repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Fix gmx h2order -d option
2019-10-02
Ca
r
sten Kutzne
r
Up
d
ate the
www
link
to the Do
x
ygen d
o
cum
e
ntation in
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
Berk Hes
s
Fix harmless O
p
enMP write race
commit
|
commitdiff
|
tree
2019-10-02
Mark Abraham
Improve PME testing
commit
|
commitdiff
|
tree
2019-10-01
Berk
H
ess
Use gmx::Range in domdec
commit
|
commitdiff
|
tree
2019-10-01
Artem Zh
m
urov
StateP
r
o
pagator
D
ataGpu object to manage GPU for
c
e
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Mark Abraha
m
Fix i
c
c warnings
commit
|
commitdiff
|
tree
2019-10-01
Berk H
e
ss
Completely rem
o
ve
c
harge grou
p
s
commit
|
commitdiff
|
tree
2019-10-01
Paul Baue
r
Fix chai
n
ID hand
l
ing in make_ndx
commit
|
commitdiff
|
tree
2019-10-01
Christoph Jungha
n
s
c
make: ad
d
missing
hea
d
er
t
o leg
a
cy api
commit
|
commitdiff
|
tree
2019-10-01
Mark Abra
h
am
Removed dependency on commrec of mdrun setup
commit
|
commitdiff
|
tree
2019-09-30
C
a
r
s
ten
K
utzner
Move ForceProviders cla
s
s into
the
g
mx namespace
commit
|
commitdiff
|
tree
2019-09-30
Ma
r
k Abrah
a
m
Make
a b
u
i
l
d
er for DD
commit
|
commitdiff
|
tree
2019-09-30
B
erk He
s
s
Remo
v
e
char
g
e group
code from f
o
rcerec
commit
|
commitdiff
|
tree
2019-09-30
Szil
á
rd Páll
Make
t
he wait on
PME GPU
r
e
sults conditional
commit
|
commitdiff
|
tree
2019-09-27
Mark
A
braham
I
mpr
o
ve MiM
i
C
t
est imple
m
entatio
n
commit
|
commitdiff
|
tree
2019-09-27
Mark Abrah
a
m
Fix gro file output
w
ith index groups
commit
|
commitdiff
|
tree
2019-09-27
M
a
rk Abraham
Fix
g
r
o
f
ile output with index groups
commit
|
commitdiff
|
tree
2019-09-27
Ma
r
k A
b
ra
h
am
Remove le
f
tover support f
o
r pre-9
.
0
C
U
DA
commit
|
commitdiff
|
tree
2019-09-24
Paul Bau
e
r
Add test for noappend
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
F
ix no-M
P
I CUDA b
u
ild
commit
|
commitdiff
|
tree
2019-09-24
Mark Ab
r
aham
Merge "Merge
bra
n
ch release-2019 into master
"
commit
|
commitdiff
|
tree
2019-09-24
Mar
k
Abraham
Fix clan
g
unu
s
e
d
-funct
i
on warnings
commit
|
commitdiff
|
tree
2019-09-24
P
aul Bauer
Add
re
l
ease notes f
o
r modular simu
l
ator
commit
|
commitdiff
|
tree
2019-09-23
Pau
l
B
a
uer
F
i
x
iss
u
e
s
when PME
rank r
e
q
u
est becomes negative
commit
|
commitdiff
|
tree
2019-09-23
P
a
ul B
a
uer
Cha
n
ge MP
I
set
u
p to comm
u
nicate TPR as bu
f
fer
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al
M
erz
Zero pressure and virial tenso
r
s at beg
i
nni
n
g o
f
step
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
I
ntro
d
uce FEP
into modu
l
ar simulator
commit
|
commitdiff
|
tree
2019-09-22
Chr
i
stop
h
Jun
g
hans
wo
r
karou
n
d for rhel bug #1749463
,
cmake b
u
g #1834
9
commit
|
commitdiff
|
tree
2019-09-22
P
aul Bauer
Remove update flag again
commit
|
commitdiff
|
tree
2019-09-22
B
erk Hess
Remo
v
e cgs_
g
l from gmx_
d
omd
e
c_comm_t
commit
|
commitdiff
|
tree
2019-09-20
Mark Abraham
Refactor t
o
create a
G
p
u
TaskAs
s
i
g
nments ob
j
ect
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove bLocalCG from DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove obsol
e
te
m
ak
e
_exclusions_zone_cg()
commit
|
commitdiff
|
tree
2019-09-19
Christia
n
Blau
Ch
e
ck input
r
ecord also in test
s
commit
|
commitdiff
|
tree
2019-09-19
Mark Abra
h
am
Use GP
U
h
alo exchange only when compa
t
i
b
le
DD is availabl
e
commit
|
commitdiff
|
tree
2019-09-19
Mark
Abraham
Fu
r
t
h
er improve getDDGridSetu
p
commit
|
commitdiff
|
tree
2019-09-19
Paul Bauer
Add basic inter
f
ace to r
u
n
u
pdate on
G
PU
commit
|
commitdiff
|
tree
2019-09-19
Berk
H
ess
Add haveFre
e
En
e
r
g
y
W
or
k
to Dom
a
i
nLifetimeWorkload flags
commit
|
commitdiff
|
tree
2019-09-19
Christia
n
B
l
au
Consistently
change densityfitting
s
prea
d
i
ng
we
i
ght
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Berk
H
e
s
s
Added free-
e
nergy
k
ernel performance no
t
e
commit
|
commitdiff
|
tree
2019-09-18
B
er
k
Hess
Fix incorrect DD
n
dim assertion
commit
|
commitdiff
|
tree
2019-09-18
Pascal Merz
v-re
s
cale thermosta
t
for
modular simu
l
a
to
r
commit
|
commitdiff
|
tree
2019-09-18
Pa
u
l Bauer
Read
T
PR file body in b
u
ffer
commit
|
commitdiff
|
tree
2019-09-18
Ala
n
Gray
G
P
U Force Halo Exchan
g
e
commit
|
commitdiff
|
tree
2019-09-17
Pas
c
a
l
Merz
Fi
x
positi
o
n
pinning for modular simulator
commit
|
commitdiff
|
tree
2019-09-16
Be
r
k
Hess
Remove ob
s
olete mdp option ns-type
commit
|
commitdiff
|
tree
2019-09-16
ejjordan
Add some cool quot
e
s
commit
|
commitdiff
|
tree
2019-09-16
Paul Bauer
Fo
r
ma
t
ting fi
x
e
s for referenc
e
manual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Eri
c
Irrgan
g
Add gm
x
ap
i
release
notes
.
commit
|
commitdiff
|
tree
2019-09-16
Alan
G
ray
GPU halo exc
h
ange
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add virt
u
al site
type
2
FD
commit
|
commitdiff
|
tree
2019-09-16
Ma
r
k Abr
a
ham
Avoid short-r
a
nge GPU o
p
erations with no w
o
rk
commit
|
commitdiff
|
tree
2019-09-16
Berk He
s
s
Remove cut-off
s
c
h
emes fr
o
m
manual
commit
|
commitdiff
|
tree
2019-09-16
Szilárd Páll
Elim
i
nate
u
nne
c
essa
r
y GP
U
stream de
p
end
e
ncy call
commit
|
commitdiff
|
tree
2019-09-16
Berk H
e
s
s
A
d
d option req
u
est
1
D DD with
1 pulse
commit
|
commitdiff
|
tree
2019-09-16
K
evin Bo
y
d
Re
m
o
v
e group scheme
fro
m
deprec
a
ted releas
e
notes
commit
|
commitdiff
|
tree
2019-09-15
Pascal Merz
Int
r
oduce the
modular simulato
r
commit
|
commitdiff
|
tree
2019-09-15
Peter Kasso
n
Patch gmxapi for Python 3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
Normalize usag
e
of GMX
T
OOLCHAI
N
DIR in gmxa
p
i
s
e
tup
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irr
g
an
g
Do not use gr
o
macs-
t
oolchain in d
a
rwin
g
mxapi builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrg
a
ng
Update gmxapi s
e
tup
.
py
commit
|
commitdiff
|
tree
2019-09-12
M
a
rk
A
braham
Disable re
p
ort-metho
d
s end-
t
o-end test
commit
|
commitdiff
|
tree
2019-09-12
S
zilárd Páll
Reorgan
i
ze on
-
GPU PME force reduction fl
a
g handling
commit
|
commitdiff
|
tree
2019-09-12
Art
e
m Zhmur
o
v
Change Padd
e
dV
e
ct
o
r to Padde
d
H
o
stVec
t
or
f
o
r force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
C
h
ristian Blau
A
d
d re
l
eas
e
note fo
r
de
n
sity fitting
.
commit
|
commitdiff
|
tree
2019-09-12
Pas
c
al Merz
Update modular
s
imulator t
e
sts
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindahl
A
dded SIMD
log2 and pow
m
ath f
u
nctions
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindahl
Update SIMD math tests and impr
o
v
e
a
cc
u
racy
commit
|
commitdiff
|
tree
2019-09-11
Paul
B
a
u
er
Remove -s
u
b
option from trjconv
commit
|
commitdiff
|
tree
2019-09-11
Art
e
m Z
h
murov
Fix f
o
r
the pos
t
-submit failure
commit
|
commitdiff
|
tree
2019-09-11
Art
e
m
Z
hmurov
Dec
o
uple GPU force buffer man
a
g
ement from
b
uffer ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irr
g
a
ng
Use
G
ROMACS CMake toolc
h
ain
f
i
l
e
for gmxapi P
y
thon
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Paul Bauer
B
a
sic
toolchain
t
o facilitate
G
M
XAPI build
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Add
g
mxap
i
.
modify_input operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric
I
rrgang
P
r
ovide a gmxa
p
i
.
r
e
ad_tp
r
operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Er
i
c
Irrgan
g
Update gmx
a
pi
.
simulation
.
c
ontext details
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
r
ic Irrgang
U
p
da
t
e gmxapi Python package infrastructu
r
e for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
No
r
malize some t
e
sting res
o
urce
s
for the Python packages
.
commit
|
commitdiff
|
tree
2019-09-11
Mag
n
u
s
Lundborg
Tid
y
u
p the
F
E kernel
commit
|
commitdiff
|
tree
2019-09-10
P
a
ul Baue
r
Fix nightly build
commit
|
commitdiff
|
tree
2019-09-10
Szilárd Páll
Use thread-MP
I
in the gpu
c
o
mm matrix
commit
|
commitdiff
|
tree
2019-09-10
P
ascal Merz
Coordinate Propagators
commit
|
commitdiff
|
tree
2019-09-10
Pa
s
cal Merz
StatePropagatorData: Introduced co
n
st box access
o
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal Me
r
z
Add
trivial
c
onst
qualifiers to shellfc and Ener
g
yOutput
commit
|
commitdiff
|
tree
2019-09-10
P
a
scal Merz
Constraint element fo
r
the mo
d
ular s
i
m
u
lator
commit
|
commitdiff
|
tree
2019-09-09
Szilár
d
Páll
Pass gmx::For
c
eF
l
a
g
s
t
o CPU nbnxm dispatch
code
commit
|
commitdiff
|
tree
2019-09-09
Szi
l
árd Páll
Pass the
n
ew gmx::ForceFlags to the nbnxm
modul
e
commit
|
commitdiff
|
tree
2019-09-09
Berk H
e
ss
R
e
move incorrect check with rf-zero
commit
|
commitdiff
|
tree
2019-09-09
Pascal Merz
Domain decomposi
t
ion and PME load bal
a
ncing for modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Re
l
a
t
iv
e
entropy
as density simil
a
rity
measure
commit
|
commitdiff
|
tree
2019-09-09
Paul
Bauer
A
d
d gmx convert
-
trj
commit
|
commitdiff
|
tree
2019-09-09
Berk
H
e
ss
Rename DD
S
etup to DD
G
rid
S
etup
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Clean
up
PME rank var
i
ables
commit
|
commitdiff
|
tree
2019-09-09
Berk H
e
ss
Refactor init_dom
a
i
n_decompo
s
ition()
commit
|
commitdiff
|
tree
2019-09-07
Pascal Mer
z
Make p
m
e_
l
oadbal_do() independent of t_state
commit
|
commitdiff
|
tree
2019-09-07
P
a
scal M
e
rz
Forc
e
E
l
em
e
n
t
and She
l
lFCElement f
o
r the mo
d
ul
a
r sim
u
lator
commit
|
commitdiff
|
tree
2019-09-06
Szil
á
r
d
P
á
ll
Add gpuupdate and gp
u
comm OnDemand
t
o
kens
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
E
x
t
r
a
c
t getting of DDRank
S
etup
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
A
d
d PP grid info to DDRankSetup
commit
|
commitdiff
|
tree
2019-09-05
M
ark A
b
r
aham
Up
d
ate mdrun te
s
t compari
s
on i
n
frastructu
r
e
commit
|
commitdiff
|
tree
next