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Fix complexity for large exclusion orders
2018-01-03
Erik Li
n
dahl
Fix
complexity
for large exclusio
n
or
d
ers
commit
|
commitdiff
|
tree
2018-01-03
Mark Abraha
m
Fi
x
d
uplicate warning
commit
|
commitdiff
|
tree
2018-01-03
Erik
L
ind
a
h
l
D
o
n't all
o
w multip
l
e energy groups for GPU runs
commit
|
commitdiff
|
tree
2018-01-02
Erik
Lindahl
Do
c
u
m
ent required
position restraint files
commit
|
commitdiff
|
tree
2018-01-02
Erik Lindah
l
Al
l
ow empty lines in hdb files
commit
|
commitdiff
|
tree
2018-01-02
Mark
A
b
r
aham
Fix membed by callin
g
the proper mtop finalization
.
.
.
commit
|
commitdiff
|
tree
2018-01-01
Eri
k
L
inda
h
l
C
l
ar
i
fy XTC error message
commit
|
commitdiff
|
tree
2017-12-29
Mark Abrah
a
m
Separate canDetectGpus
a
n
d
find
G
pus
futh
e
r, and fix
.
.
.
commit
|
commitdiff
|
tree
2017-12-28
Roland
Schu
l
z
Replace G
M
X_ALIGNED with alignas
and SIMD
a
lignmen
t
.
.
.
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupinov
Remove pote
n
t
ially wrong "per
u
s
er
r
eq
u
es
t
" note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-15
R
o
l
and Schul
z
R
e
move incorr
e
ct/misl
e
ading
O
penMP message
commit
|
commitdiff
|
tree
2017-12-15
R
oland Schulz
Revert
"Use table Ewa
l
d for S
k
y
la
k
e"
commit
|
commitdiff
|
tree
2017-12-15
Mark Abraha
m
M
a
ke OpenCL implementation of
g
pu_u
t
ils tests con
f
orm
commit
|
commitdiff
|
tree
2017-12-14
Mark Abraham
Avoid
c
o
n
fu
s
i
n
g message
a
t end of n
o
n-dynamical ru
n
s
commit
|
commitdiff
|
tree
2017-12-14
Mark Abraham
F
i
x
return values
of frame-reading functions
commit
|
commitdiff
|
tree
2017-12-14
Mark Abraham
Make AVX-5
1
2 CM
a
ke detction
wo
r
k
commit
|
commitdiff
|
tree
2017-12-14
Paul Bauer
R
e
move PB
C
before generating TPR with group scheme
commit
|
commitdiff
|
tree
2017-12-14
R
o
land Sc
h
ulz
Simplify CMAP loop
commit
|
commitdiff
|
tree
2017-12-14
Erik
L
indah
l
Work a
r
ound AVX-512 issues in g
c
c-5
.
4 and 7
.
1
commit
|
commitdiff
|
tree
2017-12-12
Erik Lind
a
h
l
Documented power spect
r
um t
o
gmx
velacc
commit
|
commitdiff
|
tree
2017-12-12
B
e
r
k
Hess
Check fo
r
large ene
r
gy at first
step
commit
|
commitdiff
|
tree
2017-12-12
B
e
rk He
s
s
Avoi
d
yellin
g
about
thread pinning tw
i
ce
commit
|
commitdiff
|
tree
2017-12-11
M
a
r
k Abraha
m
Lea
v
e N
V
ML use o
f
f by d
e
fault
commit
|
commitdiff
|
tree
2017-12-11
Mark Abraham
Check for GPU detection support before detecting
commit
|
commitdiff
|
tree
2017-12-11
Mark Abrah
a
m
Avoid signed
-
ov
e
rflow warning
wi
t
h gcc 7
commit
|
commitdiff
|
tree
2017-12-11
Mark Abra
h
am
Rem
o
ve SIMD shi
f
t operato
r
s
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Re
m
ove
SIMD warning f
o
r AM
D
Z
e
n
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Tone down note ab
o
ut
n
o
t pin
n
ing thread
s
commit
|
commitdiff
|
tree
2017-12-10
Szilá
r
d Pál
l
Di
s
able
d
efault-on NVML suppor
t
in CMake
commit
|
commitdiff
|
tree
2017-12-07
Roland Schu
l
z
Fix C++11
library che
c
k's thr
e
a
d
dependency
commit
|
commitdiff
|
tree
2017-12-03
B
e
rk Hess
C
l
ear vs
i
te velociti
e
s for simple i
n
t
egrators
commit
|
commitdiff
|
tree
2017-12-03
Mark Abraham
F
i
x fft5d pinning
commit
|
commitdiff
|
tree
2017-12-02
Berk
Hess
Av
o
id assertio
n
failure
in AWH
commit
|
commitdiff
|
tree
2017-11-29
Be
r
k Hess
Cha
n
g
e
the GPU SMT cut-off to quadra
t
ic
commit
|
commitdiff
|
tree
2017-11-28
Erik Lind
a
hl
F
ix AVX-512 SIMD
test
f
or C
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Do not
f
or
c
e separate PME r
a
nk to
rec
o
mpu
t
e recipr
o
cal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Erik
L
i
nd
a
hl
Test
m
ore A
V
X-512F instructions b
e
fore enab
l
ing
sup
p
ort
commit
|
commitdiff
|
tree
2017-11-24
Erik Lindahl
Det
e
ct AVX
-
512 FMA uni
t
s to cho
o
se best SIMD
commit
|
commitdiff
|
tree
2017-11-24
Be
r
k Hess
Limit SMT with PME on GP
U
commit
|
commitdiff
|
tree
2017-11-20
V
i
vec
a
Li
n
d
a
h
l
A
d
d r
e
ading and w
r
iting to AWH modul
e
commit
|
commitdiff
|
tree
2017-11-20
Mar
k
Abraham
Fix nightly m
a
t
r
ix c
o
nfig
commit
|
commitdiff
|
tree
2017-11-19
Berk Hess
Add SIMD f
o
r
A
WH
commit
|
commitdiff
|
tree
2017-11-18
Ma
g
nus Lundborg
Added Magn
u
s L
u
ndbo
r
g as co
n
tributor in the m
a
nu
a
l
.
commit
|
commitdiff
|
tree
2017-11-18
A
l
eksei Iu
p
inov
Asynchronous CUDA transfers a
r
e
a
ssert
e
d
to a
l
ways
.
.
.
commit
|
commitdiff
|
tree
2017-11-10
R
o
land
Schulz
Revert "Use -mavx
2
-
mfma instead of -march
w
ith AVX2"
commit
|
commitdiff
|
tree
2017-11-08
Roland Schulz
Fix scalar bl
e
nd
commit
|
commitdiff
|
tree
2017-11-08
Magnus Lundbor
g
Update to T
N
G
v 1
.
8
.
1
commit
|
commitdiff
|
tree
2017-09-09
Berk
H
ess
A
vo
i
d i
n
f in
SIMD doubl
e
sqrt()
commit
|
commitdiff
|
tree
2017-07-19
Ma
r
k Abra
h
am
Improve CMake implementation fo
r
GMX_
S
IMD
commit
|
commitdiff
|
tree
2017-06-29
T
eemu M
u
r
t
o
l
a
G
e
neralize IF
o
r
c
e
Provid
e
r
commit
|
commitdiff
|
tree
2017-06-15
Szil
á
r
d Pál
l
Al
l
o
w disablin
g
the expl
i
c
i
t use of CUDA t
e
xture
s
commit
|
commitdiff
|
tree
2017-06-14
Mark
A
braham
Simplify repor
t
ing fro
m
init_gpu
commit
|
commitdiff
|
tree
2017-06-13
Erik
L
indah
l
M
o
re
quo
t
es
commit
|
commitdiff
|
tree
2017-06-07
Vedran
M
iletić
Docu
m
ent fl
o
ating-point
arithmetic
commit
|
commitdiff
|
tree
2017-05-29
Szi
l
árd Páll
Quotes are cool, ty
p
o-free ones are
e
ven "cooler"
commit
|
commitdiff
|
tree
2017-05-27
Ma
r
k Abraham
Q
u
otes fro
m
Gottingen worksho
p
commit
|
commitdiff
|
tree
2017-05-14
Be
r
k H
e
ss
Fix b
u
gs in double Simd4 impl
e
mentat
i
ons
commit
|
commitdiff
|
tree
2017-03-19
Erik
Lindahl
Use
Op
e
nMP up to
1
6
t
hre
a
ds wi
t
h AMD Ryzen
commit
|
commitdiff
|
tree
2017-03-19
Erik Lindahl
128-b
i
t
AVX2 SIMD for AMD
R
yzen
commit
|
commitdiff
|
tree
2017-03-19
M
ark Abra
h
am
Fix
s
t
ring handl
i
ng f
o
r gcc 7
commit
|
commitdiff
|
tree
2017-03-14
Erik Lind
a
hl
F
ix
gcc compiles of AVX-512 SIM
D
commit
|
commitdiff
|
tree
2017-02-14
Mark Abraham
Fix handl
i
ng o
f
pre
v
iou
s
v
ir
i
als
commit
|
commitdiff
|
tree
2017-02-10
Roland
S
chulz
R
emove duplicate AVX512 gat
h
e
r definitions
commit
|
commitdiff
|
tree
2017-02-09
Eri
k
Lindahl
Wo
r
k
around false xl
c
-13
.
1
.
5 bug in SI
M
D tes
t
commit
|
commitdiff
|
tree
2017-02-09
Mark
A
braham
R
e
move
E
ST_DISTR
from stat
e
.
h
commit
|
commitdiff
|
tree
2017-02-09
M
ark Ab
r
aham
Enhanc
e
warninp
commit
|
commitdiff
|
tree
2017-02-08
Roland
Schulz
AVX512: Use double-sized gather for
pairs of
fl
o
ats
commit
|
commitdiff
|
tree
2017-02-07
M
ark Abr
a
h
a
m
Introduced sys
t
em preparation section
to user guide
commit
|
commitdiff
|
tree
2017-02-03
D
a
vid
v
an der Spoel
F
i
xes
S
E
GV in gmx or
d
er
.
commit
|
commitdiff
|
tree
2017-01-11
Rol
a
nd Schulz
Tid
y
:
m
ode
r
ni
z
e-use-nullptr
commit
|
commitdiff
|
tree
2016-11-03
Rol
a
n
d Schulz
Su
p
ress
I
CC 16 on Windows false po
s
tives
commit
|
commitdiff
|
tree
2016-10-30
T
e
e
mu Murtola
S
u
pport normalizing val
u
es
i
n KeyValueTree
commit
|
commitdiff
|
tree
2016-10-30
Rol
a
nd
Schulz
R
e
place qsort/bsea
r
c
h
wit
h
std::sor
t
/lower_bo
u
nd
commit
|
commitdiff
|
tree
2016-10-11
M
ark
A
braham
U
pdate
for FFTW
3
.
3
.
5
commit
|
commitdiff
|
tree
2016-09-26
David van der
S
poel
F
ixes
issue with
R
el
e
ase build in cor
r
ela
t
ion functions
.
commit
|
commitdiff
|
tree
2016-09-18
R
oland
S
chulz
Fix math-t
e
st fal
s
e positive
commit
|
commitdiff
|
tree
2016-09-18
Roland Schulz
Better optimized IC
C
release f
l
ag
s
commit
|
commitdiff
|
tree
2016-09-12
Mark Abraham
Prelimi
n
ary
clea
n
up of NVML code
commit
|
commitdiff
|
tree
2016-09-12
Berk Hess
A
dd const to thread
-
MPI functi
o
ns
commit
|
commitdiff
|
tree
2016-09-12
Ve
d
ran M
i
l
etić
Documen
t
wallcycle counters and subcounters
commit
|
commitdiff
|
tree
2016-09-12
Tee
m
u Murtola
Fi
x
vario
u
s memo
r
y
leaks
commit
|
commitdiff
|
tree
2016-07-31
James G
r
aham
Avoid blank l
i
ne
i
n writing index fil
e
commit
|
commitdiff
|
tree
2016-07-30
R
o
l
and Sc
h
ulz
Updat
e
GCC
version for referenc
e
b
u
ild
commit
|
commitdiff
|
tree
2016-07-30
Vedran M
i
letić
Document gmx
_
cgso
r
t_t
a
n
d gmx_d
o
mdec_sort
_
t s
t
r
ucts
commit
|
commitdiff
|
tree
2016-07-09
Eri
k
Lindahl
P
revent fragile use cases of checkpoint appending
commit
|
commitdiff
|
tree
2016-07-08
Erik
Lin
d
ahl
Update affinity checking for In
t
e
l
compiler
commit
|
commitdiff
|
tree
2016-07-08
Eri
k
L
i
ndahl
Wo
r
k around
compiler i
s
s
u
e wi
t
h random
te
s
t
commit
|
commitdiff
|
tree
2016-07-08
S
zil
á
rd Páll
Add PDF
m
etadata t
o
t
he manual
commit
|
commitdiff
|
tree
2016-07-07
Erik Lind
a
hl
Reduce
h
wloc &
c
p
uid test
r
equirements
commit
|
commitdiff
|
tree
2016-07-07
T
e
emu Murt
o
la
Chan
g
e handling for mis
s
ing releng docs
commit
|
commitdiff
|
tree
2016-07-07
Szilárd
P
áll
Add
u
ser
guide
info
o
n CUD
A
application clocks
commit
|
commitdiff
|
tree
2016-07-07
M
a
rk A
b
raham
Fix build if
l
ibcuda i
s
found but
nvcc
is n
o
t
commit
|
commitdiff
|
tree
2016-06-07
Se
m
en Ye
s
yle
v
s
k
yy
A
d
ded man
u
al s
e
ction
about e
m
bedding prot
e
ins
t
o membranes
.
commit
|
commitdiff
|
tree
2016-06-05
Szilárd P
á
ll
Add supp
o
rt for CUDA
C
C 6
.
0/6
.
1
commit
|
commitdiff
|
tree
2016-06-03
Berk He
s
s
Hand
l
e partially froze
n
and con
s
t
rai
n
ed
atoms
commit
|
commitdiff
|
tree
2016-06-02
Szil
á
rd Páll
Add
e
n
v
.
va
r
.
to enable OpenCL caching
commit
|
commitdiff
|
tree
2016-06-02
S
z
ilárd Pál
l
Fix Ope
n
CL
b
inary cache file nam
e
gener
a
tion
commit
|
commitdiff
|
tree
2016-06-02
Rol
a
nd
S
chulz
Fi
x
ICC 16u3
build
commit
|
commitdiff
|
tree
2016-06-02
Patric
k
W
elche
Ensur
e
IMD
include
d
ependen
c
ies work
commit
|
commitdiff
|
tree
2016-05-29
Mark Abraham
Simpl
i
fied and updated OpenCL compilation
commit
|
commitdiff
|
tree
next