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Merge branch release-5-1 into release-2016
2016-06-30
Mark Abraham
Merge branc
h
releas
e
-5-1 int
o
rele
a
se-201
6
commit
|
commitdiff
|
tree
2016-06-29
Mark Abraham
Refactor
s
ys
c
onf chec
k
ing
commit
|
commitdiff
|
tree
2016-06-29
Mark Abraham
Work
around glibc
2
.
2
3 w
i
t
h C
U
DA
commit
|
commitdiff
|
tree
2016-06-28
Berk Hess
Prop
e
rly reset C
U
DA application clo
c
k
s
commit
|
commitdiff
|
tree
2016-06-28
Mark Abraham
Update to include a gc
c
6
.
1 configuration
commit
|
commitdiff
|
tree
2016-06-28
Mark
Abraham
F
i
x SIMD configura
t
ion m
a
n
a
gem
e
nt
commit
|
commitdiff
|
tree
2016-06-27
Mark Abraham
Removed unneces
s
ary
int
e
r-sim
u
lation signa
l
ling
commit
|
commitdiff
|
tree
2016-06-27
Berk
H
ess
Us
e
sysconf(
_
SC_NPROCESSORS_ONLN
)
commit
|
commitdiff
|
tree
2016-06-27
Mar
k
Abraham
Merge branch relea
s
e-5-1 into release-2016
commit
|
commitdiff
|
tree
2016-06-24
Berk He
s
s
Fix Verl
e
t buffer ca
l
culation wit
h
nstli
s
t=1
commit
|
commitdiff
|
tree
2016-06-23
Berk Hess
M
ore ac
c
urate GPU list sp
l
itting
commit
|
commitdiff
|
tree
2016-06-23
Mark A
b
raham
Allow use of external lmfit p
a
ckag
e
commit
|
commitdiff
|
tree
2016-06-23
Mark
Abraham
Pre
v
e
n
t use of md
r
un -maxh -multi
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
U
p
date
d
OpenCL
T
ODOL
i
st
.
txt
commit
|
commitdiff
|
tree
2016-06-22
Mark
Abraham
Fix configuration-time
c
pui
n
fo code
commit
|
commitdiff
|
tree
2016-06-22
Davi
d
va
n
der
S
poel
Remov
e
d spu
r
ious r_ij
in
f
o
rce for Mo
r
se potent
i
a
l
.
.
.
commit
|
commitdiff
|
tree
2016-06-22
M
ark Abraham
Merge br
a
nch rel
e
ase-5
-
1
i
n
to release-2
0
16
commit
|
commitdiff
|
tree
2016-06-22
Berk He
s
s
A
d
d nbnxn pair-l
i
s
t
rebalancing
commit
|
commitdiff
|
tree
2016-06-22
Berk He
s
s
Remo
v
e Open
M
P overhead
at high paralleliza
t
i
on
commit
|
commitdiff
|
tree
2016-06-22
Ber
k
Hess
Correc
t
GP
U
pair estimate fo
r
l
ist s
p
lit
t
i
n
g
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
Adj
u
st and document C++11 compiler tests
commit
|
commitdiff
|
tree
2016-06-20
Mark Abrah
a
m
U
p
date
pre-submit
matrix cont
e
n
t
s
commit
|
commitdiff
|
tree
2016-06-19
B
e
r
k H
e
ss
Remov
e
warni
n
g
s on chec
k
point mismatch
commit
|
commitdiff
|
tree
2016-06-19
Mark A
b
raham
Imp
r
o
v
e d
o
cs for l
i
n
k
ing stdlibc++ nee
d
ed by icc
commit
|
commitdiff
|
tree
2016-06-17
Berk H
e
s
s
Remove std::
t
hread:
:
hardware_concurren
c
y()
commit
|
commitdiff
|
tree
2016-06-17
Vedra
n
Miletić
Report the fi
l
enam
e
and
t
he line nu
m
ber on failure
commit
|
commitdiff
|
tree
2016-06-17
Mark Abr
a
ham
Merge bra
n
c
h release-5-
1
into release-2016
commit
|
commitdiff
|
tree
2016-06-17
M
a
r
k A
b
r
a
h
a
m
F
i
x multi-sim + DD + simple di
s
tance
restraint
s
commit
|
commitdiff
|
tree
2016-06-13
Be
r
k
Hess
Han
d
le constraint
erro
r
s with
EM
commit
|
commitdiff
|
tree
2016-06-10
Mark
A
b
raham
F
ind python
f
or docs build qu
i
etly
commit
|
commitdiff
|
tree
2016-06-08
Erik Lindahl
Dis
a
bl
e
st
a
ti
c
libcudart on
O
S X
commit
|
commitdiff
|
tree
2016-06-07
Mark Abraham
Re
-
add support for linking against
e
xternal TinyXML-2
commit
|
commitdiff
|
tree
2016-06-07
Mark Abraha
m
U
pdates to d
o
cumen
t
ation
commit
|
commitdiff
|
tree
2016-06-07
Berk Hess
Fix
d
ata race in hwi
n
fo wit
h
thread
-
MPI
commit
|
commitdiff
|
tree
2016-06-02
Mark A
b
raham
F
i
x
c
ompatibility
w
ith o
l
der CMake
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Ma
k
e
m
o
re CMake variable
s
advanced
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Ignore
s
t
derr when
d
etecting SIMD
a
nd build in
f
o
commit
|
commitdiff
|
tree
2016-05-31
Mark Ab
r
aham
Fix reference to vmdio
.
c to be vmd
i
o
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
Sec
o
nd 2016
be
t
a release
commit
|
commitdiff
|
tree
2016-05-31
B
e
rk Hess
Re
p
osition nbnxn fi
l
ler particles
commit
|
commitdiff
|
tree
2016-05-31
B
erk Hess
Avoid nu
m
erica
l
ove
r
flow
wit
h
o
verlapping atoms
commit
|
commitdiff
|
tree
2016-05-31
B
erk H
e
ss
Add check f
o
r
fini
t
e energ
i
es
commit
|
commitdiff
|
tree
2016-05-28
Roland
Sc
h
ulz
Fix
bu
i
l
d
wi
t
h clang 3
.
1+3
.
2
commit
|
commitdiff
|
tree
2016-05-27
Mark Abrah
a
m
Fix reading of bonded tabl
e
s
commit
|
commitdiff
|
tree
2016-05-26
Mark Abr
a
ham
New quo
t
e
commit
|
commitdiff
|
tree
2016-05-21
E
rik Lindahl
Disable automat
e
d FFTW
3
builds o
n
Wind
o
ws
commit
|
commitdiff
|
tree
2016-05-17
Ro
l
and Sch
u
lz
Add
r
eference to TopoTools 1
.
6
commit
|
commitdiff
|
tree
2016-05-17
Teemu Murtola
Fix
s
ome thread affin
i
ty c
a
ses
commit
|
commitdiff
|
tree
2016-05-13
Rol
a
n
d
Sch
u
lz
Don't use a
b
ort for
fa
t
al errors
commit
|
commitdiff
|
tree
2016-05-12
M
ark Abraham
Merge branch release-
5
-1 into release-2016
commit
|
commitdiff
|
tree
2016-05-12
M
ar
k
Abrah
a
m
G
R
OMACS 2016 beta1 re
l
ease
commit
|
commitdiff
|
tree
2016-05-12
Vedra
n
Mileti
ć
Re
m
ove sta
t
i
c function qu
a
lifier in OpenCL kernel utils
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
Additional
Je
n
kins
d
ocument
a
tion
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Bump clang static
a
n
alyzer to ver
s
ion
3
.
8
commit
|
commitdiff
|
tree
2016-05-10
M
a
rk Abraham
M
i
nor updat
e
to
s
phinx d
e
pe
n
dency
commit
|
commitdiff
|
tree
2016-05-10
Teemu
M
urtola
Include releng documentation to deve
l
oper
guide
commit
|
commitdiff
|
tree
2016-05-10
Erik
L
in
d
a
hl
Fi
x
precis
i
on loss
in tabulated norm
a
l
d
istribution
commit
|
commitdiff
|
tree
2016-05-10
Mar
k
Abraham
Facilitate linking
with libcxx
commit
|
commitdiff
|
tree
2016-05-10
E
rik Lindahl
Fl
u
s
h
s
trea
m
s
w
he
n
not writing newline char
a
c
t
er
commit
|
commitdiff
|
tree
2016-05-10
Ber
k
Hess
Optimized the vsite
t
hreadi
n
g
commit
|
commitdiff
|
tree
2016-05-10
Roland Schu
l
z
Add OpenMP for functio
n
s limiting sc
a
ling
commit
|
commitdiff
|
tree
2016-05-08
M
a
rk Abraha
m
Fixes for clang
3
.
7 on PowerPC
commit
|
commitdiff
|
tree
2016-05-08
James
W
.
Ba
r
ne
t
t
Correc
t
and clarify
o
utput units fo
r
fluct_
p
rops
commit
|
commitdiff
|
tree
2016-05-08
Erik Lin
d
ah
l
Fix Luza
r
/Chander litera
t
ure reference in g
_
hb
o
n
d
commit
|
commitdiff
|
tree
2016-05-08
David v
a
n
der Spoel
Modify l
m
fit
l
ibrary
t
o
avoid
c
las
h
e
s with other
v
e
rsion
s
.
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtol
a
U
se HardwareTopology
t
o
s
et nthreads_h
w
_a
v
ail
commit
|
commitdiff
|
tree
2016-04-28
Teem
u
Murtola
R
emove gmx_hw_info_t::ncore
commit
|
commitdiff
|
tree
2016-04-28
S
z
i
l
árd Páll
Workar
o
un
d
f
or gcc false posit
i
ve
w
arning
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtol
a
Imp
r
o
v
e release workf
l
o
w t
e
sting
commit
|
commitdiff
|
tree
2016-04-27
T
eemu
M
urtola
Disable multipl
e
ranks for non-MPI unit tests
commit
|
commitdiff
|
tree
2016-04-27
Mark Abrah
a
m
Me
r
ge branch release-5
-
1
commit
|
commitdiff
|
tree
2016-04-27
Szi
l
árd Páll
Fix mu
l
tiple MPI ra
n
ks per node with OpenCL
commit
|
commitdiff
|
tree
2016-04-27
T
e
emu Mu
r
tola
Fix
i
ssues with
f
aili
n
g
t
hrea
d
affinity setti
n
g
commit
|
commitdiff
|
tree
2016-04-19
Rol
a
nd Schulz
Fix
numerically unstable selection test
commit
|
commitdiff
|
tree
2016-04-19
Szilárd Páll
Move out CUDA
p
rofiler
triggers from
NBNXN
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Allow rco
u
lomb>rvdw wi
t
h
P
ME
commit
|
commitdiff
|
tree
2016-04-19
Mark A
b
raham
Repl
a
ce libxml2 with ti
n
yxml2 for use in te
s
t code
commit
|
commitdiff
|
tree
2016-04-19
R
o
la
n
d Sc
h
ulz
Tune nst
l
i
s
t incre
a
se for
K
NL
commit
|
commitdiff
|
tree
2016-04-19
M
a
rk Ab
r
aham
F
ix pars
e
_digits_from_string
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Br
o
adcast pull e
x
t
ernal potential prov
i
der string
commit
|
commitdiff
|
tree
2016-04-19
Ma
r
k Abrah
a
m
Fix mdp label
g
eneration
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Fix gmx hb
o
nd group ove
r
l
a
p
check
commit
|
commitdiff
|
tree
2016-04-14
Mark Abraham
Merg
e
b
ranch release-5
-
1
commit
|
commitdiff
|
tree
2016-04-14
Carsten Kutzner
Correct
e
d
va
l
ue
o
f
ele
c
tric
c
onversion
f
actor f
in
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
Roland S
c
hul
z
AVX512
tra
n
sposeScat
t
erIncr
/
DecrU with load/store
commit
|
commitdiff
|
tree
2016-04-04
Erik Lindahl
Fix c
o
mp
i
le error for IBM
VM
X
on ppc64
commit
|
commitdiff
|
tree
2016-04-04
Erik Lind
a
hl
Fix
S
IMD detection on new AMD AVX CPUs w/o fma
commit
|
commitdiff
|
tree
2016-04-03
E
rik Lindahl
Fi
x
unit test s
e
gfa
u
lts
wit
h
gcc-6
.
0
commit
|
commitdiff
|
tree
2016-04-03
E
rik Lindahl
Fix in
c
orrect return type
f
or sc
a
la
r
version of sim
d
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Semen
Yesylevsk
y
y
Adde
d
references to ProtSqueeze and g_membed to
the
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
Roland Schulz
Fix coolquotes
commit
|
commitdiff
|
tree
2016-04-01
M
ark Abraham
R
e
vert
to treating
-
1 as "generate a seed" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Berk
H
e
s
s
Add opti
o
n
for ex
t
e
rnal p
u
ll pot
e
ntial
commit
|
commitdiff
|
tree
2016-03-31
James W
.
Barnett
Revert behavior for hand
l
in
g
SETTL
E
e
rrors
commit
|
commitdiff
|
tree
2016-03-31
Sz
i
lár
d
Páll
refac
t
or CU
D
A
texture-
b
ased table in
i
tialization
commit
|
commitdiff
|
tree
2016-03-31
S
zilard Pall
avoid CPU
over
s
ubscri
p
tion wit
h
G
PUs
commit
|
commitdiff
|
tree
2016-03-30
Szilárd P
á
ll
LJ combination rule kernels for
Op
e
nCL
commit
|
commitdiff
|
tree
2016-03-30
Szi
l
árd Páll
Re-enable i-atom type l
o
c
a
l
mem prefetch i
n
Ope
n
CL
commit
|
commitdiff
|
tree
2016-03-30
B
e
r
k Hess
Correct md
r
un t
M
P
I
(
non-)par
a
ll
e
l er
r
or mess
a
ge
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtola
Make incl
u
desort
e
r
.
py
work with Doxygen 1
.
8
.
10
+
commit
|
commitdiff
|
tree
next