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Make nbnxn_grid_t counts and sizes arrays
2018-06-05
Berk H
e
ss
Mak
e
nbnxn_gr
i
d
_
t c
o
un
t
s and si
z
es arrays
commit
|
commitdiff
|
tree
2018-06-05
Mark Abraham
M
ake Constrain
t
s a prop
e
r class
commit
|
commitdiff
|
tree
2018-06-04
Mark Abraham
Upd
a
te
A
wh initi
a
lization a
n
d l
i
fe
t
ime management
commit
|
commitdiff
|
tree
2018-06-04
Szilárd Páll
F
i
x
timing of clFFT kernel
s
commit
|
commitdiff
|
tree
2018-06-04
Magnus L
u
n
d
borg
W
r
ite
lambdas a
n
d box
to TNG at correct intervals
commit
|
commitdiff
|
tree
2018-06-01
Ke
v
in Boy
d
Cosmetic fixes to m
d
p documentation
commit
|
commitdiff
|
tree
2018-05-31
A
l
ekse
i
Iupinov
Merge pme
.
cu into pme-gpu-int
e
rnal
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Mo
v
e
pme-timings
.
cu
t
o pm
e
-gpu-timings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleks
e
i Iupinov
Pref
e
r link
i
ng to system clFFT
r
ather
than b
u
ndled
o
ne
commit
|
commitdiff
|
tree
2018-05-31
Alekse
i
Iupinov
Move the Pme
G
puSpec
i
fi
c
structure int
o
pme-gpu
-
types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Alekse
i
Iupinov
Added the bund
l
ed
clF
F
T i
n
to Ope
n
CL builds
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iup
i
nov
Gat
h
er
t
h
e PME GPU constants/macro
s
in a sing
l
e header
commit
|
commitdiff
|
tree
2018-05-28
Aleksei Iupinov
S
up
p
ort pe
r
sistent device context-derived
d
a
ta in
P
ME
.
.
.
commit
|
commitdiff
|
tree
2018-05-25
Mark Abraham
Clean up f
o
rce
.
h and
i
t
s use
commit
|
commitdiff
|
tree
2018-05-24
M
ark Abra
h
am
Remove
b
Do
m
Dec fr
o
m t_forcerec
commit
|
commitdiff
|
tree
2018-05-24
Berk Hes
s
Fix
g
r
o
m
pp bug wit
h
bl
o
cks of same molecules
commit
|
commitdiff
|
tree
2018-05-24
M
a
rk A
b
raham
Refor
m
Ew
a
ld-module
c
make handling
commit
|
commitdiff
|
tree
2018-05-23
Roland Schulz
Rename GMX_OCL_CLUSTER_SIZE to GMX
_
OCL_N
B
_
CLUSTER_SIZE
commit
|
commitdiff
|
tree
2018-05-23
Berk Hes
s
Sp
l
it off collect
.
cpp from
d
omdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Convert nbnxn
_
s
e
arch to
C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Change nbnxn grid rea
l
location
commit
|
commitdiff
|
tree
2018-05-22
B
e
r
k
Hess
U
s
e std::vector in nbnxn_search_
t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use s
t
d::
v
ecto
r
in nbn
x
n_grid
_
t
commit
|
commitdiff
|
tree
2018-05-22
Kevi
n
Boyd
C
os
m
etic documentati
o
n changes
commit
|
commitdiff
|
tree
2018-05-22
Kevin Boyd
Minor fixes
to md
r
un
perfo
r
mance document
a
tion
commit
|
commitdiff
|
tree
2018-05-18
Alekse
i
I
up
i
nov
p
r
epa
r
eGpuKernel
A
rgu
m
ent
s
()
a
nd launchGp
u
Kernel(
)
are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split of
f
domdec
d
i
stribution an
d
c
e
llsizes
commit
|
commitdiff
|
tree
2018-05-17
B
e
rk Hess
Split a
t
om redistributio
n
off from domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Remov
e
commrec
f
rom s
e
t_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
Rolan
d
Sc
h
ulz
U
se same OpenC
L
ke
r
nel for diffe
r
ent
V
e
n
dors
commit
|
commitdiff
|
tree
2018-05-10
Carst
e
n Kutzner
Introd
u
ce h
e
lper cl
a
sses
for for
c
e provider
i
nput a
n
d
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
P
a
ul Bauer
Fix m
d
-cpi -noa
p
pend
commit
|
commitdiff
|
tree
2018-05-04
Mark Abraham
M
e
rg
e
"Merge bra
n
c
h release-
2
018
"
commit
|
commitdiff
|
tree
2018-05-04
Mark Ab
r
aham
More const correctness
commit
|
commitdiff
|
tree
2018-05-03
Mark Abraham
Merge branch release-2018
commit
|
commitdiff
|
tree
2018-05-02
Rola
n
d Schul
z
E
nab
l
e
uncrustify for
O
p
enCL
commit
|
commitdiff
|
tree
2018-05-02
Roland Schulz
Sup
p
ort 4 sized cluster
f
or G
P
U
NBL search
commit
|
commitdiff
|
tree
2018-04-27
Berk
H
ess
Re
m
o
ve pull MPI code
d
u
plication
commit
|
commitdiff
|
tree
2018-04-26
Pau
l
Bauer
Reorganize files fo
r
re
f
erence m
a
nual
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
S
p
l
i
t
up analysi
s
chapter in ref
e
r
ence ma
n
ual
commit
|
commitdiff
|
tree
2018-04-26
P
aul Bauer
Split up
spe
c
i
a
l
t
o
pics sec
t
ion in manua
l
commit
|
commitdiff
|
tree
2018-04-25
Paul Bau
e
r
Add
page breaks in
r
efer
e
n
c
e manual
commit
|
commitdiff
|
tree
2018-04-25
P
aul
B
auer
Split up Interacti
o
n functions manual page
commit
|
commitdiff
|
tree
2018-04-25
Mark Ab
r
aham
Refactor SD update
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
Cha
n
ge image c
o
nv
e
rsion to only be build once
commit
|
commitdiff
|
tree
2018-04-23
A
leksei I
u
pinov
Devi
c
eBuf
f
er
h
eaders
are
a
dded
commit
|
commitdiff
|
tree
2018-04-23
Szilárd Páll
Fix icc warning
in po
s
t-submi
t
commit
|
commitdiff
|
tree
2018-04-21
Szilá
r
d Pál
l
A
d
d
post-
s
u
bmit
with ARM HPC Toolchain
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Páll
Tweak PME r
u
n mode che
c
ks
commit
|
commitdiff
|
tree
2018-04-21
Pa
u
l
Ba
u
er
C
o
nvert
m
anual from
L
a
TeX
t
o Markup
commit
|
commitdiff
|
tree
2018-04-21
P
a
ul B
a
uer
S
econd
c
h
ange t
r
a
cki
n
g commit
commit
|
commitdiff
|
tree
2018-04-21
P
a
ul
Bauer
Intermed
i
a
te commit
to tra
c
k
changes to
manual
commit
|
commitdiff
|
tree
2018-04-17
V
iveca Li
n
dahl
Di
s
al
l
ow -skip va
l
ues <= 0 for gmx t
r
jconv
.
commit
|
commitdiff
|
tree
2018-04-17
Paul Bauer
Fix legacy
top
o
logy memo
r
y
error
commit
|
commitdiff
|
tree
2018-04-17
Ma
r
k Abraham
S
hift per-
s
tep control
logic to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark Ab
r
aham
B
r
e
ak apart update_const
r
aints
commit
|
commitdiff
|
tree
2018-04-16
Szilárd Páll
A
d
d
post-submit
test with hwlo
c
off
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
M
ove
n
at
o
ms_mol
o
ut o
f
gmx_molblock_t
commit
|
commitdiff
|
tree
2018-04-16
Mar
k
Abraham
Upda
t
ed mdru
n
comparis
o
n
i
nf
r
astructure
commit
|
commitdiff
|
tree
2018-04-13
Mark
Abraham
C
l
ea
n
up constrain
t
s
c
ode
commit
|
commitdiff
|
tree
2018-04-12
Ma
r
k Abraham
Remove use of wh
e
r
e
(), if DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraha
m
Reo
r
ganize energy evaluatio
n
for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
Prevent OpenC
L
timing
m
emory leak
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Conver
t
gmx_
m
olblock_t to
C++
commit
|
commitdiff
|
tree
2018-04-05
Mark Abr
a
ham
Simplified h
a
ndli
n
g of simula
t
ion runners
commit
|
commitdiff
|
tree
2018-04-05
M
a
rk Abraham
Create gromacs/md
r
un modu
l
e and move
c
o
d
e
there
commit
|
commitdiff
|
tree
2018-04-05
Szilár
d
P
áll
Refactor cj pr
e
lo
a
d in the
n
onbonded OpenCL kernels
commit
|
commitdiff
|
tree
2018-04-04
Mark Abraha
m
Qu
i
e
t checkpoint readi
n
g
commit
|
commitdiff
|
tree
2018-04-04
P
a
s
cal Merz
Move checkNumberOfBondedInteractio
n
s
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
C
onvert gmx_mto
p
_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraha
m
R
emov
e
lef
t
over
m
e
ntio
n
o
f
twin-ra
n
ge scheme
commit
|
commitdiff
|
tree
2018-04-03
Ma
r
k Abraham
Merge
"
Merge branch
release-2018"
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Move file open
i
ng
o
ut of init_pull()
commit
|
commitdiff
|
tree
2018-03-29
S
z
ilárd Páll
T
weak/enable icc 18 post-sub
m
it tests
commit
|
commitdiff
|
tree
2018-03-29
Magnus Lundborg
Impro
v
ed check o
f
if only forc
e
s are c
o
mputed
in do_pairs()
commit
|
commitdiff
|
tree
2018-03-29
P
a
u
l Bauer
Fix cmake Sphin
x
detection for ve
r
s
ions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szil
á
rd Pá
l
l
Switch CUDA 9
.
0/gcc
5
t
e
s
t to CUDA 9
.
1
/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
B
e
rk Hess
M
o
d
ularize pu
l
l_coord_work_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Fre
e
m
or
e
memo
r
y i
n
grompp and
mdrun
commit
|
commitdiff
|
tree
2018-03-28
Be
r
k Hess
Re
m
ove mols from g
m
x_mtop_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark
A
braham
M
e
rge branch
release-2018
commit
|
commitdiff
|
tree
2018-03-27
Ma
r
k Abraham
Clarified mdp options
r
elating to bonds
commit
|
commitdiff
|
tree
2018-03-27
Mark Abra
h
am
More g
c
c
-
8 fixes for
POWER
commit
|
commitdiff
|
tree
2018-03-21
David van der Spoel
Re
n
amed entropy
.
*
t
o
thermoche
m
i
s
try
.
*
commit
|
commitdiff
|
tree
2018-03-21
M
ark Abraham
V
ersio
n
2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abra
h
a
m
Mer
g
e "Merge branc
h
rele
a
se-2016 int
o
r
elease-
2
018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
M
a
rk Abrah
a
m
Update rel
e
ase notes fo
r
2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
braham
Mer
g
e branch
r
e
lease-2016 into re
l
ease-2018
commit
|
commitdiff
|
tree
2018-03-20
Ma
r
k Abraha
m
Update
u
se o
f
g
p
u_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Berk He
s
s
Disall
o
w single simulation with
multisim
commit
|
commitdiff
|
tree
2018-03-20
M
a
r
k
Abraham
Upd
a
t
e
us
e
of
gpu_id in
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
U
p
date
u
se of gpu_i
d
i
n
J
enkins
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abraham
Add helper function to make a vect
o
r from an ArrayRef
commit
|
commitdiff
|
tree
2018-03-19
Mark Abraham
Fix VSX SIMD with gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
Only f
r
e
e
topology when allocated
commit
|
commitdiff
|
tree
2018-03-16
B
e
rk H
e
ss
Corr
e
c
t PMF sign er
r
or in AWH bias shari
n
g
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
I
m
p
rove
i
nt
e
r-simul
a
tion
signa
l
ing
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
Mak
e
a persiste
n
t physical node co
m
municator
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix mdr
u
n signalling with AWH
b
i
as sh
a
rin
g
commit
|
commitdiff
|
tree
2018-03-13
B
erk Hess
Add
A
WH
fi
x
e
s
t
o
r
e
leas
e
notes
commit
|
commitdiff
|
tree
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