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Third beta release of 2018
2017-12-19
Mark A
b
ra
h
a
m
Third beta release
o
f 2018
commit
|
commitdiff
|
tree
2017-12-19
Mark Ab
r
aham
Fix ta
b
l
e tests an
d
improve table construction
commit
|
commitdiff
|
tree
2017-12-19
Berk He
s
s
Make ov
e
rsu
b
s
cription war
n
i
n
g consistent
commit
|
commitdiff
|
tree
2017-12-19
Carsten Kutz
n
e
r
Fix electric fi
e
l
d
.
mdp documentation
commit
|
commitdiff
|
tree
2017-12-19
E
rik
Lindahl
Use r
e
duced de
f
ault tolerances for
t
px compariso
n
commit
|
commitdiff
|
tree
2017-12-18
R
o
lan
d
S
ch
u
lz
Fix
cm
a
k
e error
with ema
c
s lock file
s
in place
commit
|
commitdiff
|
tree
2017-12-17
Roland Schulz
Change
avx
_
12
8
_fm
a
build to double
commit
|
commitdiff
|
tree
2017-12-17
Rola
n
d Schulz
Support Simd4N
for SimdRealWidth<4
commit
|
commitdiff
|
tree
2017-12-14
E
r
i
k Lind
a
hl
Fix
PBC error in g
m
x_spat
i
al
commit
|
commitdiff
|
tree
2017-12-14
Mark Abra
h
a
m
M
e
rge "Merge branch
release-2016 i
n
to relea
s
e-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-12
Erik
Lindahl
Disallow ascii formats for g
m
x
trj
c
a
t
commit
|
commitdiff
|
tree
2017-12-12
Mark Abraham
Impr
o
v
e gr
o
mpp missing-param
e
ters
e
rror
message
commit
|
commitdiff
|
tree
2017-12-12
Mark
Abraham
Merge branch
rel
e
ase-
2
0
1
6 into release-20
1
8
commit
|
commitdiff
|
tree
2017-12-11
Mark Abraham
Second
b
eta rele
a
se of 2
0
18
commit
|
commitdiff
|
tree
2017-12-11
Erik Lind
a
h
l
R
emove du
p
licate
d
lines
f
rom
O
PLS ffbonded
.
itp
commit
|
commitdiff
|
tree
2017-12-11
Rola
n
d
S
chulz
Repl
a
ce intrinsic with in
l
i
ne asm for AVX512 unit test
commit
|
commitdiff
|
tree
2017-12-11
Er
i
k Lind
a
hl
Don't warn about NVML
c
locks that are
a
t
max
commit
|
commitdiff
|
tree
2017-12-11
Berk
H
ess
Add gromp
p
note for PR
p
co
u
ple + position res
t
ra
i
nts
commit
|
commitdiff
|
tree
2017-12-10
Erik Lindahl
Revert
"
Di
s
able def
a
ult-on
NVML
suppor
t
in
CMake
"
commit
|
commitdiff
|
tree
2017-12-07
Erik Lindahl
Added cool quo
t
e fr
o
m Viveca's def
e
nse
commit
|
commitdiff
|
tree
2017-12-07
Roland
Schulz
Fix AWH test accura
c
y
commit
|
commitdiff
|
tree
2017-12-07
Berk
Hess
Choose f
a
ster nbnxn SIMD kernels
o
n AMD Zen
commit
|
commitdiff
|
tree
2017-12-07
Ro
l
an
d
Sc
h
u
lz
Fi
x
e
xp test fo
r
ICC
in double
commit
|
commitdiff
|
tree
2017-12-07
R
oland
Schulz
F
i
x R
e
lWithAssert
w
ith ICC
commit
|
commitdiff
|
tree
2017-12-07
A
l
eksei Iupin
o
v
Rel
a
x
e
d pre
c
ision in spline i
n
t
erpo
l
ation
tests
commit
|
commitdiff
|
tree
2017-12-06
Szilár
d
Páll
Implem
e
nt
alternating
G
PU wait
commit
|
commitdiff
|
tree
2017-12-05
A
leksei I
u
pi
n
o
v
Do not acce
p
t
un
s
up
p
ort
e
d
c
ombinat
i
on
"
-pme cpu
-pmef
f
t
.
.
.
commit
|
commitdiff
|
tree
2017-12-05
Rolan
d
Schul
z
Fix Arra
y
Ref
<
S
imdDInt
3
2> for SS
E
/AVX1
2
8
commit
|
commitdiff
|
tree
2017-12-05
Mark Abraham
Updat
e
testing
to i
n
clude cmake 3
.
1
0
.
0
commit
|
commitdiff
|
tree
2017-12-05
Magnus
L
u
ndborg
SIMD accelerated Ur
e
y-Brad
l
e
y
commit
|
commitdiff
|
tree
2017-12-05
B
e
rk Hess
Fi
x
DD exa
c
t continuati
o
n
b
u
g
commit
|
commitdiff
|
tree
2017-12-04
Mark Abr
a
ham
Fix fr
e
e_gpu
commit
|
commitdiff
|
tree
2017-12-04
Mark A
b
raham
Merge
b
ranc
h
relea
s
e
-2016 i
n
to releas
e
-2018
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk He
s
s
U
p
date mdr
u
n signa
l
help
t
ext
commit
|
commitdiff
|
tree
2017-12-04
B
erk Hess
Only stop at nstlist
s
t
eps with -rep
r
od
commit
|
commitdiff
|
tree
2017-12-04
Erik Lindahl
Fi
x
compilat
i
on issue
s
f
o
r AVX-512
commit
|
commitdiff
|
tree
2017-11-28
Mark Abraham
GRO
M
AC
S
2018 first beta release
commit
|
commitdiff
|
tree
2017-11-28
Ber
k
Hess
Refactor
nbnxn
e
x
cl
u
sion setti
n
g
commit
|
commitdiff
|
tree
2017-11-28
Erik
Lin
d
ah
l
Improv
e
status m
e
s
s
ages fo
r
SIMD checks
commit
|
commitdiff
|
tree
2017-11-27
Szilárd Páll
Time FFT/gather in mixed mode
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
Iupinov
D
i
s
able failing sep
a
r
a
te PM
E
rank tests
commit
|
commitdiff
|
tree
2017-11-27
Paul Bauer
Add GP
U
task information to user-gui
d
e
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupinov
Ena
b
le se
p
a
r
ate P
M
E GPU
rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iupinov
Ac
t
ivate
m
ixed mode of
P
M
E
o
n
GPU
commit
|
commitdiff
|
tree
2017-11-24
Szi
l
á
rd Páll
Add GPU sharing post-submit co
n
f
i
g
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
Update
de
v
eloper guide
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
Activa
t
e PME on GPUs
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Remove o
u
tdated (alre
a
dy implemented) p
i
nnin
g
TODO
commit
|
commitdiff
|
tree
2017-11-24
Mark
Abr
a
ham
Add PME i
n
tegra
t
io
n
test
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
E
xtend ta
s
k assignment
c
ode
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei
Iupino
v
Ment
i
on gmx_install_he
a
d
ers() in the
deve
l
oper
manual
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei
Iu
p
inov
Make FFT
real-s
p
ace grid use CUDA
pinning f
o
r m
i
xe
d
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ks
e
i Iupinov
Pin coord
i
nates,
for
c
es
a
n
d charges f
o
r P
M
E on
G
PU
commit
|
commitdiff
|
tree
2017-11-22
P
a
scal Merz
Proof of
c
oncept: Physical val
i
da
t
i
o
n
s
uite
commit
|
commitdiff
|
tree
2017-11-21
Erik Lindah
l
Separate
S
IMD flag detect
i
on
from
management
commit
|
commitdiff
|
tree
2017-11-21
Mark
Ab
r
a
h
am
Support pinning in HostAllo
c
ator
commit
|
commitdiff
|
tree
2017-11-21
Viveca Li
n
dahl
Add force correlation
to AWH module
commit
|
commitdiff
|
tree
2017-11-21
Paul B
a
uer
First
g
enera
l
additi
o
ns to
the docume
n
tation
commit
|
commitdiff
|
tree
2017-11-19
Viveca Lindahl
Ad
d
AWH section to
m
anual
.
commit
|
commitdiff
|
tree
2017-11-19
Viveca L
i
ndahl
Add AWH bi
a
s
i
n
g module
+
test
s
commit
|
commitdiff
|
tree
2017-11-17
M
ark Abraham
Use HostAllocatio
n
Policy for cha
r
geA
commit
|
commitdiff
|
tree
2017-11-17
M
ark Abraham
Add ch
e
c
k
ing functi
o
n
f
o
r whether a b
u
ffer is p
i
nned
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
Improve handling of PME GPU force
bu
f
fer
commit
|
commitdiff
|
tree
2017-11-15
Alek
s
ei Iupinov
Rename and expose "generic" GPU memo
r
y
tr
a
nsfer func
t
ion
s
commit
|
commitdiff
|
tree
2017-11-10
Mark Abr
a
ham
I
mpor
t
cmake Module
s
/FindCUDA
.
cmak
e
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupino
v
Rena
m
e sync
h
r
o
nous
G
PU transfer functions to
match
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Mark A
b
raham
Prepar
e
d t_mdato
m
s f
o
r us
i
ng vect
o
r
commit
|
commitdiff
|
tree
2017-11-09
Mar
k
Abraha
m
Intr
o
d
uce HostAllocationPo
l
icy
commit
|
commitdiff
|
tree
2017-11-09
Roland Sch
u
lz
ICC should use ZM
M
if c
o
de an
y
how use
s
ZMM
commit
|
commitdiff
|
tree
2017-11-07
Mark Abr
a
h
am
R
eform
gmx
_
p
m
e
_
p
p
alloc a
n
d use v
e
ct
o
r
commit
|
commitdiff
|
tree
2017-11-07
Mark Abr
a
ha
m
Introduce gmxopencl
.
h
commit
|
commitdiff
|
tree
2017-11-07
M
ark Abraham
Test clang on ARM in ni
g
htly matrix
commit
|
commitdiff
|
tree
2017-11-07
Szil
á
r
d Páll
A
d
d
w
allcy
c
le timer for the PME GPU
F reduction
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Split off nbnxn GPU timing
a
nd s
t
agin
g
reduction
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
I
m
prove PME includes
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Pá
l
l
Deduplicate CUDA and Open
C
L
timer struct
commit
|
commitdiff
|
tree
2017-11-06
Davi
d
van der Spoel
Fixed check for water in ge
n
_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
Mark Abraham
Merg
e
"Merge branch re
l
ease-2
0
16"
commit
|
commitdiff
|
tree
2017-11-02
Da
v
id van d
e
r Sp
o
e
l
N
e
w mdp
inpu
t
for e
l
ectric fields
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei Iupino
v
Replace mat
h
.
h by c
m
ath i
n
cl
u
des in
c
p
p
f
i
l
es
commit
|
commitdiff
|
tree
2017-11-02
Mar
k
Abraham
Merge branch
r
elease-2
0
16
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
Sm
a
ll change
to LaT
e
X manual generation
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Fix
t
hread-MPI rank choice
f
o
r
orientation
r
e
s
traints
commit
|
commitdiff
|
tree
2017-11-01
Alek
s
ei I
u
pino
v
Remove u
n
use
d
PME GP
U
decl
a
rations
commit
|
commitdiff
|
tree
2017-11-01
Al
e
ksei
I
upinov
Move pme_gpu_finish_computation() documentation
t
o
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
Fixing missing
r
efe
r
ences in
w
e
b
d
o
cumentation
commit
|
commitdiff
|
tree
2017-11-01
Ale
k
sei Iupinov
Fix erroneou
s
PME
G
P
U
"step" n
a
mings
commit
|
commitdiff
|
tree
2017-11-01
M
ark Abra
h
am
Improve handlin
g
of
GPU IDs
commit
|
commitdiff
|
tree
2017-11-01
Alekse
i
Iupinov
Simplif
y
PME GPU synchro
n
iza
t
ion code
commit
|
commitdiff
|
tree
2017-10-31
Aleksei Iupinov
Reuse ep
b
cXY logic
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Fix nstli
s
t incr
e
ase
warn
i
ng print
commit
|
commitdiff
|
tree
2017-10-31
Szi
l
árd P
á
ll
Check CUD
A
available/
c
om
p
iled
c
o
de
c
ompatibilit
y
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupi
n
ov
Fix
reference mo
d
e buil
d
unused
function
warnin
g
s
commit
|
commitdiff
|
tree
2017-10-30
B
e
rk
H
e
s
s
Remo
v
e u
n
used sign paramete
r
from di
h
_angle()
commit
|
commitdiff
|
tree
2017-10-30
Roland Schulz
ArrayRe
f
:
Repla
c
e from
V
ecto
r
w
it
h
sub
A
rra
y
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
Added
opt
i
on -water tip
s
3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-30
Ale
k
sei Iupinov
Bring
P
ME
GPU
/
CUDA int
e
r
n
al structure names to CamelCase
commit
|
commitdiff
|
tree
2017-10-27
Mark
A
bra
h
am
Fi
x
hw d
e
t
ection
m
ore
commit
|
commitdiff
|
tree
2017-10-26
Mark A
b
raham
New quote
commit
|
commitdiff
|
tree
2017-10-20
Mark A
b
raha
m
C
l
arify do
c
s for Fma
x
in EM
commit
|
commitdiff
|
tree
next