborg
I
nline fun
c
tions of calculations of FE intera
c
t
i
on
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Berk Hes
s
Change DD pme for
c
e buffe
r
to std:
:
ve
c
t
o
r
commit
|
commitdiff
|
tree
2019-09-04
Berk H
e
ss
Initialize a
l
l members
of gmx_domdec_t
commit
|
commitdiff
|
tree
2019-09-03
M
.
Eri
c
I
r
rgang
Python wrappi
n
g code for gmxapi mdrun b
i
n
d
ings
.
commit
|
commitdiff
|
tree
2019-09-03
Pas
c
al Merz
Introduce energy element for mod
u
lar simulator
commit
|
commitdiff
|
tree
2019-09-03
Mark
A
braham
Simpli
f
y e
n
erg
y
-file com
p
aris
o
n
s in tests
commit
|
commitdiff
|
tree
2019-09-03
Artem Zhmurov
Add Parr
i
nello-R
a
hman pressure coupling
t
o CUDA
Leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-02
B
e
rk
Hes
s
Only
u
s
e fshift
w
hen needed
commit
|
commitdiff
|
tree
2019-09-01
C
hristian
B
lau
Add checkpointing for MdModu
l
es
commit
|
commitdiff
|
tree
2019-08-30
Christi
a
n
B
la
u
LocalAtomSet
c
onstruction with vectors of gmx::index
commit
|
commitdiff
|
tree
2019-08-30
M
.
E
r
ic Irrg
a
n
g
Import bas
e
code for Python-driven simul
a
tion from
.
.
.
commit
|
commitdiff
|
tree
2019-08-30
Magnus Lundborg
C
h
a
nged some v
a
riables f
r
om
S
C
Real t
o
r
e
al in FE ke
r
nel
.
commit
|
commitdiff
|
tree
2019-08-30
Christi
a
n Blau
I
m
plementing the
density fitting f
o
rc
e
provid
e
r
commit
|
commitdiff
|
tree
2019-08-29
M
a
rk Abra
h
a
m
More quo
t
es
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Introduce signallers for modular
i
n
tegrator
commit
|
commitdiff
|
tree
2019-08-28
Pau
l
Bauer
Fix ret
u
rn value
commit
|
commitdiff
|
tree
2019-08-28
Mark Abraham
Fix int
e
gration issues
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
In
t
r
oduce the mai
n
modul
a
r simulator interfac
e
s
a
nd
.
.
.
commit
|
commitdiff
|
tree
2019-08-28
Paul Ba
u
er
Change tole
r
ance
for norm
a
l
mode te
s
ts
commit
|
commitdiff
|
tree
2019-08-28
Szilárd Páll
Add cl
a
ng-tidy
nightly
t
est with
SIMD + OpenCL
commit
|
commitdiff
|
tree
2019-08-28
Szilár
d
Páll
M
ove nonb
o
nded
G
P
U wait timing in
t
o t
h
e GPU module
commit
|
commitdiff
|
tree
2019-08-27
Mark Abraham
Add i
n
teg
r
ation tests for exact restarts
commit
|
commitdiff
|
tree
2019-08-27
Christian Bla
u
Add
d
ens
i
ty fitting
parameters
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Access to Gaus
s
Transfor
m
3D
data
commit
|
commitdiff
|
tree
2019-08-27
Chris
t
ia
n
Blau
A
d
d
index
g
roup
o
ption
to
d
ensity f
i
tting
commit
|
commitdiff
|
tree
2019-08-26
P
a
ul Bauer
Remove se
c
t
ion checking api
l
evel
commit
|
commitdiff
|
tree
2019-08-26
Pa
u
l Ba
u
e
r
R
e
mo
v
e installed
h
e
aders from CMak
e
commit
|
commitdiff
|
tree
next