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Fix race condition in GPU X halo exchange with GPU update
2019-11-25
Alan Gray
Fix race con
d
ition in GPU
X halo exchange with
GPU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
Christ
i
an Blau
InM
e
morySeria
l
izer
w
i
th end
i
aness s
w
ap
.
commit
|
commitdiff
|
tree
2019-11-21
Mar
k
Abraham
New cool quote
commit
|
commitdiff
|
tree
2019-11-20
Art
e
m Zhmurov
A
dd
D
2H copies
f
or the
c
hec
k
pointing
commit
|
commitdiff
|
tree
2019-11-20
A
r
t
e
m Zhmurov
M
ove the copy of the
v
el
o
cities for the output clo
s
er
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
Be
r
k Hess
Quiet p
d
b2gmx and
u
se
gmx_
f
atal
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric Irrgang
Remove st
u
b cont
e
nt fr
o
m
g
m
xapi do
c
s
.
commit
|
commitdiff
|
tree
2019-11-16
Mark A
b
r
aham
R
e
laxed
li
s
te
d
forces te
s
t
tol
e
r
a
n
ces
commit
|
commitdiff
|
tree
2019-11-06
Berk Hess
Depre
c
a
t
ed
sc-r
-
power=48
commit
|
commitdiff
|
tree
2019-11-04
Paul Bauer
Add build for clang-
f
ormat
commit
|
commitdiff
|
tree
2019-11-04
Paul Bauer
Split
up source code forma
t
ting scripts
commit
|
commitdiff
|
tree
2019-11-04
T
e
emu Murtola
Update clang-format c
o
nfi
g
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
r
i
c
Irrgang
Improve uniformity
o
f
O
S X CMake config
u
ration
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrg
a
n
g
Rest
o
re CM
a
ke conve
n
ience target
s
for sampl
e
_r
e
s
traint
.
commit
|
commitdiff
|
tree
2019-10-31
Al
a
n Gray
Remove dead code for nbnxm H2D coordi
n
at
e
copy event
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
Bug fix fo
r
e
v
en
t
pa
s
sed to GPU comm
f
eatu
r
es
commit
|
commitdiff
|
tree
2019-10-31
P
a
sca
l
Merz
Check for contradicting environment variables (mo
d
u
l
ar
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Mark Abraham
Tes
t
s for vali
d
periodic acti
o
ns
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrga
n
g
Disable
its test
s
when sample_restraint i
s
not the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
Decrease
t
he
m
ax
i
mum allowed Pytho
n
version
for gmxapi
.
commit
|
commitdiff
|
tree
2019-10-29
A
rt
e
m Zhmurov
Disable G
P
U
upda
t
e whe
n
c
oord
i
na
t
e
s
swapping is enable
d
commit
|
commitdiff
|
tree
2019-10-24
Ber
k
H
e
ss
Add bool useDomainDecompositi
o
n
in mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add gmx_mtop_i
n
teract
i
on_cou
n
t()
commit
|
commitdiff
|
tree
2019-10-23
ejjo
r
dan
M
ak
e
t_nextnb an i
m
plement
a
tion detail
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Corr
e
c
t fo
r
ske
w
e
d
box b
e
fore domain dec
o
mpos
i
ti
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Ala
n
Gra
y
E
n
a
b
le GPU Peer
A
ccess in GPU Utilities
commit
|
commitdiff
|
tree
2019-10-22
ejjor
d
an
Remove unused fu
n
ctions from gm
x
pre
p
roces
s
commit
|
commitdiff
|
tree
2019-10-22
B
er
k
H
e
ss
R
e
q
uire -ei for essenti
a
l dy
n
amics
commit
|
commitdiff
|
tree
2019-10-22
ejjord
a
n
Remove un
u
sed functio
n
generate_excls and m
a
ke c
l
ean
_
excls
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
B
erk
H
ess
Const correctness for
g
e
nhydro
commit
|
commitdiff
|
tree
2019-10-15
P
a
ul
B
auer
Fi
x
b
ug in preprocessing
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eric
I
r
rga
n
g
Fix logic
e
r
ror in gmxapi
.
version
.
api_
i
s_at_least()
.
commit
|
commitdiff
|
tree
2019-10-13
Mark Ab
r
a
h
am
Ensure
e
nvironment
v
ariable
u
s
e
does
not
g
i
ve warning
s
commit
|
commitdiff
|
tree
2019-10-12
Berk Hes
s
Add
class
FixedCapacit
y
Vector
commit
|
commitdiff
|
tree
2019-10-12
A
r
te
m
Z
h
murov
Cen
t
ralize m
a
nag
e
ment of coordinates ready on GP
U
even
t
commit
|
commitdiff
|
tree
2019-10-08
Pras
h
anth Kandur
i
Fused two if b
r
anches with the sam
e
condi
t
ional
commit
|
commitdiff
|
tree
2019-10-02
Cars
t
en K
u
tzn
e
r
Update the www link t
o
the
D
oxygen
doc
u
mentation in
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
Berk H
e
ss
Fix harmless OpenMP write
r
ace
commit
|
commitdiff
|
tree
2019-10-02
Mark Abraha
m
Improve P
M
E t
e
sting
commit
|
commitdiff
|
tree
2019-10-01
Berk Hes
s
Use gmx::Ra
n
ge in domd
e
c
commit
|
commitdiff
|
tree
2019-10-01
Ar
t
em Zhmurov
StatePro
p
aga
t
orData
G
pu object to man
a
ge GPU
f
or
c
es
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Mark Ab
r
aham
Fix icc warnings
commit
|
commitdiff
|
tree
2019-10-01
Berk
Hess
Completely r
e
move charge groups
commit
|
commitdiff
|
tree
2019-10-01
Paul Bauer
F
i
x chain
ID handlin
g
in ma
k
e_
n
d
x
commit
|
commitdiff
|
tree
2019-10-01
Christoph J
u
n
g
hans
cmake: add missi
n
g header to legacy api
commit
|
commitdiff
|
tree
2019-10-01
Mark Abr
a
ham
Removed dependency on commrec
of mdrun
setup
commit
|
commitdiff
|
tree
2019-09-30
Car
s
t
e
n K
u
tzne
r
Move
ForceProvid
e
rs cla
s
s
into the gmx namespace
commit
|
commitdiff
|
tree
2019-09-30
Mark Abraham
Mak
e
a bui
l
der for DD
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Remov
e
c
h
arge group
code from f
o
rcer
e
c
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Páll
Make the wait on PME GP
U
r
esults c
o
n
d
itional
commit
|
commitdiff
|
tree
2019-09-27
M
a
rk
A
braham
Impr
o
ve MiMiC test implementation
commit
|
commitdiff
|
tree
2019-09-27
Mark Abrah
a
m
Fix gro f
i
l
e
output
w
i
th i
n
dex
g
r
oup
s
commit
|
commitdiff
|
tree
2019-09-27
Mark Abr
a
ham
F
ix
gro
file output with i
n
dex groups
commit
|
commitdiff
|
tree
2019-09-27
Ma
r
k
Abraham
Remov
e
leftover support for pre-9
.
0 CUDA
commit
|
commitdiff
|
tree
2019-09-24
Paul Ba
u
er
Add test for n
o
a
p
pend
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraha
m
Fix n
o
-MPI CUDA build
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
Me
r
ge "Merge branch
r
el
e
ase-
2
019 into
master
"
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
Fix clang
u
nused-function warnin
g
s
commit
|
commitdiff
|
tree
2019-09-24
Paul Bauer
Add release notes for mod
u
lar
s
imul
a
to
r
commit
|
commitdiff
|
tree
2019-09-23
Paul Bauer
Fix issues when
PME rank reque
s
t becomes negativ
e
commit
|
commitdiff
|
tree
2019-09-23
P
a
ul Bauer
Chan
g
e MPI setup to commun
i
cate TPR as buffer
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al
M
erz
Zer
o
p
r
e
s
sure
and v
i
rial tensors at
b
egi
n
ning
of step
commit
|
commitdiff
|
tree
2019-09-23
Pascal
M
erz
Introduce FEP into modular simulator
commit
|
commitdiff
|
tree
2019-09-22
C
h
r
isto
p
h J
u
nghans
workarou
n
d
f
or rhel bug #174946
3
, cmak
e
bug #18349
commit
|
commitdiff
|
tree
2019-09-22
P
a
ul Bauer
Remove update flag again
commit
|
commitdiff
|
tree
2019-09-22
Ber
k
Hes
s
Remove cgs_g
l
from gmx_domde
c
_
c
omm_t
commit
|
commitdiff
|
tree
2019-09-20
Mark A
b
r
a
h
am
Refa
c
tor to create a
G
puTaskA
s
signments objec
t
commit
|
commitdiff
|
tree
2019-09-19
Berk
H
ess
Remove
b
Lo
c
a
lCG from DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove obsol
e
te make_excl
u
sions_
z
on
e
_c
g
()
commit
|
commitdiff
|
tree
2019-09-19
Chr
i
sti
a
n Blau
Check
in
p
u
t
recor
d
al
s
o in tests
commit
|
commitdiff
|
tree
2019-09-19
Mark
Abraham
Use GP
U
halo ex
c
han
g
e
only when compat
i
ble DD is available
commit
|
commitdiff
|
tree
2019-09-19
M
ark Abraham
Fu
r
ther improve getDDGr
i
dSetup
commit
|
commitdiff
|
tree
2019-09-19
P
aul Bauer
Add basic
i
nt
e
rface to run
u
pdate on G
P
U
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Add haveF
r
eeEnergyWork
t
o
D
omainLifetimeWorkload flags
commit
|
commitdiff
|
tree
2019-09-19
C
hristian Blau
Consistently chang
e
d
ensityfitting
spreadin
g
weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Added
f
r
e
e
-e
n
ergy kern
e
l
p
e
r
formanc
e
note
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Fix inco
r
rect
D
D nd
i
m asserti
o
n
commit
|
commitdiff
|
tree
2019-09-18
Pascal Mer
z
v-r
e
scal
e
thermostat for modular simulator
commit
|
commitdiff
|
tree
2019-09-18
Paul Bauer
R
e
ad TPR f
i
le body
i
n buffer
commit
|
commitdiff
|
tree
2019-09-18
Alan
Gray
GPU Fo
r
ce Halo Exchange
commit
|
commitdiff
|
tree
2019-09-17
P
a
scal
Merz
Fix po
s
ition pin
n
i
n
g for modula
r
sim
u
lator
commit
|
commitdiff
|
tree
2019-09-16
B
e
rk Hess
Remove o
b
s
olete
mdp optio
n
ns-type
commit
|
commitdiff
|
tree
2019-09-16
ejjordan
Add some coo
l
qu
o
tes
commit
|
commitdiff
|
tree
2019-09-16
Paul Bauer
F
o
rmatting
f
ixes for reference manu
a
l
commit
|
commitdiff
|
tree
2019-09-16
M
.
Er
i
c
Ir
r
gang
Add gmxa
p
i release notes
.
commit
|
commitdiff
|
tree
2019-09-16
Alan G
r
ay
GPU ha
l
o exchange
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
H
e
s
s
Add virtual
s
ite
t
y
pe
2FD
commit
|
commitdiff
|
tree
2019-09-16
Mark Abr
a
ham
Avoid short-
r
ange GPU o
p
e
r
ations with
no
w
ork
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remove cu
t
-
o
ff schemes from
m
anual
commit
|
commitdiff
|
tree
2019-09-16
Szilárd Páll
Eliminate unnecessary GPU
s
tream dependency
c
all
commit
|
commitdiff
|
tree
2019-09-16
Berk Hes
s
Add option req
u
es
t
1D DD with 1 pulse
commit
|
commitdiff
|
tree
2019-09-16
Ke
v
in Boyd
Remo
v
e group sc
h
e
m
e fr
o
m
deprecated release notes
commit
|
commitdiff
|
tree
2019-09-15
P
a
scal M
e
rz
Introduce the modular s
i
m
u
lator
commit
|
commitdiff
|
tree
2019-09-15
P
eter Kasson
Patch
gmx
a
pi f
o
r
Python 3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irr
g
ang
No
r
malize usage of GMXTOOL
C
HAINDIR
i
n gmxapi
setup
.
p
y
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
D
o
n
o
t
use groma
c
s
-
toolchain in
d
arwin gmxapi builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
E
r
i
c Irrgang
Update
g
m
x
api
s
etup
.
py
commit
|
commitdiff
|
tree
2019-09-12
Mark Abraha
m
Disa
b
le r
e
p
o
r
t
-
m
ethods end-to
-
e
nd test
commit
|
commitdiff
|
tree
2019-09-12
Szilárd Páll
Reor
g
a
n
ize
o
n-GPU PM
E
f
o
rce r
e
duc
t
ion flag handl
i
n
g
commit
|
commitdiff
|
tree
2019-09-12
Artem Z
h
murov
Cha
n
ge Padde
d
Ve
c
tor to PaddedHostVector
f
or
force CPU
.
.
.
commit
|
commitdiff
|
tree
next