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Improve mdrun performance user guide
2018-02-15
Aleksei Iupi
n
ov
Ad
d
freeDe
v
iceBuffe
r
GPU utility fun
c
tion
commit
|
commitdiff
|
tree
2018-01-18
Mark Abra
h
am
B
ump version
numbers fo
r
2019 development
commit
|
commitdiff
|
tree
2017-11-27
Berk H
e
ss
Enable aut
o
thread pinnin
g
w
ith
t
h
read
l
imit
i
ng
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
Also pr
i
n
t 1
x
1 pai
r
-list se
t
up to log
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Use
-m
a
vx2 -
m
fma i
n
stead of
-march wi
t
h
AVX2
commit
|
commitdiff
|
tree
2017-11-07
S
z
ilár
d
Páll
Merge comm
o
n nbnxn CU
D
A/OpenCL GP
U
w
ait cod
e
-
p
aths
commit
|
commitdiff
|
tree
2017-10-19
Szilárd Pál
l
Disab
l
e OpenMP
w
i
th clan
g
3
.
4 post-subm
i
t config
commit
|
commitdiff
|
tree
2017-10-12
Szilár
d
Páll
Remove the size_t f
r
om
the PME gather
CUDA kenels
commit
|
commitdiff
|
tree
2017-10-03
Szilárd Páll
Enable co
m
pilin
g
CUDA device code with clang
commit
|
commitdiff
|
tree
2017-10-03
Berk Hess
Move calling of special force functions
commit
|
commitdiff
|
tree
2017-08-29
Szilárd Páll
F
ix typo
a
nd
t
weak env var
d
o
c
s
commit
|
commitdiff
|
tree
2017-08-29
Berk He
s
s
Set de
f
a
u
l
t
G
MX_OPENMP_MAX_THREADS to 64
commit
|
commitdiff
|
tree
2017-07-19
Mark Abraham
Ma
d
e post-s
u
bmit con
f
ig to test clang+op
e
nmp
.
commit
|
commitdiff
|
tree
2017-07-09
Berk Hess
Res
t
ru
c
ture the load b
a
l
a
ncing timing
commit
|
commitdiff
|
tree
2017-05-22
Ro
l
and Schulz
Re
m
ove TMPI_ATOMI
C
S
from conf
i
g
.
h
commit
|
commitdiff
|
tree
2017-03-29
Szilárd Páll
Refactor CUDA kernel use
o
f
t
ables
commit
|
commitdiff
|
tree
2017-03-17
Szil
á
rd Pá
l
l
Allow bypassing OpenCL devi
c
e comp
a
ti
b
il
i
ty c
h
eck
commit
|
commitdiff
|
tree
2017-01-30
Ma
r
k Abraham
Fix mu
l
ti-dom
a
in reruns
commit
|
commitdiff
|
tree
2017-01-05
Berk He
s
s
Fix flat-bottom
p
osi
t
ion restr
a
int
s
+ D
D
+
OpenMP
commit
|
commitdiff
|
tree
2016-12-01
Mark
A
bra
h
am
A
dd IN
S
TALL-dev to ai
d
people doing unusual buil
d
s
commit
|
commitdiff
|
tree
2016-12-01
Alekse
i
Iupinov
Move GPU assignme
n
t function
s
int
o
a
s
ep
a
rat
e
f
i
le
commit
|
commitdiff
|
tree
2016-11-17
Szilá
r
d
Pál
l
Correct kerne
l
launch
bo
u
nds f
o
r CUDA sm_60
commit
|
commitdiff
|
tree
2016-11-01
Szil
á
rd
Páll
Me
r
ge "Merge
b
ran
c
h
release-2
0
16"
commit
|
commitdiff
|
tree
2016-10-26
Szilárd Páll
Add GMX_DISABLE_GPU_TIM
I
NG env va
r
commit
|
commitdiff
|
tree
2016-10-09
Szilárd Pá
l
l
Correct kernel launch
b
ounds for CUDA sm_60
commit
|
commitdiff
|
tree
2016-09-22
B
er
k
Hess
Fix gcc war
n
ing in
Al
i
gne
d
A
llocator
commit
|
commitdiff
|
tree
2016-08-24
M
ark
A
b
raham
Remove hacks for outdated
B
l
ueGene support
commit
|
commitdiff
|
tree
2016-07-05
Szilárd
P
áll
Docu
m
e
n
t
G
MX_
G
P
U_APPLICATIO
N
_
CLOCKS
commit
|
commitdiff
|
tree
2016-06-08
Mark Abraha
m
Merge
b
ranch release-5-1 i
n
t
o
release-
2
016
commit
|
commitdiff
|
tree
2016-06-03
Vedr
a
n Miletić
Wri
t
e
O
penCL buil
d
log prio
r
to checking
build status
commit
|
commitdiff
|
tree
2016-05-10
Berk
Hess
Fix C
U
DA
s
h
mem bug
commit
|
commitdiff
|
tree
2016-05-06
Berk H
e
ss
O
penMP parallelization for pull
commit
|
commitdiff
|
tree
2016-04-26
Ved
r
an Miletić
Disable
C
UDA profil
e
r whe
n
us
i
ng Op
e
nCL
commit
|
commitdiff
|
tree
2016-04-26
S
zilárd Pá
l
l
Fix OpenCL asserti
o
n
commit
|
commitdiff
|
tree
2016-04-13
Szilárd Páll
S
p
elling fixes
commit
|
commitdiff
|
tree
2016-04-13
Szil
á
rd Páll
Do
n
ot create empt
y
man/ma
n
7 dir
e
ctory
commit
|
commitdiff
|
tree
2016-04-04
Szilárd Pál
l
Mark m
o
re va
r
iables as advance
d
commit
|
commitdiff
|
tree
2016-03-31
Szilárd Páll
Fix mul
t
iple tMPI rank
s
per
O
penCL device
commit
|
commitdiff
|
tree
2016-03-22
B
e
r
k He
s
s
Avoid assertion failure in p
m
e
_
loadbal_do
commit
|
commitdiff
|
tree
2016-03-05
M
ark Abraham
Ad
d
SETTLE unit tests
commit
|
commitdiff
|
tree
2016-02-17
Szilá
r
d
P
áll
r
eintroduce supercl interaction mask co
n
s
t
a
nt
commit
|
commitdiff
|
tree
2016-02-17
Szilárd Páll
c
h
a
nge macr
o
s to co
n
stants in GP
U
code
commit
|
commitdiff
|
tree
2016-02-15
S
zilárd Páll
Allo
w
GMX_NB_MIN_CI=0
t
o
be pass
e
d
commit
|
commitdiff
|
tree
2016-02-11
Szilárd Páll
Re-enable
LJ-PME + L
o
rentz-Berthel
o
t on
G
PUs
commit
|
commitdiff
|
tree
2016-02-06
Szilard Pall
Use cu
d
aLaunchKernel with CUDA 7
.
0 and later
commit
|
commitdiff
|
tree
2016-01-20
S
z
ilárd Páll
Me
r
ge r
e
m
o
te-track
i
ng branch 'or
i
gi
n
/
release-5
-
1'
i
nto
.
.
.
commit
|
commitdiff
|
tree
2016-01-05
Szilard P
a
ll
remov
e
dupl
i
cate macros and
e
nable Wundef in CUDA
commit
|
commitdiff
|
tree
2015-11-04
Szila
r
d Pal
l
Tweak NVML-related m
e
s
sage
s
commit
|
commitdiff
|
tree
2015-11-01
Szila
r
d
P
all
Fix
bug in cycle
s
ubc
o
u
n
te
r
m
anagement
commit
|
commitdiff
|
tree
2015-10-15
Szi
l
ard Pall
F
i
x reset error mes
s
age
commit
|
commitdiff
|
tree
2015-09-17
Szilard Pall
Fix broken OpenCL de
t
ec
t
ion
commit
|
commitdiff
|
tree
2015-06-29
Szilard P
a
ll
Fix
CUDA int
e
r-str
e
a
m
synchroniza
t
i
o
n iss
u
e
commit
|
commitdiff
|
tree
2015-06-17
Szi
l
a
r
d
P
al
l
fix
minor CUDA NB
k
ernel perfor
m
ance regression
commit
|
commitdiff
|
tree
2015-06-08
Szilard Pa
l
l
add last two GROMACS paper citations
commit
|
commitdiff
|
tree
2015-05-14
Szilard Pal
l
Merge release-4-6 into rel
e
ase-5-0
commit
|
commitdiff
|
tree
2015-03-11
Berk Hes
s
Reduced cost of Berendsen pressure c
o
up
l
ing
commit
|
commitdiff
|
tree
2015-01-16
Sz
i
lard Pall
Improve an
d
clarify m
d
run
b
e
havior with nst
e
ps
<
0
commit
|
commitdiff
|
tree
2014-12-10
Szi
l
ar
d
Pall
Fix nstep comman
d
l
i
ne
override print
commit
|
commitdiff
|
tree
2014-11-14
Sz
i
lárd Páll
Start nvpr
o
f pro
f
i
ling at c
o
unter reset
commit
|
commitdiff
|
tree
2014-07-27
Ro
l
a
n
d S
c
hulz
Remove
individ
u
al cuda l
i
braries
commit
|
commitdiff
|
tree
2014-06-17
B
e
rk Hess
Updated
m
d
r
un
-np
m
e document
a
tion
commit
|
commitdiff
|
tree
2014-05-24
Rossen Apost
o
lov
Allow
t
rjconv
t
o
keep som
e
box dimensions un
c
h
an
g
ed
.
commit
|
commitdiff
|
tree
2014-02-28
Szilard P
a
ll
Improved CUDA no
n
-bonded
k
ernel performance
commit
|
commitdiff
|
tree