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Fix warnings with clang 9
2019-10-31
M
.
Eric Irrgang
R
esto
r
e
CMake convenience targets for sample_r
e
straint
.
commit
|
commitdiff
|
tree
2019-10-31
Alan Gr
a
y
Remove dead code for n
b
nxm H2D
c
oordin
a
te
c
opy event
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
Bug fix fo
r
event pa
s
sed to
G
PU comm features
commit
|
commitdiff
|
tree
2019-10-31
Pascal Merz
Check for contradicting en
v
ironment
varia
b
les (mo
d
ular
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Mark Abraham
Tests fo
r
va
l
id
p
e
riodi
c
ac
t
ions
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgan
g
Disable it
s
tests when
s
ample_rest
r
aint is not
the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
Decrease the maxim
u
m allowed Python version for
g
mxapi
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhm
u
rov
Disab
l
e GPU update when coordinat
e
s
s
w
apping
i
s
enabled
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add bool use
D
omainDecomposition in
mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add
g
mx_mtop_interaction_c
o
unt()
commit
|
commitdiff
|
tree
2019-10-23
ejjor
d
an
Make t_nextn
b
a
n
i
m
plementation detail
commit
|
commitdiff
|
tree
2019-10-23
P
ascal M
e
rz
Correct for skewed box before
d
omain decomposition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Alan Gray
Enable GPU Peer Access in GPU
Util
i
t
i
es
commit
|
commitdiff
|
tree
2019-10-22
ejj
o
r
d
an
Re
m
ove unused fu
n
c
t
i
ons
from
g
m
xprepr
o
cess
commit
|
commitdiff
|
tree
2019-10-22
Berk Hess
Re
q
uire -ei for e
s
sential
d
y
n
amics
commit
|
commitdiff
|
tree
2019-10-22
ejjordan
Rem
o
ve unused function generate_excls and
m
a
k
e
clean_excl
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Berk
Hess
Const c
o
rrectness for ge
n
hy
d
r
o
commit
|
commitdiff
|
tree
2019-10-15
Paul Bauer
F
ix bug
i
n pr
e
processing
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eri
c
Irrgang
Fix log
i
c
error in gmxapi
.
v
ersion
.
ap
i
_is_at_least()
.
commit
|
commitdiff
|
tree
2019-10-13
Mark Abr
a
h
a
m
Ensure
env
i
ronment variable use d
o
es not give
w
arnings
commit
|
commitdiff
|
tree
2019-10-12
B
erk Hess
Add class Fixed
C
apa
c
ity
V
ector
commit
|
commitdiff
|
tree
2019-10-12
Arte
m
Zhmurov
C
e
ntralize management
o
f
c
o
o
r
dina
t
es
ready o
n
GPU event
commit
|
commitdiff
|
tree
2019-10-08
Pr
a
shanth
K
andur
i
Fus
e
d t
w
o
if
b
ranches with the
s
ame conditiona
l
commit
|
commitdiff
|
tree
2019-10-02
Carsten Kutzner
Update the w
w
w l
i
nk
t
o
the
Doxygen
d
ocume
n
tation in
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
Ber
k
Hess
Fix
h
arm
l
es
s
O
pe
n
MP write race
commit
|
commitdiff
|
tree
2019-10-02
Mar
k
Abraham
I
m
pro
v
e
P
M
E te
s
ting
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Use gmx::Range in domdec
commit
|
commitdiff
|
tree
2019-10-01
Artem Zhmurov
S
tateP
r
o
p
agat
o
rDataGpu
object
t
o manage
G
PU forces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Mark Ab
r
a
ham
Fix icc warnin
g
s
commit
|
commitdiff
|
tree
2019-10-01
Ber
k
Hess
Completely remove c
h
arge groups
commit
|
commitdiff
|
tree
2019-10-01
Paul Bauer
Fix chain ID handling
i
n make_ndx
commit
|
commitdiff
|
tree
2019-10-01
Christoph Junghans
cmake: add miss
i
ng header to legacy api
commit
|
commitdiff
|
tree
2019-10-01
Mark
A
b
ra
h
am
Removed dependency on commrec of mdrun se
t
up
commit
|
commitdiff
|
tree
2019-09-30
C
a
rsten Kutzner
Move ForceP
r
oviders class into
the gmx namespace
commit
|
commitdiff
|
tree
2019-09-30
Mark
A
b
rah
a
m
Make a builder for DD
commit
|
commitdiff
|
tree
2019-09-30
Berk
H
ess
R
e
mo
v
e charg
e
group code
from forcerec
commit
|
commitdiff
|
tree
2019-09-30
S
z
ilárd
Pál
l
Ma
k
e the wait on PME GPU resu
l
ts
co
n
diti
o
nal
commit
|
commitdiff
|
tree
2019-09-27
Mark
A
braham
Imp
r
ove MiMiC
t
est implementation
commit
|
commitdiff
|
tree
2019-09-27
Mark
A
braham
Fix gro file
o
ut
p
ut with
i
ndex groups
commit
|
commitdiff
|
tree
2019-09-27
M
ark Ab
r
aham
Fix g
r
o
f
ile o
u
tput wit
h
i
n
dex
groups
commit
|
commitdiff
|
tree
2019-09-27
Mark
A
braham
Remove left
o
ver
s
upport
for pre-9
.
0 CUDA
commit
|
commitdiff
|
tree
2019-09-24
P
a
u
l
Bauer
Add test for noap
p
end
commit
|
commitdiff
|
tree
2019-09-24
Mark
A
braham
Fix no-MPI
CUDA bui
l
d
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
M
erge "Merge
b
r
anc
h
release-2019 into master"
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
Fix clang unused-fu
n
ction warning
s
commit
|
commitdiff
|
tree
2019-09-24
Paul
Bauer
Add re
l
ease notes fo
r
modular simul
a
t
o
r
commit
|
commitdiff
|
tree
2019-09-23
Paul B
a
uer
Fi
x
issues
w
hen PME rank
r
equest become
s
negative
commit
|
commitdiff
|
tree
2019-09-23
Paul Bauer
C
han
g
e MPI set
u
p t
o
communi
c
ate TPR as bu
f
fe
r
commit
|
commitdiff
|
tree
2019-09-23
Pascal M
e
rz
Z
e
ro
pre
s
sure and virial t
e
ns
o
rs at beginning of step
commit
|
commitdiff
|
tree
2019-09-23
P
a
scal Merz
I
ntroduce F
E
P
i
nto mod
u
lar
s
im
u
l
at
o
r
commit
|
commitdiff
|
tree
2019-09-22
Christoph J
u
nghans
w
orkaround f
o
r rhel bug
#1749463, cmake
bug #18349
commit
|
commitdiff
|
tree
2019-09-22
Paul Bauer
Rem
o
ve upd
a
te flag aga
i
n
commit
|
commitdiff
|
tree
2019-09-22
Berk H
e
ss
Remove cgs
_
g
l from
g
mx_domd
e
c_c
o
mm_t
commit
|
commitdiff
|
tree
2019-09-20
M
ark Abrah
a
m
Refactor to create a Gp
u
Ta
s
kAssignments
o
b
ject
commit
|
commitdiff
|
tree
2019-09-19
Ber
k
Hess
Remove bL
o
calCG from
D
D
code
commit
|
commitdiff
|
tree
2019-09-19
Berk Hes
s
Remove obso
l
ete ma
k
e_excl
u
s
ions_zone_cg(
)
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Check input
record also in tests
commit
|
commitdiff
|
tree
2019-09-19
M
ark
Abraham
Use
G
P
U
halo exc
h
ange
only
w
hen compati
b
l
e
DD
i
s availa
b
le
commit
|
commitdiff
|
tree
2019-09-19
Mark
A
braham
Fur
t
her improve getDDGri
d
Setu
p
commit
|
commitdiff
|
tree
2019-09-19
P
aul Bauer
Ad
d
basic interfac
e
t
o run upda
t
e
on
G
P
U
commit
|
commitdiff
|
tree
2019-09-19
Berk Hes
s
A
dd hav
e
F
r
eeEnergyWork to
D
omainLif
e
timeWorkload flags
commit
|
commitdiff
|
tree
2019-09-19
Chri
s
t
i
an
B
lau
Con
s
is
t
e
n
tly change densityfitt
i
n
g
spread
i
ng
w
eight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Berk
H
e
ss
A
dded fr
e
e
-
ener
g
y ke
r
nel perfo
r
mance note
commit
|
commitdiff
|
tree
2019-09-18
Berk
Hess
Fix
i
ncorrect DD
ndim ass
e
rtion
commit
|
commitdiff
|
tree
2019-09-18
Pasca
l
Merz
v-rescale
t
her
m
ostat for modu
l
ar si
m
u
lator
commit
|
commitdiff
|
tree
2019-09-18
Paul Ba
u
er
Read TPR file
b
ody in buffer
commit
|
commitdiff
|
tree
2019-09-18
Alan Gray
GPU F
o
rc
e
Halo Exchange
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix position pinning f
o
r
modular simulato
r
commit
|
commitdiff
|
tree
2019-09-16
Be
r
k Hess
Rem
o
ve obsolete
mdp o
p
tion
ns-type
commit
|
commitdiff
|
tree
2019-09-16
ejjordan
Add some co
o
l quotes
commit
|
commitdiff
|
tree
2019-09-16
P
a
u
l
Bauer
Fo
r
m
a
ttin
g
fixes for ref
e
rence
ma
n
ual
commit
|
commitdiff
|
tree
2019-09-16
M
.
E
r
i
c Irrga
n
g
Ad
d
gmxa
p
i releas
e
notes
.
commit
|
commitdiff
|
tree
2019-09-16
A
lan
Gray
GPU h
a
lo ex
c
h
a
nge
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add virtual site type
2FD
commit
|
commitdiff
|
tree
2019-09-16
Mark Abraham
Avoid shor
t
-range GPU oper
a
tions with no wor
k
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Re
m
ove cut-off
s
chemes from manual
commit
|
commitdiff
|
tree
2019-09-16
Szilárd P
á
ll
Elimi
n
ate unnecessary
GPU stream dependency call
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add option requ
e
s
t
1D
D
D
with 1 p
u
l
s
e
commit
|
commitdiff
|
tree
2019-09-16
Kevin Boy
d
Remove group scheme f
r
om deprecated
release notes
commit
|
commitdiff
|
tree
2019-09-15
Pascal Merz
Introduce the modul
a
r
simulator
commit
|
commitdiff
|
tree
2019-09-15
Peter Kasson
Patch gmxapi fo
r
Python 3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric I
r
rgang
Norma
l
ize usa
g
e
of
GM
X
T
OOLCHAINDIR in gmxapi setup
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
E
r
ic
Irr
g
ang
Do not use g
r
o
m
acs-
t
oolch
a
in in da
r
win gmxapi buil
d
s
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irr
g
ang
Update
gmxapi
setup
.
py
commit
|
commitdiff
|
tree
2019-09-12
Mark Abrah
a
m
Disable report
-
m
e
thods
e
nd-to-end test
commit
|
commitdiff
|
tree
2019-09-12
Szilárd Páll
Reorga
n
ize on-
G
PU PME force reduction flag handling
commit
|
commitdiff
|
tree
2019-09-12
Artem Zhmurov
Change PaddedVect
o
r to Pad
d
edHost
V
e
c
tor for force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Christian
B
la
u
Add release
not
e
for density fitting
.
commit
|
commitdiff
|
tree
2019-09-12
Pascal Merz
Update modular simulator tests
commit
|
commitdiff
|
tree
2019-09-12
Er
i
k Lindahl
Added S
I
MD l
o
g2 a
n
d po
w
mat
h
functions
commit
|
commitdiff
|
tree
2019-09-12
Er
i
k
L
inda
h
l
Update SI
M
D
mat
h
tests and improve
a
ccur
a
cy
commit
|
commitdiff
|
tree
2019-09-11
Paul Ba
u
er
Remove -sub option from trjco
n
v
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
F
ix f
o
r the
p
ost-submit fail
u
re
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmu
r
ov
Decouple
GPU force buffe
r
man
a
gement from buffer ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Use GROMACS
C
Make
too
l
chai
n
file fo
r
gm
x
api Pyt
h
on
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Paul B
a
u
e
r
B
a
sic toolchain t
o
facil
i
tate GM
X
API buil
d
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Add gmxapi
.
m
od
i
f
y_input operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric I
r
r
g
a
n
g
P
rov
i
de a gmx
a
pi
.
r
ead_tpr operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Update gmxapi
.
simulation
.
c
o
ntext de
t
ails
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
r
ic Ir
r
gang
Update
gmxapi Python package
infrastructure
for ne
w
.
.
.
commit
|
commitdiff
|
tree
next