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Mark HWLOC cmake cache variable as advanced
2019-11-04
Tee
m
u Murtola
U
p
dat
e
clang-format config
commit
|
commitdiff
|
tree
2019-10-31
M
.
Er
i
c
I
rrg
a
ng
Improve
uniformity of
O
S X CMake confi
g
uration
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
r
i
c
Irrgang
Restore C
M
ake convenience
t
argets
for
s
a
m
p
le
_
restraint
.
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
R
emove dead cod
e
for nbnxm H2
D
coordinate copy e
v
ent
commit
|
commitdiff
|
tree
2019-10-31
Alan
Gra
y
Bug
f
ix fo
r
event pa
s
sed to GPU
c
omm
f
eatures
commit
|
commitdiff
|
tree
2019-10-31
Pascal
Merz
C
h
e
ck for con
t
radic
t
ing envir
o
n
m
ent variables (modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
M
a
r
k
A
braham
Tests for v
a
l
i
d
periodic acti
o
n
s
commit
|
commitdiff
|
tree
2019-10-29
M
.
E
ric
Irrgang
D
isable its tests
w
he
n
sam
p
le_restraint is not the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
D
ecrea
s
e the maximum a
l
lowed
Python
version for gmxapi
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmuro
v
Disable GPU u
p
d
a
t
e
when coordinates swappi
n
g is enabled
commit
|
commitdiff
|
tree
2019-10-24
B
e
r
k
Hess
A
dd bool useDom
a
inDe
c
o
m
positi
o
n in mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add gmx
_
mtop_int
e
raction_
c
ount()
commit
|
commitdiff
|
tree
2019-10-23
ejjordan
Make t_
n
extnb an implemen
t
ation detail
commit
|
commitdiff
|
tree
2019-10-23
P
a
scal Merz
C
o
r
rect
f
or skewed box
bef
o
re domain decomposition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Alan Gray
Enable GPU Peer Access in GP
U
Utilities
commit
|
commitdiff
|
tree
2019-10-22
ejjor
d
an
Remove
u
n
u
sed
f
u
nctions from gmxpreproc
e
ss
commit
|
commitdiff
|
tree
2019-10-22
Berk
H
ess
Requir
e
-
e
i f
o
r essential dynam
i
cs
commit
|
commitdiff
|
tree
2019-10-22
ejjordan
Remove u
n
used func
t
ion
g
ener
a
te_excls
a
nd m
a
ke clean_
e
xcls
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Be
r
k
H
ess
Const corr
e
ctness for genhydro
commit
|
commitdiff
|
tree
2019-10-15
Pau
l
Bauer
Fix bu
g
in prepr
o
cessing
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eric Irrgang
Fi
x
logi
c
error in gmxapi
.
version
.
api_is_a
t
_least()
.
commit
|
commitdiff
|
tree
2019-10-13
Mark Abraham
E
n
sure envir
o
nmen
t
var
i
a
b
le use does not
g
ive
w
arnings
commit
|
commitdiff
|
tree
2019-10-12
B
erk Hess
A
dd clas
s
FixedCa
p
acityVector
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmuro
v
Centralize management of coord
i
nates re
a
d
y
o
n
GPU even
t
commit
|
commitdiff
|
tree
2019-10-08
P
r
ashanth Kanduri
Fused two if
br
a
nches with the sam
e
conditio
n
a
l
commit
|
commitdiff
|
tree
2019-10-02
C
a
rste
n
K
utzner
Update th
e
w
w
w l
i
nk to t
h
e Do
x
y
g
en documenta
t
i
on i
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
Berk Hes
s
Fix
harmles
s
OpenMP write race
commit
|
commitdiff
|
tree
2019-10-02
Ma
r
k Abr
a
ham
I
m
prove PME testin
g
commit
|
commitdiff
|
tree
2019-10-01
Berk He
s
s
Use gmx
:
:Range in
d
o
mdec
commit
|
commitdiff
|
tree
2019-10-01
Artem
Z
hmurov
StateProp
a
ga
t
orDataGpu
o
bj
e
ct to manage GP
U
f
o
rces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Ma
r
k Abraham
Fix icc warnings
commit
|
commitdiff
|
tree
2019-10-01
Be
r
k Hess
C
omplete
l
y remo
v
e charge groups
commit
|
commitdiff
|
tree
2019-10-01
Paul
Bauer
Fix
c
hain ID ha
n
dli
n
g i
n
ma
k
e_n
d
x
commit
|
commitdiff
|
tree
2019-10-01
Christo
p
h J
u
nghans
c
m
ake: add missing
h
ea
d
er to legacy api
commit
|
commitdiff
|
tree
2019-10-01
Mark Abraham
Removed de
p
endency on commrec of mdrun
s
etup
commit
|
commitdiff
|
tree
2019-09-30
Ca
r
s
ten Kut
z
ner
M
ove For
c
eProvid
e
rs cl
a
s
s into the gmx n
a
m
e
space
commit
|
commitdiff
|
tree
2019-09-30
Ma
r
k Abraha
m
Ma
k
e a builder
f
or DD
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
R
emove charge group code from fo
r
cer
e
c
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Pá
l
l
Ma
k
e the wa
i
t
o
n P
M
E GPU resul
t
s
c
on
d
itional
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
I
m
pro
v
e MiMiC test imp
l
e
menta
t
ion
commit
|
commitdiff
|
tree
2019-09-27
Mark A
b
r
a
h
am
Fi
x
gro file output with index groups
commit
|
commitdiff
|
tree
2019-09-27
Mark
A
braham
Fix gro file ou
t
put with
i
ndex group
s
commit
|
commitdiff
|
tree
2019-09-27
Mark Ab
r
aham
Remo
v
e leftover
s
upport for pre-9
.
0 CUDA
commit
|
commitdiff
|
tree
2019-09-24
Paul
B
au
e
r
A
dd test for
noappend
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
F
ix no-MP
I
C
U
DA build
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
M
erge "Merg
e
b
r
anch release-2019 into master"
commit
|
commitdiff
|
tree
2019-09-24
M
ark
A
braham
Fix clan
g
unused-funct
i
on w
a
rnin
g
s
commit
|
commitdiff
|
tree
2019-09-24
Pau
l
Baue
r
Add
r
elease notes for
m
o
dular simulato
r
commit
|
commitdiff
|
tree
2019-09-23
P
a
ul Bauer
Fix
i
s
sues
when P
M
E ran
k
request beco
m
e
s n
e
gative
commit
|
commitdiff
|
tree
2019-09-23
Paul Bauer
C
h
a
nge MPI setup
to communi
c
a
te TPR as
b
u
ffer
commit
|
commitdiff
|
tree
2019-09-23
Pa
s
ca
l
Merz
Ze
r
o pres
s
ure an
d
viria
l
tensors
a
t be
g
i
nning o
f
step
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Introduce F
E
P
in
t
o modular
simulator
commit
|
commitdiff
|
tree
2019-09-22
Ch
r
istoph Junghans
workaround for rhe
l
bug #17
4
9
4
63, cm
a
k
e bug #18349
commit
|
commitdiff
|
tree
2019-09-22
P
a
u
l
B
aue
r
R
e
move upd
a
t
e
fla
g
again
commit
|
commitdiff
|
tree
2019-09-22
Berk Hess
Re
m
ove cgs_gl from gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-20
Mark Abraham
Refac
t
or
to create a
G
p
u
T
askAssignme
n
t
s
o
b
j
ec
t
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
R
e
move bLocalCG from DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove obsolet
e
make_exclusions_
z
one
_
cg()
commit
|
commitdiff
|
tree
2019-09-19
Christ
i
an Blau
Check
i
nput r
e
cord also in tests
commit
|
commitdiff
|
tree
2019-09-19
Mark Ab
r
aham
Use GPU h
a
lo
e
xchange only when
compatibl
e
DD is availabl
e
commit
|
commitdiff
|
tree
2019-09-19
Mark A
b
raham
F
u
rther improve
g
etDDGr
i
dSetup
commit
|
commitdiff
|
tree
2019-09-19
Paul Baue
r
A
d
d basic inter
f
ace to run
u
pdate on GPU
commit
|
commitdiff
|
tree
2019-09-19
Berk
Hess
Ad
d
haveFreeE
n
e
rgyWork
t
o DomainLif
e
timeWorkloa
d
flags
commit
|
commitdiff
|
tree
2019-09-19
C
h
r
i
stian Blau
Co
n
sistent
l
y change densi
t
yfitting
spreading
w
e
ight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Berk H
e
s
s
Add
e
d
f
ree-energy kernel perfor
m
ance note
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Fix incorrect DD ndim assertion
commit
|
commitdiff
|
tree
2019-09-18
Pascal Merz
v-resca
l
e thermostat for modular simulator
commit
|
commitdiff
|
tree
2019-09-18
Paul Bauer
Read
T
PR file
bod
y
in bu
f
fer
commit
|
commitdiff
|
tree
2019-09-18
Alan Gray
G
P
U Force Halo Exchan
g
e
commit
|
commitdiff
|
tree
2019-09-17
P
ascal M
e
r
z
Fix position pi
n
ning for modular simulato
r
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remove obsole
t
e
m
dp
o
pt
i
on ns-typ
e
commit
|
commitdiff
|
tree
2019-09-16
ejjord
a
n
Ad
d
some cool quotes
commit
|
commitdiff
|
tree
2019-09-16
P
a
u
l Bauer
Fo
r
matting fi
x
es for refere
n
ce
m
anual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Eri
c
I
r
rgang
Add gmxapi releas
e
notes
.
commit
|
commitdiff
|
tree
2019-09-16
A
l
an Gray
GP
U
hal
o
exc
h
ange
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
Hess
Add vir
t
ual
s
ite type 2FD
commit
|
commitdiff
|
tree
2019-09-16
Mar
k
Abraham
Avoid short-range
GPU operations with no
work
commit
|
commitdiff
|
tree
2019-09-16
Berk H
e
ss
Remove cut-off schemes from manual
commit
|
commitdiff
|
tree
2019-09-16
Szilár
d
Pál
l
Elimi
n
ate unn
e
cessary GPU stream depe
n
dency
c
all
commit
|
commitdiff
|
tree
2019-09-16
Berk
Hess
Add option request 1
D
DD with 1
pu
l
se
commit
|
commitdiff
|
tree
2019-09-16
Kevin B
o
yd
Remove gro
u
p scheme from deprec
a
ted release
notes
commit
|
commitdiff
|
tree
2019-09-15
Pasca
l
Merz
I
n
tro
d
uce the mo
d
ula
r
si
m
ula
t
or
commit
|
commitdiff
|
tree
2019-09-15
Peter
K
a
sson
Patch gmxa
p
i for Python 3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrg
a
n
g
Normalize u
s
age of GMXTOOLCHAINDIR in gmx
a
pi setu
p
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
Er
i
c Irrgang
D
o not use
g
r
omacs-toolcha
i
n
in darwin
g
mxapi builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Ir
r
gang
Update g
m
xa
p
i setup
.
p
y
commit
|
commitdiff
|
tree
2019-09-12
Mark Abraham
Disable report-
m
ethods en
d
-to-
e
n
d
test
commit
|
commitdiff
|
tree
2019-09-12
S
zi
l
ár
d
Páll
Reorga
n
ize
o
n
-
GPU
P
ME force reductio
n
flag ha
n
d
li
n
g
commit
|
commitdiff
|
tree
2019-09-12
Ar
t
em Zhmurov
C
h
a
n
ge Pad
d
e
d
V
e
c
t
o
r t
o
PaddedHostVector f
o
r force
C
PU
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Christian Bl
a
u
A
dd release note for
d
e
nsit
y
f
itting
.
commit
|
commitdiff
|
tree
2019-09-12
Pascal Merz
Update modul
a
r
simulator test
s
commit
|
commitdiff
|
tree
2019-09-12
E
r
ik Lindahl
Added
S
IMD log2 and pow math functions
commit
|
commitdiff
|
tree
2019-09-12
Erik
L
indahl
Update SIMD math tests and improve accur
a
c
y
commit
|
commitdiff
|
tree
2019-09-11
P
aul Bauer
Remove
-
sub option from trjconv
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Fix f
o
r the post-submi
t
fail
u
r
e
commit
|
commitdiff
|
tree
2019-09-11
Ar
t
em Zh
m
urov
Dec
o
uple GPU forc
e
b
u
ffer
managemen
t
from buffer ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
ric I
r
rgang
Use
GROMAC
S
CMa
k
e toolchain file for
gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Paul Bauer
Basic toolch
a
in
t
o facil
i
tate GMXAPI build
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Add gmxapi
.
modify_i
n
put operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
P
r
ovide a gmxapi
.
read_tpr
op
e
ratio
n
.
commit
|
commitdiff
|
tree
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