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Update Awh initialization and lifetime management
2018-06-04
Mark Abraham
Update Awh initialization and lifet
i
me
management
commit
|
commitdiff
|
tree
2018-06-04
Szilá
r
d
P
áll
Fix t
i
mi
n
g o
f
clFFT
k
erne
l
s
commit
|
commitdiff
|
tree
2018-06-04
Magnu
s
Lundb
o
rg
Wri
t
e lambdas
a
nd box to
T
NG
at correct interval
s
commit
|
commitdiff
|
tree
2018-06-01
K
e
vin Boy
d
C
o
sm
e
tic fixes to mdp doc
u
m
e
ntation
commit
|
commitdiff
|
tree
2018-05-31
Alekse
i
Iu
p
inov
Merge pm
e
.
c
u
in
t
o
pme-gpu-internal
.
cp
p
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei Iupi
n
o
v
Move
pme-timin
g
s
.
cu
to pme-gpu-timings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
sei Iupinov
P
refer linking
to system c
l
FFT
rather than bun
d
led
o
n
e
commit
|
commitdiff
|
tree
2018-05-31
A
leksei Iupinov
Move
t
he PmeGpuS
p
eci
f
i
c
s
t
ruc
t
ure into pme-gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
upinov
Added the b
u
n
d
l
e
d
c
l
FFT into Op
e
nCL build
s
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Gather the
P
ME GPU constants/macros in a singl
e
h
e
ade
r
commit
|
commitdiff
|
tree
2018-05-28
Aleksei
I
upinov
Support pers
i
stent de
v
ice conte
x
t-der
i
ve
d
da
t
a in P
M
E
.
.
.
commit
|
commitdiff
|
tree
2018-05-25
Mark
A
brah
a
m
Clean up f
o
rce
.
h and i
t
s use
commit
|
commitdiff
|
tree
2018-05-24
Mark Abraham
R
e
move bD
o
mDec
from t_for
c
ere
c
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Fi
x
gr
o
mpp bug
w
ith blocks of
s
am
e
mo
l
e
cules
commit
|
commitdiff
|
tree
2018-05-24
M
a
r
k
Abraham
Reform Ewald-modul
e
cmak
e
handl
i
ng
commit
|
commitdiff
|
tree
2018-05-23
Roland Schulz
Rename GMX_OCL_CLUSTER_S
I
ZE to GMX_OCL_NB_CLUSTE
R
_SIZE
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Split
off col
l
ect
.
cpp from do
m
d
e
c
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Convert
nbnxn_searc
h
t
o C++
commit
|
commitdiff
|
tree
2018-05-22
B
e
r
k Hess
Change nbnxn g
r
id reallocati
o
n
commit
|
commitdiff
|
tree
2018-05-22
B
e
rk H
e
s
s
U
se std::vec
t
or in n
b
nxn_se
a
rch_t
commit
|
commitdiff
|
tree
2018-05-22
Ber
k
Hess
Use std
:
:vector
in nbnxn_
g
rid_t
commit
|
commitdiff
|
tree
2018-05-22
Kev
i
n
Bo
y
d
Cosmetic do
c
umen
t
ation chan
g
es
commit
|
commitdiff
|
tree
2018-05-22
Kev
i
n Boyd
Minor
f
ix
e
s to mdru
n
performance
d
ocumentation
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iupinov
prepareGpu
K
ernelArgu
m
ents(
)
and launchGpuKernel
(
) are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Berk
H
ess
Split off domdec dis
t
rib
u
tion and c
e
ll
s
izes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
S
p
lit atom
redistributi
o
n off from domde
c
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Be
r
k
Hess
Remove commrec from set_ddbox(
)
commit
|
commitdiff
|
tree
2018-05-15
Rol
a
nd
S
chulz
Use same
O
penCL kern
e
l
fo
r
diff
e
rent Ve
n
d
o
rs
commit
|
commitdiff
|
tree
2018-05-10
Carsten Kutzner
Introduce helper
classes for force provider input
and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Paul Bauer
Fi
x
md -
c
pi -noa
p
pend
commit
|
commitdiff
|
tree
2018-05-04
Mar
k
Abraham
Merge "Merge
b
ranch release-20
1
8
"
commit
|
commitdiff
|
tree
2018-05-04
Mar
k
Abraham
More cons
t
cor
r
e
c
t
ness
commit
|
commitdiff
|
tree
2018-05-03
Mark A
b
r
a
ham
Me
r
ge branch release-2018
commit
|
commitdiff
|
tree
2018-05-02
Roland Sc
h
ulz
En
a
ble uncrustif
y
for OpenC
L
commit
|
commitdiff
|
tree
2018-05-02
Rol
a
nd Schulz
Support 4 sized cl
u
ster fo
r
GPU NBL search
commit
|
commitdiff
|
tree
2018-04-27
Berk H
e
ss
Remove p
u
ll MPI cod
e
dupli
c
a
tion
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
Reo
r
g
anize files for re
f
erence manual
commit
|
commitdiff
|
tree
2018-04-26
Paul Bau
e
r
Spl
i
t up analysis c
h
apter in reference m
a
nual
commit
|
commitdiff
|
tree
2018-04-26
Paul
B
a
uer
Split
up special topics
s
ection in manual
commit
|
commitdiff
|
tree
2018-04-25
P
a
ul
Bauer
Add page breaks
in r
e
ferenc
e
m
anual
commit
|
commitdiff
|
tree
2018-04-25
Paul
B
a
u
e
r
Split up Inte
r
a
c
tion funct
i
on
s
m
anual p
a
ge
commit
|
commitdiff
|
tree
2018-04-25
Mark Abrah
a
m
Refac
t
or SD update
commit
|
commitdiff
|
tree
2018-04-25
Paul
B
auer
C
ha
n
ge image conversion to on
l
y be build once
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
DeviceBuffe
r
headers are
a
dded
commit
|
commitdiff
|
tree
2018-04-23
Szilá
r
d Páll
Fi
x
i
c
c warni
n
g i
n
post-sub
m
it
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Páll
Add po
s
t-
s
ubmit
w
ith ARM H
P
C
T
oolchain
commit
|
commitdiff
|
tree
2018-04-21
Szi
l
árd
P
áll
Twea
k
PME run mode checks
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
C
onvert m
a
nual from L
a
TeX to Markup
commit
|
commitdiff
|
tree
2018-04-21
P
a
ul
B
auer
Se
c
ond change
t
racking commit
commit
|
commitdiff
|
tree
2018-04-21
Paul Bau
e
r
In
t
e
r
mediate comm
i
t to trac
k
cha
n
ges to ma
n
u
al
commit
|
commitdiff
|
tree
2018-04-17
Vivec
a
L
i
nd
a
h
l
D
isallow -ski
p
values <= 0 for gmx
trjconv
.
commit
|
commitdiff
|
tree
2018-04-17
Pa
u
l Bauer
F
i
x legacy topology
m
e
mory error
commit
|
commitdiff
|
tree
2018-04-17
Mark Abr
a
ham
Shift p
e
r-step control logic to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark Abraham
Break ap
a
rt u
p
da
t
e_c
o
ns
t
raint
s
commit
|
commitdiff
|
tree
2018-04-16
Szilárd Páll
Add post-submit
test with
hwloc
o
f
f
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
M
o
v
e
n
atoms_mol out of gmx_
m
o
l
blo
c
k_t
commit
|
commitdiff
|
tree
2018-04-16
Mark Abra
h
am
U
p
dated m
d
run
comparison infrastructure
commit
|
commitdiff
|
tree
2018-04-13
Mark
A
braham
C
lean up constra
i
nt
s
cod
e
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
R
emove u
s
e of where(), if
D
EBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraha
m
Reorganize
ene
r
gy
evaluatio
n
fo
r
EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
Prevent Open
C
L
t
i
ming me
m
ory leak
commit
|
commitdiff
|
tree
2018-04-09
B
e
r
k Hess
Convert gmx_molblock_t to C++
commit
|
commitdiff
|
tree
2018-04-05
Mark
A
braham
Simplified h
a
n
d
li
n
g o
f
s
i
mulatio
n
runners
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Cr
e
at
e
gro
m
a
cs/mdru
n
module and move
code th
e
re
commit
|
commitdiff
|
tree
2018-04-05
Szilárd Páll
Refactor cj pre
l
oad in the nonbonde
d
OpenCL k
e
rnel
s
commit
|
commitdiff
|
tree
2018-04-04
Mark
A
braham
Q
u
iet checkpo
i
nt reading
commit
|
commitdiff
|
tree
2018-04-04
P
as
c
al Merz
Move checkNumb
e
rOfB
o
ndedIn
t
e
ractions
commit
|
commitdiff
|
tree
2018-04-03
Be
r
k Hes
s
Co
n
v
ert gm
x
_
mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Remov
e
leftover mention of twin-range s
c
h
e
me
commit
|
commitdiff
|
tree
2018-04-03
M
a
rk Ab
r
aham
Mer
g
e "
M
erge
b
ranch release-2018"
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Move
f
i
le
o
pening out
o
f init_pull
(
)
commit
|
commitdiff
|
tree
2018-03-29
Szilárd Páll
Twe
a
k/ena
b
le icc 18 post-submi
t
tests
commit
|
commitdiff
|
tree
2018-03-29
M
agnus Lund
b
org
Improved check o
f
if only forces are comp
u
ted in do
_
pa
i
rs()
commit
|
commitdiff
|
tree
2018-03-29
Paul Bauer
F
ix
c
mak
e
Sphinx detection for version
s
>1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd Páll
Swit
c
h CUDA 9
.
0/gcc 5 test to CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk He
s
s
Modu
l
arize pull
_
coor
d
_work_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Fre
e
more
memory
i
n
grompp a
n
d mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Remove mols
f
r
o
m
gmx_m
t
op_
t
commit
|
commitdiff
|
tree
2018-03-28
M
a
r
k
Abr
a
ham
Merge branch release-2018
commit
|
commitdiff
|
tree
2018-03-27
Mark A
b
r
a
ham
Cla
r
if
i
ed mdp
o
p
tions re
l
ating to bond
s
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
More gcc-8 fixes for POWER
commit
|
commitdiff
|
tree
2018-03-21
David van der Spoel
Ren
a
med ent
r
opy
.
*
to
thermochemist
r
y
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark
Abraham
Ve
r
si
o
n
2
018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Merge "Merge branch releas
e
-2016 into
r
elease-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Upda
t
e
r
elease n
o
tes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abraham
Merge bran
c
h release-2016 in
t
o
r
elease-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update use
of gpu_
i
d
i
n Jenki
n
s
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallow si
n
gl
e
sim
u
lation with m
u
ltisim
commit
|
commitdiff
|
tree
2018-03-20
M
a
rk Abraham
Update use of gpu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abrah
a
m
Update use of gpu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
braham
Add help
e
r
function to make a vector from a
n
Arra
y
Ref
commit
|
commitdiff
|
tree
2018-03-19
Mark Abraham
Fix VSX
SI
M
D with gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Paul B
a
ue
r
Only free
t
opology when
a
l
l
ocated
commit
|
commitdiff
|
tree
2018-03-16
Berk He
s
s
Correct PMF sign error
in AWH b
i
as sh
a
ring
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
I
m
prove in
t
er-
s
i
m
u
lation signaling
commit
|
commitdiff
|
tree
2018-03-14
Mark A
b
ra
h
am
Make a persistent physical node communicator
commit
|
commitdiff
|
tree
2018-03-14
B
erk Hess
Fix mdrun sign
a
llin
g
with AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-13
Berk
Hes
s
Add
A
WH
f
ix
e
s to
release notes
commit
|
commitdiff
|
tree
2018-03-13
Szilárd
P
áll
Require O
p
e
nCL
1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ensemble checkpointin
g
commit
|
commitdiff
|
tree
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