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Merge branch release-5-1 into release-2016
2016-03-31
S
z
ilard Pall
a
v
oid CPU oversubscripti
o
n
with GPUs
commit
|
commitdiff
|
tree
2016-02-06
S
zilard
Pall
Use
c
udaLaunchKernel with CUDA 7
.
0 and later
commit
|
commitdiff
|
tree
2016-01-05
Szilard Pall
remove dupli
c
a
t
e
m
acro
s
and enable Wundef
i
n CUDA
commit
|
commitdiff
|
tree
2016-01-01
Szilard Pall
Fix xlc
+
C
UDA workaround in
g
mx
M
a
nageNvccCo
n
fig
commit
|
commitdiff
|
tree
2015-12-26
Szilard
P
all
Improve docu
m
entation
o
n
Ope
n
CL issue w
i
th NVIDIA
commit
|
commitdiff
|
tree
2015-12-13
Szilard Pall
Open
C
L cod
e
cleanup
commit
|
commitdiff
|
tree
2015-11-04
S
zilar
d
Pa
l
l
Tweak NVML-related messa
g
e
s
commit
|
commitdiff
|
tree
2015-11-02
Szilard
P
al
l
Fix sign
a
l type
commit
|
commitdiff
|
tree
2015-11-01
S
zilard Pall
F
i
x bug in cycle sub
c
ounter manageme
n
t
commit
|
commitdiff
|
tree
2015-10-24
Szilard Pall
A
void using
incompatible NV
M
L version
commit
|
commitdiff
|
tree
2015-10-22
Szi
l
ard
Pal
l
Quiet Find
N
VML
commit
|
commitdiff
|
tree
2015-10-15
S
zil
a
rd Pa
l
l
Fix
r
eset
error message
commit
|
commitdiff
|
tree
2015-09-27
Szilard Pall
Tweak th
e
C
U
DA
G
PU shared mem/L1 con
f
ig
commit
|
commitdiff
|
tree
2015-09-17
Szilard
Pall
Fix broken OpenCL dete
c
tion
commit
|
commitdiff
|
tree
2015-09-16
Szi
l
ard Pall
Fix OpenCL
build
commit
|
commitdiff
|
tree
2015-08-13
Szilard P
a
ll
add clFlus
h
t
o
ki
c
k of
Open
C
L work
commit
|
commitdiff
|
tree
2015-07-02
Szil
a
rd Pall
Fix O
p
e
nC
L
compilation erro
r
s
.
commit
|
commitdiff
|
tree
2015-06-29
Szila
r
d
P
a
ll
Fi
x
CU
D
A inter
-
stre
a
m synchroni
z
ation
issue
commit
|
commitdiff
|
tree
2015-06-27
Szilard P
a
ll
Fix CUDA arc
h
i
tecture dep
e
ndent issues
commit
|
commitdiff
|
tree
2015-06-25
Szilard Pall
Add missing mac
r
o undef
i
n C
U
DA NB kerne
l
commit
|
commitdiff
|
tree
2015-06-21
S
zilard Pall
fi
x
CPU core over
s
ubscription detection
commit
|
commitdiff
|
tree
2015-06-17
Szilard Pall
fix
minor CU
D
A N
B
ke
r
nel
perfor
m
anc
e
regression
commit
|
commitdiff
|
tree
2015-06-08
Szilard Pall
add last t
w
o GROM
A
C
S
paper c
i
ta
t
ions
commit
|
commitdiff
|
tree
2015-06-06
Szilard
P
a
l
l
Op
t
imize a
t
omic accum
u
lation in CUDA NB kernel
commit
|
commitdiff
|
tree
2015-05-15
Szil
a
r
d Pal
l
A
s
sert the size of n
o
n
-bonded G
P
U work
u
nits
commit
|
commitdiff
|
tree
2015-05-14
Szilar
d
Pall
Merge release-4-6 in
t
o rel
e
ase-5-0
commit
|
commitdiff
|
tree
2015-05-13
Szilard Pa
l
l
Fix auto-do
w
nloade
d
regr
e
ssion te
s
t ex
e
cution
commit
|
commitdiff
|
tree
2015-01-16
Szilard Pa
l
l
Improv
e
and clarify mdrun beha
v
ior with n
s
teps
<
0
commit
|
commitdiff
|
tree
2014-12-10
Szi
l
ard P
a
l
l
Fix nstep co
m
mand line
o
ver
r
ide
print
commit
|
commitdiff
|
tree
2014-09-30
Szilard
P
all
Fix inc
o
rrect LJ cut
-
off with G
P
U +
P
ME tuning
commit
|
commitdiff
|
tree
2014-03-01
Szilard Pall
Added CUDA LJ-PME
nbnxn ker
n
els
commit
|
commitdiff
|
tree
2014-02-28
Szilard Pall
Im
p
roved CUDA non-bonded kernel
p
er
f
or
m
ance
commit
|
commitdiff
|
tree
2014-02-27
S
z
ilard Pal
l
CUDA ker
n
el
s
for swi
t
ched
LJ
commit
|
commitdiff
|
tree
2014-02-21
Szilard Pall
po
r
tabilit
y
a
spects in instal
l
guid
e
+ minor tweaks
commit
|
commitdiff
|
tree
2013-12-02
Szilard Pall
remo
v
e
l
egacy CUDA no
n
-bo
n
ded kernels
commit
|
commitdiff
|
tree
2013-11-13
Szilard Pall
Clarified
G
P
U
selecti
o
n
o
utput and mdrun help
commit
|
commitdiff
|
tree
2013-11-06
Szilard Pall
en
a
bl
e
GPU sharing a
m
ong tMP
I
ranks
commit
|
commitdiff
|
tree
2013-10-15
Sz
i
la
r
d Pall
make u
s
e of CUDA s
t
ream
p
ri
o
ri
t
ies
commit
|
commitdiff
|
tree
2013-10-14
S
z
i
l
a
rd Pall
use C
U
D
A
t
e
x
ture
objects
w
h
e
n supp
o
r
t
ed
commit
|
commitdiff
|
tree
2013-09-29
Szil
a
rd Pa
l
l
allow co
m
pilation
to optimize for CUDA
c
ompute cap
.
.
.
commit
|
commitdiff
|
tree
2013-06-27
Szilard Pall
A
d
apted
c
lang-AMD-FM
A
work
a
r
ound for both
C
a
n
d C++
commit
|
commitdiff
|
tree
2013-06-25
S
z
i
lard Pal
l
added CUDA compiler flags to version header
commit
|
commitdiff
|
tree
2013-05-30
Szilar
d
Pall
f
i
x thread-safety issue in
a
f
finity layout dete
c
tion
commit
|
commitdiff
|
tree
2013-05-30
Szilard Pal
l
add workaround for
clang on AMD wi
t
h FMA
commit
|
commitdiff
|
tree
2013-05-30
S
zi
l
ard Pall
f
i
x
t
hread
o
ffset + st
r
ide c
h
eck
commit
|
commitdiff
|
tree
2013-05-27
Szilard Pall
minor
funct
i
on argument cleanup
commit
|
commitdiff
|
tree
2013-04-17
Szi
l
ard
Pall
C
UD
A
PME kernel
s
with analytical Ewald correc
t
ion
commit
|
commitdiff
|
tree
2013-01-24
Szi
l
ard Pall
added back cuda
.
h
in
c
ludes to fix missing
C
UDA_VE
R
SION
commit
|
commitdiff
|
tree
2013-01-18
Szilard Pall
rem
o
ve
unnecessary cma
k
e
messages
commit
|
commitdiff
|
tree
2013-01-17
Sz
i
lar
d
Pa
l
l
don
'
t use polling with new driver
commit
|
commitdiff
|
tree
2013-01-11
Szilard Pall
ti
m
e the GP
U
force clea
r
ing
a
sync
l
aunch overhead
commit
|
commitdiff
|
tree
2013-01-11
Szil
a
rd P
a
ll
c
o
nsole
a
n
d
l
og output improvements
commit
|
commitdiff
|
tree
2013-01-02
Szil
a
rd Pall
improved reporting
of faile
d
a
f
finity s
e
tti
n
g
commit
|
commitdiff
|
tree
2012-12-20
S
zilar
d
P
a
ll
fix
i
ncorre
c
t
gmx_
f
atal argument
o
rder
commit
|
commitdiff
|
tree
2012-12-18
Szi
l
ard Pall
i
s
sue err
o
r if G
P
U I
D
is
prov
i
ded with GPU acc
.
off
commit
|
commitdiff
|
tree
2012-12-05
Szil
a
rd
Pall
don't warn durin
g
confi
g
uring i
f
n
o
G
PUs were
fo
u
nd
commit
|
commitdiff
|
tree
2012-12-05
Szilard Pall
first ste
p
toward m
o
ving O
p
en
M
M support to contrib
commit
|
commitdiff
|
tree
2012-12-05
Szilard
Pall
don'
t
a
u
to-set nvcc host compiler with cmake >2
.
8
.
9
commit
|
commitdiff
|
tree
2012-11-30
Szilar
d
Pall
force C++ li
n
king of t
h
e gpu_
u
tils
commit
|
commitdiff
|
tree
2012-11-29
Sz
i
lard Pall
made errors during GPU detection non-fatal
commit
|
commitdiff
|
tree
2012-11-29
Szilard Pa
l
l
fix cmak
e
re
-
running failure
i
nt
r
odu
c
ed
b
y ef11
2
7f
commit
|
commitdiff
|
tree
2012-11-29
S
z
i
lard Pall
aut
o
m
a
t
i
on for set
t
ing GMX_GPU
&
cmake GPU detection
commit
|
commitdiff
|
tree
2012-11-29
Szil
a
rd Pall
don't print nonbonde
d
k
e
rnel info with G
M
X_NO_
N
ONBONDED
commit
|
commitdiff
|
tree
2012-11-28
Szilard Pall
enable GPU emulati
o
n withou
t
G
PU support
commit
|
commitdiff
|
tree
2012-11-28
Szilar
d
Pall
us
e
t
M
PI
API for threa
d
a
f
finit
y
setti
n
g
commit
|
commitdiff
|
tree
2012-11-23
Szilard Pa
l
l
r
e
mo
v
ed group non-bone
d
e
d call with verlet s
c
heme
commit
|
commitdiff
|
tree
2012-11-22
Szilard Pall
u
nset MPI detection
l
eftover ca
c
he va
r
iables
commit
|
commitdiff
|
tree
2012-11-19
Szilard Pall
alw
a
y
s mark as advanced
leftove
r
F
i
ndCUDA v
a
riabl
e
s
commit
|
commitdiff
|
tree
2012-11-09
Szilard Pall
o
n
l
y use CPU_COUNT if
i
t's a
v
a
ilable
commit
|
commitdiff
|
tree
2012-11-09
Szi
l
ard Pa
l
l
als
o
prefer
e
ntiate
.
lib wi
t
h GMX_PREFER_STATI
C
_
LIBS
commit
|
commitdiff
|
tree
2012-11-07
Szilard Pall
auto-set n
v
cc host co
m
piler with FindMPI detection
commit
|
commitdiff
|
tree
2012-11-07
Szilard Pall
detect
e
xte
r
n
a
lly set CPU
a
ffinity
commit
|
commitdiff
|
tree
2012-11-02
Szilar
d
Pall
don't execut
e
any mpi_info/mpin
a
m
e
i
n t
h
e path
commit
|
commitdiff
|
tree
2012-10-31
S
zilard P
a
ll
fix i
n
ternal/
e
xt
e
rna
l
OpenMP thr
e
ad affinity clash
commit
|
commitdiff
|
tree
2012-10-22
Szila
r
d Pall
fix CUDA
n
o
n
-bonded kernel poin
t
er assignment
commit
|
commitdiff
|
tree
2012-10-02
Szilard Pall
added Verlet
s
cheme
and
NxN no
n
-bon
d
ed functi
o
nality
commit
|
commitdiff
|
tree
2012-09-03
S
z
il
a
rd
P
all
Me
r
ge bra
n
c
h
'
relea
s
e-4-5-patches' int
o
release-4-6
commit
|
commitdiff
|
tree
2012-06-27
S
z
i
lar
d
Pall
fixes typo gmx_omp
in
t
roduced by 69
7
bc
d
c
commit
|
commitdiff
|
tree
2012-06-25
Szi
l
ar
d
Pall
introduc
e
gmx_omp wrapp
e
r for the OpenMP
A
PI
commit
|
commitdiff
|
tree
2012-05-22
S
z
ilard P
a
ll
added ex
p
licit s
q
rtf to the flo
a
t versio
n
of
n
orm
commit
|
commitdiff
|
tree
2012-05-02
Sz
i
lard P
a
ll
removed -fi
n
l
i
ne-funct
i
o
ns from
t
h
e release
g
c
c
f
lags
commit
|
commitdiff
|
tree
2012-04-26
Szilard Pall
Corrected fo
u
ri
e
r
s
p
a
cing descriptio
n
commit
|
commitdiff
|
tree
2012-04-19
Szilard
Pall
compiler flag f
i
x
e
s
commit
|
commitdiff
|
tree
2012-04-18
S
z
i
l
ard
P
al
l
added missing
#ifdef arou
n
d
#
include "thread_mpi
.
h"
commit
|
commitdiff
|
tree
2012-04-15
Szilard Pall
enabl
e
command line optio
n
ch
e
king in mdrun
commit
|
commitdiff
|
tree
2012-03-28
S
z
i
l
a
r
d Pall
Me
r
ge branch
'release-
4
-
5-patches' into release-4-6
commit
|
commitdiff
|
tree
2012-03-14
S
z
ila
r
d Pall
fi
x
ed appendin
g
OpenMP compile
r
option t
o
flag lis
t
commit
|
commitdiff
|
tree
2012-02-29
Szilard Pall
M
e
rge
b
ranch 'release-4-5-patches'
i
nto
rel
e
ase-4-6
commit
|
commitdiff
|
tree
2012-02-09
S
z
i
lard Pall
r
enamed GMX_THRE
A
DS to GMX_THRE
A
D_MPI
commit
|
commitdiff
|
tree
2012-02-02
Sz
i
lard Pal
l
fixed confusin
g
n
onbonded k
e
rnel p
o
inter initialization
commit
|
commitdiff
|
tree
2012-01-17
Szilard Pall
Fixe
d
timing measur
e
me
n
ts
.
commit
|
commitdiff
|
tree
2011-04-08
Szilard Pal
l
fixed g_tu
n
e_pme to pass cor
r
e
c
tl
y
boolean
arguments
.
.
.
commit
|
commitdiff
|
tree
2011-02-23
Szilard Pall
added cmake warning
w
hen the ca
c
he generated
o
n
another
.
.
.
commit
|
commitdiff
|
tree
2011-02-11
Szilard
P
all
fixed buggy detection of h
o
stname and time of
build
.
.
.
commit
|
commitdiff
|
tree
2010-11-08
S
z
i
lard Pall
Merge branch 'r
e
lease-
4
-5-patc
h
es' of
g
i
t
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-11-05
Szilard
Pall
Me
r
ge branch '
r
e
l
e
a
se-
4
-
5
-
patches'
of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-11-03
Sz
i
lard Pall
now it'
s
possible to run bin
a
r
ies in the build t
r
e
e
.
.
.
commit
|
commitdiff
|
tree
2010-10-29
Szila
r
d
P
all
Merge branch 'release-4-5-pat
c
he
s
' of
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-29
Szila
r
d
Pall
enabled
G
MX_PREF
E
R_STATIC_LIBS CMake
o
p
tion for CYGWIN
commit
|
commitdiff
|
tree
2010-10-29
Szilard Pa
l
l
f
ixe
d
the de
f
a
u
lt for OpenMM plug
i
n di
r
location (
b
ug
.
.
.
commit
|
commitdiff
|
tree
next