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Update Awh initialization and lifetime management
2018-06-04
Mark Ab
r
aham
Upda
t
e Aw
h
ini
t
ial
i
z
ation and lifetime management
commit
|
commitdiff
|
tree
2018-06-04
Szi
l
árd
P
á
l
l
Fix
timing of
c
lFFT k
e
rnels
commit
|
commitdiff
|
tree
2018-06-04
M
agn
u
s Lundborg
Write lambdas and b
o
x to TNG at co
r
rect interv
a
ls
commit
|
commitdiff
|
tree
2018-06-01
Kevin B
o
yd
C
o
smetic fixes to mdp
do
c
umentation
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
u
pinov
M
e
rge pme
.
cu
i
nt
o
pme-gpu-internal
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
u
p
in
o
v
Move pme-timings
.
cu to pme-gpu-timings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
Iup
i
nov
Prefer linking t
o
system
clFF
T
r
a
the
r
than bundled one
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
sei Iupino
v
M
o
v
e the
P
meGpuSpeci
f
ic s
t
r
uct
u
re into pme-g
p
u-
t
ypes
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
sei Iupinov
Added
t
h
e bundled clFFT
i
nto OpenCL builds
commit
|
commitdiff
|
tree
2018-05-31
A
leksei
Iupinov
G
a
ther the PME GPU
c
ons
t
a
n
ts/mac
r
os in a s
i
ngle h
e
ader
commit
|
commitdiff
|
tree
2018-05-28
Al
e
ksei Iupinov
Suppor
t
p
ersistent device context-der
i
ve
d
data in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-25
Mark
Abraham
Clean
u
p force
.
h and its use
commit
|
commitdiff
|
tree
2018-05-24
Ma
r
k Ab
r
aham
Remove bDomDec from t
_
for
c
erec
commit
|
commitdiff
|
tree
2018-05-24
Berk
He
s
s
Fix grompp bug with bloc
k
s
of
s
ame
m
olecule
s
commit
|
commitdiff
|
tree
2018-05-24
Mark Abraham
Ref
o
rm
E
wald-module cm
a
ke
h
andling
commit
|
commitdiff
|
tree
2018-05-23
Roland S
c
hulz
R
e
n
a
me GMX
_
OCL
_
CLUSTER_SIZE
to GM
X
_OCL_NB_CLUSTER_SIZE
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Spl
i
t
o
f
f
collec
t
.
cpp fr
o
m domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Berk Hes
s
Convert
n
b
nxn_search to C
+
+
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
C
hange nbnxn
g
rid reallocati
o
n
commit
|
commitdiff
|
tree
2018-05-22
Ber
k
Hess
Use std
:
:vecto
r
in nbnxn_search
_
t
commit
|
commitdiff
|
tree
2018-05-22
Be
r
k
Hess
U
s
e
std::vect
o
r
in nbn
x
n_grid
_
t
commit
|
commitdiff
|
tree
2018-05-22
Kevin
Boyd
Cos
m
etic doc
u
mentatio
n
changes
commit
|
commitdiff
|
tree
2018-05-22
Kevin
B
oy
d
Minor fixes to mdru
n
per
f
or
m
ance documentation
commit
|
commitdiff
|
tree
2018-05-18
Alek
s
ei Iupino
v
p
r
epare
G
puKernelArguments()
and launchGpuKern
e
l()
are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Ber
k
H
e
ss
Split off domdec di
s
trib
u
tion an
d
cellsizes
commit
|
commitdiff
|
tree
2018-05-17
B
erk Hess
Spl
i
t ato
m
redistribution off from domd
e
c
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Remov
e
co
m
m
r
ec
f
ro
m
set_ddb
o
x()
commit
|
commitdiff
|
tree
2018-05-15
Ro
l
a
n
d Schu
l
z
Use same
O
p
enCL kernel f
o
r different
V
e
ndors
commit
|
commitdiff
|
tree
2018-05-10
Carsten Kutzn
e
r
Introduce h
e
l
per classes for force provider input and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
P
a
ul Bauer
Fix md -cpi -noap
p
end
commit
|
commitdiff
|
tree
2018-05-04
Mark Abra
h
am
Merge
"M
e
rge
branch rel
e
a
s
e
-2018"
commit
|
commitdiff
|
tree
2018-05-04
Mar
k
Abra
h
a
m
More const corre
c
tness
commit
|
commitdiff
|
tree
2018-05-03
Mark Ab
r
aham
Merge b
r
anch relea
s
e-2
0
1
8
commit
|
commitdiff
|
tree
2018-05-02
Rola
n
d Schulz
Enable uncrustify
for
O
penCL
commit
|
commitdiff
|
tree
2018-05-02
Roland Schulz
Support 4 siz
e
d clust
e
r
f
or
GPU NBL search
commit
|
commitdiff
|
tree
2018-04-27
Ber
k
H
ess
R
emov
e
pul
l
MPI code duplic
a
tion
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
R
e
org
a
n
ize
files for reference manual
commit
|
commitdiff
|
tree
2018-04-26
Pau
l
Bauer
Split up
a
nal
y
sis ch
a
pter in reference manual
commit
|
commitdiff
|
tree
2018-04-26
Paul
B
a
u
er
Split up special topics section in man
u
al
commit
|
commitdiff
|
tree
2018-04-25
Pau
l
Bauer
Add page bre
a
ks
i
n reference m
a
nual
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
Sp
l
i
t
u
p
Interaction fun
c
ti
o
ns man
u
a
l
page
commit
|
commitdiff
|
tree
2018-04-25
M
a
rk Abraham
R
e
factor SD u
p
date
commit
|
commitdiff
|
tree
2018-04-25
Pa
u
l
Bauer
Change image conversion to
only be
build
o
nce
commit
|
commitdiff
|
tree
2018-04-23
Alek
s
e
i
Iupinov
D
eviceBu
f
fer head
e
rs are
added
commit
|
commitdiff
|
tree
2018-04-23
S
z
ilárd Páll
Fix ic
c
warning in p
o
st-sub
m
it
commit
|
commitdiff
|
tree
2018-04-21
Szilárd P
á
ll
Add p
o
st-submit with ARM
HPC Toolch
a
i
n
commit
|
commitdiff
|
tree
2018-04-21
Szil
á
rd
P
á
l
l
Twea
k
PME run m
o
de checks
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Convert manual from LaTeX to Markup
commit
|
commitdiff
|
tree
2018-04-21
Paul
Bau
e
r
Secon
d
ch
a
nge tracking com
m
i
t
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Intermediate c
o
mmit to track change
s
to manual
commit
|
commitdiff
|
tree
2018-04-17
Vive
c
a Lind
a
hl
Disallow -skip values <= 0 for gmx
t
rj
c
onv
.
commit
|
commitdiff
|
tree
2018-04-17
Paul B
a
uer
F
i
x
l
egacy top
o
logy
m
emory error
commit
|
commitdiff
|
tree
2018-04-17
Mark Abraham
Shift per-step
con
t
rol logi
c
to do_
m
d
commit
|
commitdiff
|
tree
2018-04-17
Mark
A
b
raha
m
Break ap
a
rt update
_
constraints
commit
|
commitdiff
|
tree
2018-04-16
S
zilár
d
Páll
Add post-submit
test wit
h
hwloc off
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
Move nato
m
s_mol o
u
t
o
f gmx_molblock_t
commit
|
commitdiff
|
tree
2018-04-16
Mark Abraham
U
pdat
e
d mdrun compar
i
so
n
i
n
f
rastructure
commit
|
commitdiff
|
tree
2018-04-13
Mar
k
Abraha
m
Cl
e
an up c
o
nstrai
n
t
s code
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Remove use of where(), if
D
E
B
UG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Reorga
n
ize
e
nergy evalua
t
i
o
n for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
Prevent
O
penCL tim
i
ng memory
l
eak
commit
|
commitdiff
|
tree
2018-04-09
Be
r
k
Hess
Convert gmx_mo
l
bl
o
ck_t to C++
commit
|
commitdiff
|
tree
2018-04-05
Mark
Ab
r
aha
m
Simplified handl
i
n
g
of
simul
a
t
ion runners
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Create gromacs/mdrun module and move cod
e
t
here
commit
|
commitdiff
|
tree
2018-04-05
Sz
i
lá
r
d
Pá
l
l
Refactor cj
preload
in t
h
e nonbonded
OpenCL ker
n
el
s
commit
|
commitdiff
|
tree
2018-04-04
M
ark Abraham
Quiet
checkpoint reading
commit
|
commitdiff
|
tree
2018-04-04
P
a
sca
l
Merz
M
o
ve checkNumberOfBond
e
dI
n
teractions
commit
|
commitdiff
|
tree
2018-04-03
Berk Hes
s
Convert gmx
_
mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark
A
b
raham
Rem
o
ve leftover mention of tw
i
n-range scheme
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Merge "Merge branch
r
ele
a
se-2018"
commit
|
commitdiff
|
tree
2018-03-29
Berk H
e
ss
Move file opening out of init_pull()
commit
|
commitdiff
|
tree
2018-03-29
Szil
á
r
d
Páll
Twea
k
/
e
n
able icc 18
post-sub
m
it
tests
commit
|
commitdiff
|
tree
2018-03-29
M
a
gnus Lun
d
borg
Im
p
roved
check of if only
f
o
rces are computed in do_pairs()
commit
|
commitdiff
|
tree
2018-03-29
Paul B
a
uer
Fix cmake Sphinx d
e
tection
for versions
>
1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilá
r
d P
á
l
l
Switch C
U
DA 9
.
0/
g
c
c 5 test to
C
UDA
9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk He
s
s
Modular
i
ze
pull_coor
d
_work_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Free more memory
i
n
grompp
a
nd mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Remo
v
e mols from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Merge branch relea
s
e-2018
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraha
m
C
l
a
rified mdp
o
ptions
r
elating
t
o b
o
nds
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
M
o
re gcc-8 fixes for POWER
commit
|
commitdiff
|
tree
2018-03-21
D
avid van der Spoel
Renamed entropy
.
* to ther
m
och
e
m
istry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Ma
r
k Abraham
Vers
i
on
2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abra
h
am
Me
r
ge "Merge branch rele
a
se-2016 into re
l
eas
e
-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Update release notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Ab
r
aham
Merge bra
n
c
h
rel
e
ase-2016 into release-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
U
pdate use of gp
u
_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallow sin
g
le
simulat
i
on wit
h
mul
t
isi
m
commit
|
commitdiff
|
tree
2018-03-20
Mark Abrah
a
m
Update us
e
of gpu_id in Jenkin
s
commit
|
commitdiff
|
tree
2018-03-20
Mark A
b
raham
Up
d
ate
u
se of gpu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
A
dd helper function
t
o make a
v
ector from an ArrayRef
commit
|
commitdiff
|
tree
2018-03-19
Mark Abraham
Fix VSX SIMD w
i
th
gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Pa
u
l Ba
u
er
Only free top
o
logy when all
o
cated
commit
|
commitdiff
|
tree
2018-03-16
B
erk Hess
Correct PMF
sign err
o
r in A
W
H bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve inter-si
m
u
l
ation
sig
n
ali
n
g
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
Make a persist
e
nt
p
hysical node communi
c
a
t
o
r
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
e
s
s
F
ix m
d
r
un signal
l
in
g
with AWH b
i
as sharing
commit
|
commitdiff
|
tree
2018-03-13
B
erk H
e
ss
A
d
d
AWH
f
i
xes to r
e
l
ease
notes
commit
|
commitdiff
|
tree
2018-03-13
S
z
ilárd Pál
l
Requir
e
OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
B
erk Hess
Fix AWH en
s
emble chec
k
poin
t
i
ng
commit
|
commitdiff
|
tree
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