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Merge remote-tracking branch 'origin/release-2019'
2019-09-25
Szilárd Páll
Merge remo
t
e
-
t
racking bra
n
c
h '
o
r
i
gin/
r
elea
s
e-2019'
commit
|
commitdiff
|
tree
2019-09-18
Szilárd
P
áll
Set up w
o
rkload data structure
s
commit
|
commitdiff
|
tree
2019-09-18
Paul
B
auer
Fix MSVC warning
commit
|
commitdiff
|
tree
2019-09-17
Paul Bauer
Add
de
p
recation note for
32 bit
commit
|
commitdiff
|
tree
2019-09-16
Szilá
r
d Páll
Refa
c
tor GPU buf ops-related la
u
nche
s
i
n do_
f
orce
(
)
commit
|
commitdiff
|
tree
2019-09-13
S
zilárd Páll
Fix
GPU X buffer ops with
e
mpty domain
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Dec
o
uple coordinates
buffer manag
e
ment
from buffer
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Arte
m
Zhmurov
Reor
g
anize
P
ME c
o
de
:
commit
|
commitdiff
|
tree
2019-09-11
Szilárd Pá
l
l
Fix gpucomm matrix
commit
|
commitdiff
|
tree
2019-09-06
Mark Abraham
C
lean u
p
commrec
unifor
m
ly
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Col
l
ect settings for DD in
DDSetti
n
gs
commit
|
commitdiff
|
tree
2019-09-03
Berk
H
ess
Remove gmx_do
m
d
e
c
_t f
r
om
dd
_
choose_g
r
id()
commit
|
commitdiff
|
tree
2019-09-03
Be
r
k He
s
s
Extact UnitCellInfo from
g
mx_
d
omde
c
_t
commit
|
commitdiff
|
tree
2019-09-02
M
a
r
k
Abraham
Move i
n
itial
i
zation of clFFT
commit
|
commitdiff
|
tree
2019-08-26
Mark
A
braham
Conv
e
rted a CUDA config
to use clang host-only
c
ompilation
commit
|
commitdiff
|
tree
2019-08-23
S
z
ilá
r
d Páll
Fix clang tidy warnings i
n
CUDA build
commit
|
commitdiff
|
tree
2019-08-21
Mark Abraham
Im
p
rove
o
rganizatio
n
of LINCS repo
r
ting
commit
|
commitdiff
|
tree
2019-08-15
Al
a
n
Gray
PME reducti
o
n for CUDA
F
buffer oper
a
t
ions
commit
|
commitdiff
|
tree
2019-08-12
Szilárd Pá
l
l
Fix hwloc find p
a
ckage naming
a
nd quietness
i
ssu
e
s
commit
|
commitdiff
|
tree
2019-07-26
Ber
k
He
s
s
Remo
v
e sh_
i
nvr
c
6 from in
t
eraction_cons
t
_t
commit
|
commitdiff
|
tree
2019-07-19
Alan G
r
ay
F
b
u
f
fer oper
a
tions in CUDA
commit
|
commitdiff
|
tree
2019-07-16
Mark Abraham
Add g
p
ubufferops test matrix
commit
|
commitdiff
|
tree
2019-07-11
Sz
i
lárd Páll
Use Hos
t
Vector for
Grid/
G
r
i
dSet data need on-GPU
commit
|
commitdiff
|
tree
2019-07-04
S
z
ilárd Páll
Bump latest CUD
A
+ gc
c
in
t
he pre-su
b
mit
m
atrix
commit
|
commitdiff
|
tree
2019-07-04
Szilárd Páll
Fix a -Wformat-trun
c
ation w
a
rning in tng
commit
|
commitdiff
|
tree
2019-07-01
Alan Gray
Bu
g
fix a
n
d sim
p
lification
f
o
r
CU
D
A
X Buffer
O
ps
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
Simpli
f
y GPU nbn
x
m x c
o
nversion
commit
|
commitdiff
|
tree
2019-05-22
Alan Gray
Code quality improvem
e
nts
f
or
CUDA position
buffer ops
commit
|
commitdiff
|
tree
2019-05-20
Szilárd Páll
Improve X buf
f
e
r ops
k
ernel
commit
|
commitdiff
|
tree
2019-05-10
Alan Gr
a
y
Position b
u
ffer ops in CUDA
commit
|
commitdiff
|
tree
2019-03-27
Berk Hess
Fix
n
bnxm OpenCL
w
i
t
h
c
luster size 4
commit
|
commitdiff
|
tree
2019-02-07
Sz
i
lá
r
d Páll
Requi
r
e
a
64-bit plat
f
or
m
f
o
r OpenCL
commit
|
commitdiff
|
tree
2019-01-18
M
a
rk Abr
a
h
am
Improve
nvcc er
r
o
r reporting
commit
|
commitdiff
|
tree
2019-01-02
Szilárd Páll
Fix clang 6 wa
r
ning
commit
|
commitdiff
|
tree
2018-12-31
S
z
ilár
d
Páll
Fix release notes typo
commit
|
commitdiff
|
tree
2018-12-20
Szilárd Páll
Merge "Me
r
ge branc
h
release-2018 into r
e
lease-2019
.
.
.
commit
|
commitdiff
|
tree
2018-12-18
Szilár
d
Páll
Merge release
-
2019 branch
into master
commit
|
commitdiff
|
tree
2018-12-18
Berk Hess
Use st
d
::vector in LINCS
commit
|
commitdiff
|
tree
2018-12-17
Szilárd
P
áll
Fix GMX_BUIL
D
_O
W
N_
F
F
T
W_URL
C
Make cache entry
t
yp
e
commit
|
commitdiff
|
tree
2018-12-17
P
a
u
l
Bauer
Add ma
t
rix entry to
t
est
e
xte
r
nal FFTW build
commit
|
commitdiff
|
tree
2018-12-17
Paul Ba
u
er
F
ix FFTW build
commit
|
commitdiff
|
tree
2018-12-13
Szilárd Pá
l
l
A
v
oid spurious timing in
bonded
G
PU
launch
s
ubcount
e
r
commit
|
commitdiff
|
tree
2018-11-26
M
a
rk Ab
r
aham
C
l
ean
u
p
initial log outp
u
t
commit
|
commitdiff
|
tree
2018-11-22
Mark Abraham
Introduce PpForceWorkload
commit
|
commitdiff
|
tree
2018-11-07
Szilárd Páll
Re
-
enable the
a
r
mclang post-s
u
bmit build
commit
|
commitdiff
|
tree
2018-11-07
Mark Abraham
Suppress
cla
n
g
warnings
a
bou
t
QMMM code
commit
|
commitdiff
|
tree
2018-11-01
Mark
A
b
r
a
ha
m
Stop u
s
ing hwloc
o
n old ARM
s
lave
commit
|
commitdiff
|
tree
2018-10-31
Be
r
k Hess
Pin important
b
uffer
s
in CUDA bondeds
commit
|
commitdiff
|
tree
2018-10-22
Mark Abraham
Fix
cla
n
g
CUDA warnings
commit
|
commitdiff
|
tree
2018-10-14
Szilárd Páll
Fix more clang-6 warnings in CU
D
A code
commit
|
commitdiff
|
tree
2018-10-08
Roland Schulz
Fi
x
O
CL com
p
iler warning
s
commit
|
commitdiff
|
tree
2018-10-08
Roland Sch
u
lz
Remove ma
j
o
rit
y
of OCL command line const
a
nts
commit
|
commitdiff
|
tree
2018-10-07
Szilárd Páll
Use new
GPU slave for
A
M
D
O
penCL verify runs
commit
|
commitdiff
|
tree
2018-10-05
Ro
l
an
d
Schulz
F
i
x mu
l
tiple
b
ugs
d
e
t
ected
o
n
Wind
o
ws
commit
|
commitdiff
|
tree
2018-10-04
Roland Schulz
Use su
b
group for warp
_
any and C
J
4 pr
e
fetch
commit
|
commitdiff
|
tree
2018-10-04
Mark
A
br
a
ham
Replace C
U
D
A
call depr
e
c
ated in CUDA 10
commit
|
commitdiff
|
tree
2018-09-27
Roland Schulz
Recognize In
t
e
l
GPU as compatible
commit
|
commitdiff
|
tree
2018-09-13
Rola
n
d
S
chulz
Remove
s
pa
r
c
64
_
hpc_
a
ce nonbonded
k
e
rnel
s
commit
|
commitdiff
|
tree
2018-09-07
Ma
r
k
Ab
r
a
h
am
Minor fixe
s
to GP
U
build
s
y
s
t
e
m
commit
|
commitdiff
|
tree
2018-08-27
Aleksei Iupinov
Prepare pme
-
gpu-
t
y
pes
.
h
f
or OpenCL
commit
|
commitdiff
|
tree
2018-08-21
Szilár
d
Páll
Request flushi
n
g
denorm
s
to
ze
r
o in Open
C
L
commit
|
commitdiff
|
tree
2018-06-25
A
l
ekse
i
Iupin
o
v
Move ve
c
type_ops
.
clh into gp
u
_
u
tils
commit
|
commitdiff
|
tree
2018-06-25
Al
e
ksei Iupinov
Move
t
h
e PME
G
PU kernel la
u
nch fu
n
ctions into pme-gpu
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei Iupinov
PME OpenC
L
3
D
FFT tra
n
sfo
r
m i
s
i
m
plemented, u
s
in
g
clFFT
commit
|
commitdiff
|
tree
2018-05-30
Aleksei Iup
i
nov
Make P
M
E GPU stru
c
tures us
e
DeviceBuf
f
er
commit
|
commitdiff
|
tree
2018-05-29
S
zi
l
á
rd
P
á
ll
Switch
t
o C
U
DA
9
.
2 + gcc 7
commit
|
commitdiff
|
tree
2018-04-20
S
zilárd
P
áll
Minor fix for pre-
s
u
bmit ma
t
ri
x
docs
commit
|
commitdiff
|
tree
2018-04-19
Szilárd Páll
Move
t
he P
M
E GPU
c
leari
n
g to the
e
nd of the
s
tep
commit
|
commitdiff
|
tree
2018-04-18
Mark Abraham
Introduce g
m
x_used_in_debug
commit
|
commitdiff
|
tree
2018-04-13
Szilárd
Páll
Use tri
v
alue option for GMX_HWLOC
commit
|
commitdiff
|
tree
2018-03-20
V
e
dran M
i
le
t
ić
Doc
u
ment matri
x
_
convert fu
n
ction in
PBC
commit
|
commitdiff
|
tree
2018-03-12
Szi
l
á
r
d Páll
Avoid icc-specific -march=core-avx2
fla
g
with gcc/clan
g
commit
|
commitdiff
|
tree
2018-03-06
S
zilárd Páll
Extend "Finding out how
to run
md
r
u
n
b
e
t
ter" section
commit
|
commitdiff
|
tree
2018-03-06
Aleksei Iupinov
Isol
a
te PME GPU s
p
line pa
r
ameter indexing in
inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Alek
s
ei Iup
i
n
o
v
Sto
p
using custom
Fi
n
d
O
penCL
.
cmake, per TODO
commit
|
commitdiff
|
tree
2018-03-05
A
l
e
ksei I
u
p
ino
v
Correct t
h
e nbn
x
n_
g
p
u
_compil
e
_kernels() docs
commit
|
commitdiff
|
tree
2018-02-21
Szilárd Páll
Switch pre-sub
m
it CUD
A
8
.
0 test to 9
.
0
commit
|
commitdiff
|
tree
2018-02-20
Szilárd Páll
Avoid ab
o
rting mdrun when GPU sani
t
y chec
k
detects
.
.
.
commit
|
commitdiff
|
tree
2018-02-18
Aleksei Iupinov
Replace *_
f
ree_
b
uffered ca
l
ls b
y
fre
e
D
e
viceBuffer
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Add freeDeviceBu
f
f
e
r
GPU
utility
f
unc
t
ion
commit
|
commitdiff
|
tree
2018-01-18
Mar
k
Abraham
Bum
p
v
ersion numbers for 2019 development
commit
|
commitdiff
|
tree
2017-11-27
Berk He
s
s
Enable a
u
to thread
p
inning with
t
hread
l
imi
t
i
n
g
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
Also print 1x1 pair-l
i
st setu
p
to
l
o
g
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Use -mavx2 -mfma
i
n
s
te
a
d of -marc
h
with AVX2
commit
|
commitdiff
|
tree
2017-11-07
Szilárd
Páll
Merge commo
n
n
bnxn CUDA
/
OpenC
L
G
P
U wait code-p
a
t
hs
commit
|
commitdiff
|
tree
2017-10-19
Szilá
r
d P
á
ll
Disable OpenM
P
with
c
l
ang 3
.
4 po
s
t-submit
confi
g
commit
|
commitdiff
|
tree
2017-10-12
Szilárd Páll
Re
m
ove th
e
s
i
z
e_t from the
P
ME gathe
r
CU
D
A kenels
commit
|
commitdiff
|
tree
2017-10-03
Szi
l
árd Páll
Enable compi
l
ing CUDA device code w
i
th c
l
ang
commit
|
commitdiff
|
tree
2017-10-03
Berk Hess
Move calling of
special forc
e
functions
commit
|
commitdiff
|
tree
2017-08-29
Szil
á
rd Pá
l
l
Fix typo a
n
d tweak env var d
o
cs
commit
|
commitdiff
|
tree
2017-08-29
Be
r
k Hess
Set def
a
ult G
M
X_OPENMP_MAX_THREADS
t
o 64
commit
|
commitdiff
|
tree
2017-07-19
Mark Abraham
Made post-s
u
bmit conf
i
g
t
o
t
e
st clang+openmp
.
commit
|
commitdiff
|
tree
2017-07-09
B
e
rk Hess
Restructure
the l
o
ad balancing timing
commit
|
commitdiff
|
tree
2017-05-22
Roland Schulz
Remove T
M
PI_ATOMICS from c
o
nf
i
g
.
h
commit
|
commitdiff
|
tree
2017-03-29
Szilárd P
á
l
l
Refacto
r
CUDA kernel use of tables
commit
|
commitdiff
|
tree
2017-03-17
Szilárd Pá
l
l
Allow bypass
i
n
g
OpenCL dev
i
ce co
m
p
a
tibi
l
ity check
commit
|
commitdiff
|
tree
2017-01-30
Mark Abraha
m
Fix mul
t
i-do
m
a
i
n rer
u
ns
commit
|
commitdiff
|
tree
2017-01-05
Berk Hess
Fix fl
a
t
-
bottom positio
n
restraints
+ DD
+ OpenM
P
commit
|
commitdiff
|
tree
2016-12-01
M
a
rk A
b
r
a
ham
Add INSTALL-dev to aid people doi
n
g unusual builds
commit
|
commitdiff
|
tree
2016-12-01
Ale
k
sei Iu
p
inov
Move
G
P
U assignment functio
n
s into a
s
ep
a
rate file
commit
|
commitdiff
|
tree
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