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StatePropagatorDataGpu object to manage GPU forces, positions and velocities buffers
2019-10-01
Artem
Z
hmurov
Sta
t
e
Pr
o
pagatorDataGp
u
o
bj
e
ct to
ma
n
ag
e
GP
U
forc
e
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Mark Abraham
Fix icc wa
r
nings
commit
|
commitdiff
|
tree
2019-10-01
Berk
H
ess
C
o
mpletely re
m
ove charge gro
u
p
s
commit
|
commitdiff
|
tree
2019-10-01
Christ
o
ph Junghans
c
ma
k
e: add miss
i
ng header to legacy a
p
i
commit
|
commitdiff
|
tree
2019-10-01
Mark Ab
r
aham
Removed dependency on commre
c
of mdrun s
e
tu
p
commit
|
commitdiff
|
tree
2019-09-30
Carsten Kutzner
Move ForceP
r
o
v
iders class i
n
to the gmx n
a
mespace
commit
|
commitdiff
|
tree
2019-09-30
M
a
rk Abr
a
ham
Ma
k
e a
b
uilder f
o
r DD
commit
|
commitdiff
|
tree
2019-09-30
B
e
rk Hess
Rem
o
ve charge gr
o
up cod
e
from forcerec
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Páll
Make the
w
ait
on PME GP
U
r
esults conditiona
l
commit
|
commitdiff
|
tree
2019-09-27
M
ark Abra
h
am
Improve
M
iMiC test implementation
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraha
m
Fix
gro f
i
l
e
output with
i
ndex groups
commit
|
commitdiff
|
tree
2019-09-27
M
a
r
k Abraham
Remove leftover s
u
pport for p
r
e-9
.
0 CUD
A
commit
|
commitdiff
|
tree
2019-09-24
P
au
l
B
a
uer
Add test
for n
o
append
commit
|
commitdiff
|
tree
2019-09-24
Ma
r
k Abraham
Fi
x
n
o
-MPI CUDA
b
ui
l
d
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
Merge "
M
erge
bran
c
h re
l
eas
e
-2019
i
nto master
"
commit
|
commitdiff
|
tree
2019-09-24
M
a
rk Abra
h
am
Fix c
l
a
ng unused-funct
i
on
warnin
g
s
commit
|
commitdiff
|
tree
2019-09-24
Paul Bauer
Add
release notes for modular si
m
u
l
ator
commit
|
commitdiff
|
tree
2019-09-23
Paul
B
a
uer
F
i
x issues when
P
M
E ra
n
k re
q
ue
s
t becomes negati
v
e
commit
|
commitdiff
|
tree
2019-09-23
Paul Bauer
Change
MPI s
e
t
up to com
m
uni
c
ate TPR as
b
uffer
commit
|
commitdiff
|
tree
2019-09-23
Pasc
a
l
M
erz
Zero pressu
r
e a
n
d virial tenso
r
s
at beginning of st
e
p
commit
|
commitdiff
|
tree
2019-09-23
P
ascal Merz
I
ntr
o
duce FEP into mo
d
ular simulator
commit
|
commitdiff
|
tree
2019-09-22
Christoph Junghans
workaround for rhe
l
bug #1749463, cmake bug #18349
commit
|
commitdiff
|
tree
2019-09-22
Paul B
a
uer
Rem
o
ve
upd
a
te flag again
commit
|
commitdiff
|
tree
2019-09-22
Berk He
s
s
Re
m
ove c
g
s
_
gl from gmx_domdec
_
c
omm_t
commit
|
commitdiff
|
tree
2019-09-20
M
ark
A
brah
a
m
Refa
c
tor
to create a GpuTa
s
k
Assignment
s
o
b
j
e
ct
commit
|
commitdiff
|
tree
2019-09-19
B
e
rk Hess
Remove bLocal
C
G
fr
o
m DD co
d
e
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove obso
l
ete make_exclusions_zone_cg()
commit
|
commitdiff
|
tree
2019-09-19
Christian Bla
u
Check input record al
s
o in tests
commit
|
commitdiff
|
tree
2019-09-19
Mark Abra
h
am
U
s
e GPU
h
a
l
o e
x
ch
a
nge o
n
ly when compa
t
i
b
le DD is av
a
i
l
able
commit
|
commitdiff
|
tree
2019-09-19
M
ark
Abraham
Fu
r
ther improve getD
D
GridSetup
commit
|
commitdiff
|
tree
2019-09-19
Paul Ba
u
er
Add b
a
si
c
inter
f
ace t
o
r
un update
on GPU
commit
|
commitdiff
|
tree
2019-09-19
Berk He
s
s
Add haveFreeEn
e
rgyWork
t
o Doma
i
n
L
ifetim
e
Workl
o
ad flags
commit
|
commitdiff
|
tree
2019-09-19
C
h
r
istia
n
Blau
Consis
t
ently
chan
g
e densityf
i
tting
spreading weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Ad
d
ed free-e
n
ergy kernel perfor
m
ance
n
ote
commit
|
commitdiff
|
tree
2019-09-18
Be
r
k
H
e
s
s
Fix incorrect DD
ndim asse
r
tion
commit
|
commitdiff
|
tree
2019-09-18
Pasca
l
Me
r
z
v-rescal
e
t
h
e
r
mostat for
m
odular
s
imul
a
tor
commit
|
commitdiff
|
tree
2019-09-18
Paul Baue
r
Read
TPR file body in buffer
commit
|
commitdiff
|
tree
2019-09-18
Alan Gray
GPU Force Halo Exc
h
ange
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix position pinning
f
or
modul
a
r
si
m
ulato
r
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remove obsolete mdp optio
n
ns-
t
ype
commit
|
commitdiff
|
tree
2019-09-16
ejjordan
Ad
d
s
ome co
o
l quotes
commit
|
commitdiff
|
tree
2019-09-16
P
a
ul Bauer
Formatting fixes for refere
n
ce manual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Eric Irrgang
A
d
d
g
mxapi release notes
.
commit
|
commitdiff
|
tree
2019-09-16
Alan Gr
a
y
GP
U
halo ex
c
h
ange
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add
virtual
s
ite t
y
pe 2FD
commit
|
commitdiff
|
tree
2019-09-16
Mark Abraha
m
Avo
i
d short-rang
e
GPU operat
i
o
n
s with no work
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remove cut-off s
c
hemes from manual
commit
|
commitdiff
|
tree
2019-09-16
Szil
á
rd Páll
Eliminate unnec
e
ssary GPU stream dependency
call
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
Hess
Add
o
p
tion request 1
D
DD with
1
puls
e
commit
|
commitdiff
|
tree
2019-09-16
Kevin
Boy
d
Remove
g
roup scheme from deprecat
e
d release notes
commit
|
commitdiff
|
tree
2019-09-15
Pascal Merz
Introduce
t
he modul
a
r
simu
l
ator
commit
|
commitdiff
|
tree
2019-09-15
Pet
e
r K
a
sson
Pa
t
c
h gmxapi f
o
r Pyt
h
on 3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric
Irrgang
N
ormalize u
s
age of GMXTOOLCHAI
N
DIR in gmxapi setup
.
p
y
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
D
o not
u
se gro
m
ac
s
-to
o
lchain in darwin gmxapi b
u
i
lds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
E
ric
I
rrgang
Update gmxa
p
i setup
.
p
y
commit
|
commitdiff
|
tree
2019-09-12
Ma
r
k Abraham
Disable
re
p
ort-methods
e
nd-to-end
te
s
t
commit
|
commitdiff
|
tree
2019-09-12
Szi
l
árd Páll
Reo
r
g
a
nize on-GPU
P
ME force reduction flag handlin
g
commit
|
commitdiff
|
tree
2019-09-12
A
rtem Zhmurov
Change
P
a
ddedVec
t
or to PaddedHostVector f
o
r force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Ch
r
istian Blau
Add release note for density fitting
.
commit
|
commitdiff
|
tree
2019-09-12
Pascal Merz
Update modul
a
r simula
t
o
r tests
commit
|
commitdiff
|
tree
2019-09-12
Erik Li
n
dahl
Added SIM
D
log2
and pow math functions
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindahl
U
p
d
a
t
e SIMD
math tests and impr
o
ve accu
r
a
cy
commit
|
commitdiff
|
tree
2019-09-11
P
a
ul Bauer
Remove -sub optio
n
fro
m
trjconv
commit
|
commitdiff
|
tree
2019-09-11
Artem
Z
hmurov
Fix for the post-submit fail
u
re
commit
|
commitdiff
|
tree
2019-09-11
Artem
Zhmurov
D
e
c
o
uple GPU for
c
e buffer
m
anagement from buffer ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric
I
rrg
a
n
g
U
se GROMACS CMake tool
c
h
ain fil
e
for g
m
xapi Python
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Paul Ba
u
e
r
B
a
sic toolchain
t
o
fac
i
lit
a
te GMXAPI
b
uild
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
A
dd
g
mxapi
.
modify_input oper
a
tion
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
r
ic Irr
g
ang
Provide a gmxap
i
.
read_tpr operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
U
p
date gmxa
p
i
.
simulation
.
contex
t
details
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irr
g
ang
Update gmx
a
pi
Pytho
n
package infrastruct
u
r
e for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Ir
r
gang
Normalize some te
s
ting resources for th
e
Python packages
.
commit
|
commitdiff
|
tree
2019-09-11
M
a
gnus Lundborg
Tidy up
t
he FE ke
r
nel
commit
|
commitdiff
|
tree
2019-09-10
Pau
l
Bauer
Fix nightly build
commit
|
commitdiff
|
tree
2019-09-10
S
z
ilárd
P
áll
Us
e
thread-MP
I
i
n
the gpucom
m
m
atrix
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
Coor
d
inate Propagato
r
s
commit
|
commitdiff
|
tree
2019-09-10
Pascal
Merz
StatePropag
a
torDa
t
a: Introdu
c
e
d
const box accessor
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
A
d
d
t
rivial const qualifiers to shellfc and
EnergyOutput
commit
|
commitdiff
|
tree
2019-09-10
P
a
scal Me
r
z
Constraint elem
e
n
t for th
e
modular
simula
t
or
commit
|
commitdiff
|
tree
2019-09-09
Szilár
d
P
á
ll
Pass gmx::Force
F
l
a
g
s t
o
CPU nbnx
m
d
ispatch c
o
d
e
commit
|
commitdiff
|
tree
2019-09-09
Szilárd
P
áll
Pass the new gm
x
:
:
F
o
r
ceFla
g
s to the nb
n
xm mo
d
ule
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Re
m
o
v
e
in
c
orrect check with rf-ze
r
o
commit
|
commitdiff
|
tree
2019-09-09
P
ascal M
e
rz
Domain decompo
s
ition and PME load b
a
lancing for modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Chri
s
tian
B
lau
Re
l
ative ent
r
o
p
y a
s
density similarity measure
commit
|
commitdiff
|
tree
2019-09-09
P
aul Bauer
Add gmx con
v
ert-trj
commit
|
commitdiff
|
tree
2019-09-09
Berk He
s
s
R
en
a
me DDSetup to DD
G
ridSet
u
p
commit
|
commitdiff
|
tree
2019-09-09
Berk
Hess
Clean up PME rank variabl
e
s
commit
|
commitdiff
|
tree
2019-09-09
Be
r
k Hess
Refact
o
r in
i
t_domain_de
c
omposit
i
o
n()
commit
|
commitdiff
|
tree
2019-09-07
Pascal Merz
Make pme_loadb
a
l_do()
independent of t_state
commit
|
commitdiff
|
tree
2019-09-07
Pas
c
al Merz
ForceElement
and ShellFCElement fo
r
the modular si
m
ulator
commit
|
commitdiff
|
tree
2019-09-06
S
z
ilárd
P
áll
Add gpuupdate and gp
u
comm OnDemand tokens
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Extr
a
ct g
e
t
tin
g
of DDRankSetup
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Add
P
P gr
i
d
i
nfo to DDRank
S
etup
commit
|
commitdiff
|
tree
2019-09-05
Mark Abraham
Update mdrun test comparison infrastructure
commit
|
commitdiff
|
tree
2019-09-05
Pa
s
c
al Merz
Rename MicroState to Stat
e
PropagatorData
f
or modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
Christian Blau
Add reference den
s
i
t
y f
i
le option to de
n
sityfittin
g
commit
|
commitdiff
|
tree
2019-09-05
B
e
rk Hess
S
p
l
it off getting of th
e
DD setup
commit
|
commitdiff
|
tree
2019-09-04
Szilárd
P
áll
Bump ARM HPC
t
oolch
a
i
n
in p
o
st-
s
ubmit to
v19
.
3
commit
|
commitdiff
|
tree
2019-09-04
Szil
á
rd Páll
Add back a clan
g
-tid
y
e
xception
commit
|
commitdiff
|
tree
2019-09-04
Chris
t
ian Blau
R
ead m
r
c fi
l
e usin
g
f
ile
n
a
m
e
commit
|
commitdiff
|
tree
next