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Add nbnxn pair-list rebalancing
2016-06-22
Berk
H
ess
Add nbnxn pair-list re
b
alancing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Rem
o
ve OpenMP
overhead at high
p
aralleliza
t
ion
commit
|
commitdiff
|
tree
2016-06-22
Berk
H
e
s
s
Cor
r
ect GPU pai
r
e
s
t
im
a
t
e for list
s
pl
i
tti
n
g
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
Adjust and document C++
1
1
c
o
mpiler te
s
ts
commit
|
commitdiff
|
tree
2016-06-20
Mark
A
br
a
ham
Update pre
-
submit
m
atrix contents
commit
|
commitdiff
|
tree
2016-06-19
Berk Hess
R
e
move warnin
g
s
on
checkpoin
t
m
i
s
m
at
c
h
commit
|
commitdiff
|
tree
2016-06-19
Mark Abr
a
ham
Impr
o
ve docs for linking s
t
dlibc+
+
n
e
eded by i
c
c
commit
|
commitdiff
|
tree
2016-06-17
Berk Hess
Remove std::thread::ha
r
dware_concurr
e
ncy()
commit
|
commitdiff
|
tree
2016-06-17
Vedran Miletić
Report
t
he filename
a
nd the
l
in
e
numb
e
r
on
f
ailure
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Mer
g
e branch release-5-1 into
rel
e
ase-2016
commit
|
commitdiff
|
tree
2016-06-17
Mar
k
Abraham
Fix
m
ulti-s
i
m
+ DD + simple di
s
tance
r
e
s
tra
i
nt
s
commit
|
commitdiff
|
tree
2016-06-13
B
e
r
k
H
ess
Handle cons
t
raint errors with EM
commit
|
commitdiff
|
tree
2016-06-10
Mark Abraham
Find
python f
o
r docs build quietly
commit
|
commitdiff
|
tree
2016-06-08
Erik Lin
d
ah
l
Disable static lib
c
u
d
art on OS X
commit
|
commitdiff
|
tree
2016-06-07
M
a
rk Abraham
Re-a
d
d su
p
por
t
for linking aga
i
nst extern
a
l
TinyXML-2
commit
|
commitdiff
|
tree
2016-06-07
Mark Abraham
U
p
dates to documentation
commit
|
commitdiff
|
tree
2016-06-07
B
e
r
k
Hess
Fix data race i
n
h
winfo with
t
hread-MPI
commit
|
commitdiff
|
tree
2016-06-02
M
a
rk Ab
r
aham
Fix comp
a
tibility with olde
r
CMake
commit
|
commitdiff
|
tree
2016-06-02
Ma
r
k Abraham
Make more CMake variables advanced
commit
|
commitdiff
|
tree
2016-06-02
Mark Abr
a
ham
Ig
n
o
re stderr wh
e
n
det
e
c
t
ing SIMD and
b
uild i
n
fo
commit
|
commitdiff
|
tree
2016-05-31
Mark Abrah
a
m
F
ix r
e
f
e
renc
e
to vmdio
.
c
to
b
e vmd
i
o
.
c
pp
commit
|
commitdiff
|
tree
2016-05-31
M
a
rk A
b
raha
m
Se
c
ond 2
0
16 beta r
e
l
ea
s
e
commit
|
commitdiff
|
tree
2016-05-31
Berk Hes
s
Reposition nbnxn
fil
l
e
r
p
a
rticles
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
A
void
n
u
m
e
r
ical overflow w
i
th
o
ve
r
lapping atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Add check for
f
i
nite energies
commit
|
commitdiff
|
tree
2016-05-28
Roland Sc
h
ulz
Fix b
u
ild with cl
a
ng 3
.
1+3
.
2
commit
|
commitdiff
|
tree
2016-05-27
Mark Ab
r
aham
Fix r
e
adi
n
g of
bonded
t
ables
commit
|
commitdiff
|
tree
2016-05-26
Ma
r
k Abraham
New quote
commit
|
commitdiff
|
tree
2016-05-21
Erik
L
indahl
D
i
sable autom
a
t
e
d FFTW3
bu
i
lds
o
n Windo
w
s
commit
|
commitdiff
|
tree
2016-05-17
Roland Schulz
A
d
d
re
f
erence
to TopoTools 1
.
6
commit
|
commitdiff
|
tree
2016-05-17
Teemu Murtola
Fix so
m
e thread affin
i
ty cas
e
s
commit
|
commitdiff
|
tree
2016-05-13
Rolan
d
Schulz
Don't
u
se ab
o
rt for fat
a
l errors
commit
|
commitdiff
|
tree
2016-05-12
Mar
k
Abrah
a
m
Merge br
a
nch relea
s
e-5-1 i
n
to
re
l
ease-2016
commit
|
commitdiff
|
tree
2016-05-12
Ma
r
k Abraha
m
GR
O
MACS 2016 beta1
rele
a
se
commit
|
commitdiff
|
tree
2016-05-12
Ve
d
ran Milet
i
ć
Remove
s
t
atic functio
n
qualifier in Open
C
L
k
ern
e
l
utils
commit
|
commitdiff
|
tree
2016-05-10
Teemu
Mu
r
tola
Additional
Jenkins
d
oc
u
mentatio
n
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraha
m
Bump
clang s
t
a
tic analy
z
er to vers
i
on 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Ma
r
k
A
b
r
aham
Minor
update to s
p
hinx dependency
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtol
a
Include relen
g
d
o
cumentation to
d
eveloper gui
d
e
commit
|
commitdiff
|
tree
2016-05-10
Erik L
i
ndahl
Fix pre
c
ision l
o
s
s
in tabulat
e
d norm
a
l
d
istri
b
ution
commit
|
commitdiff
|
tree
2016-05-10
Mark
A
braham
Facilita
t
e linkin
g
with libcxx
commit
|
commitdiff
|
tree
2016-05-10
Erik Lindahl
Flush s
t
reams w
h
en not
w
riting
newl
i
ne character
commit
|
commitdiff
|
tree
2016-05-10
Berk
H
ess
Opti
m
i
z
ed the vsite threa
d
ing
commit
|
commitdiff
|
tree
2016-05-10
Roland Schulz
Add OpenMP
for
function
s
li
m
i
ting scaling
commit
|
commitdiff
|
tree
2016-05-08
M
a
rk Abra
h
am
F
i
x
es for clang 3
.
7 on PowerPC
commit
|
commitdiff
|
tree
2016-05-08
James W
.
Barn
e
tt
Correct and c
l
arif
y
output uni
t
s f
o
r
fluct_
p
rops
commit
|
commitdiff
|
tree
2016-05-08
Erik Lin
d
ahl
Fix Luz
a
r
/
Chander literature
r
e
f
e
r
enc
e
in g_h
b
ond
commit
|
commitdiff
|
tree
2016-05-08
D
a
v
i
d va
n
der Spoe
l
Mod
i
f
y
lmfit library to avoid cla
s
h
es with other
v
e
rsions
.
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murto
l
a
Use HardwareTopology t
o
s
e
t nthreads_h
w
_avail
commit
|
commitdiff
|
tree
2016-04-28
Teemu
M
u
rto
l
a
Remove
gmx_hw
_
info_t::ncor
e
commit
|
commitdiff
|
tree
2016-04-28
Szilár
d
P
á
ll
Workaround for gcc false positive warning
commit
|
commitdiff
|
tree
2016-04-27
Teemu Mur
t
ol
a
Improve rele
a
se work
f
low testing
commit
|
commitdiff
|
tree
2016-04-27
Teemu
Mu
r
tola
Disable multiple ranks for non-MPI unit t
e
sts
commit
|
commitdiff
|
tree
2016-04-27
M
ark Abraham
Merge branch releas
e
-5-1
commit
|
commitdiff
|
tree
2016-04-27
Szilárd
P
áll
Fix m
u
ltipl
e
MPI ranks per
n
ode w
i
t
h
OpenCL
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Fix issues with failing
t
hread affinity se
t
ting
commit
|
commitdiff
|
tree
2016-04-19
Ro
l
and Sch
u
lz
Fix num
e
ric
a
lly unstable selection test
commit
|
commitdiff
|
tree
2016-04-19
Szilárd
Páll
M
ove out CUDA prof
i
ler t
r
iggers f
r
o
m NBNXN
commit
|
commitdiff
|
tree
2016-04-19
Ber
k
Hes
s
A
llow rcoul
o
mb>rvdw with PM
E
commit
|
commitdiff
|
tree
2016-04-19
Mar
k
Abraham
Repla
c
e
l
i
bxml2 with tinyxm
l
2 for use in te
s
t code
commit
|
commitdiff
|
tree
2016-04-19
R
o
land
Schu
l
z
Tune nstlist incr
e
ase for KNL
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Fi
x
p
a
rse_digits_fr
o
m_string
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Broadcast p
u
ll externa
l
p
otent
i
a
l
provider string
commit
|
commitdiff
|
tree
2016-04-19
Mark
Abra
h
am
F
ix mdp labe
l
ge
n
eration
commit
|
commitdiff
|
tree
2016-04-19
Berk Hes
s
Fix gmx h
b
ond
g
roup o
v
erlap check
commit
|
commitdiff
|
tree
2016-04-14
Mark A
b
raham
Merge
b
ranch relea
s
e-5-1
commit
|
commitdiff
|
tree
2016-04-14
Ca
r
sten Ku
t
z
ner
C
orrected v
a
l
u
e of electric conve
r
sion factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
Roland Schulz
AVX
5
12 transpose
S
catte
r
Incr/Decr
U
w
i
th load/store
commit
|
commitdiff
|
tree
2016-04-04
E
r
ik Linda
h
l
Fix c
o
mpile error fo
r
IBM VMX o
n
ppc64
commit
|
commitdiff
|
tree
2016-04-04
Erik Lindahl
F
i
x SIMD detection on new AMD AVX CPUs
w/o fma
commit
|
commitdiff
|
tree
2016-04-03
Erik
L
indahl
Fix unit te
s
t
segfault
s
with gcc-6
.
0
commit
|
commitdiff
|
tree
2016-04-03
Erik Lindahl
Fix incorrect return type f
o
r s
c
a
l
a
r
vers
i
on of simd
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Sem
e
n Yesylevskyy
Added
r
eferences to ProtSquee
z
e and g_membe
d
to t
h
e
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
R
o
land Schulz
Fix coolquotes
commit
|
commitdiff
|
tree
2016-04-01
Ma
r
k
Abraham
Rever
t
to
treating -1 as "
g
enera
t
e a seed" i
n
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Add optio
n
f
or external pull pote
n
t
ial
commit
|
commitdiff
|
tree
2016-03-31
Jame
s
W
.
Barnett
Revert behavi
o
r
f
or handling S
E
TTLE errors
commit
|
commitdiff
|
tree
2016-03-31
Szilárd
Pál
l
refactor CU
D
A texture-based
t
able initialization
commit
|
commitdiff
|
tree
2016-03-31
Sz
i
lard Pal
l
avoid CPU ove
r
s
ub
s
criptio
n
with GPUs
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Pá
l
l
L
J combination r
u
le
ker
n
e
l
s
fo
r
OpenC
L
commit
|
commitdiff
|
tree
2016-03-30
Szilárd
Páll
Re-enable i-a
t
om
type loca
l
mem pr
e
fetch in Ope
n
CL
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
Correct m
d
run tMP
I
(
n
on
-
)
parall
e
l error message
commit
|
commitdiff
|
tree
2016-03-30
T
eemu Murtola
Make
incl
u
desorter
.
py work w
i
th Doxygen 1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
Szilárd
Pál
l
Descri
b
e AMD APPSDK 3
.
0
i
ssues in the guide
commit
|
commitdiff
|
tree
2016-03-30
Te
e
m
u
Murtola
Fi
x
error report
i
ng for documentation
bu
i
ld
commit
|
commitdiff
|
tree
2016-03-30
Mark Abraham
Cle
a
n
up vs
i
t
e
code
commit
|
commitdiff
|
tree
2016-03-22
Carste
n
Kutzner
Clean-up code for s
w
apcoords
.
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ com
b
i
nation rule kernels for
CUDA
commit
|
commitdiff
|
tree
2016-03-19
Ma
r
k A
b
raham
Add mor
e
const correctnes
s
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Improved some mdru
n
int
e
gration
t
ests
commit
|
commitdiff
|
tree
2016-03-18
Mark Abra
h
am
W
a
r
n about Ope
n
MPI 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fix non-
n
ormalization of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-18
M
a
rk Abraham
Fix
t
yp
o
in Fourier
dihedral equ
a
ti
o
n
commit
|
commitdiff
|
tree
2016-03-18
Viveca
L
i
nda
h
l
A
d
ded pull c
o
or
d
inate geometry an
g
le
.
commit
|
commitdiff
|
tree
2016-03-18
Da
v
id van der S
p
oel
Fixed divisio
n
by zero
i
n pola
r
ize
.
commit
|
commitdiff
|
tree
2016-03-18
Nicholas Breen
Vari
o
us minor spelling fixe
s
- messages and code
comment
s
.
.
.
commit
|
commitdiff
|
tree
2016-03-17
Carsten
Kutzner
Fix m
e
mbed in
i
t
i
alization
commit
|
commitdiff
|
tree
2016-03-15
Mark
A
braham
Merge branch release-5-0
into release-
5
-1
commit
|
commitdiff
|
tree
2016-03-11
Mar
k
Abr
a
h
am
M
erge branch
release-5-0 i
n
to
release-5-1
commit
|
commitdiff
|
tree
2016-03-10
Mar
k
Abraha
m
Require 2015 ve
r
sion for MSV
C
commit
|
commitdiff
|
tree
next