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Couple of new quotes
2016-06-22
Berk
Hess
Re
m
ove OpenMP overhead at high paralleliz
a
tion
commit
|
commitdiff
|
tree
2016-06-22
Be
r
k Hess
Correct G
P
U
pair e
s
ti
m
ate for li
s
t
sp
l
itting
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
Adjust and document C++11
compiler t
e
sts
commit
|
commitdiff
|
tree
2016-06-20
Ma
r
k Abraha
m
Upd
a
te pre-submit
m
atri
x
contents
commit
|
commitdiff
|
tree
2016-06-19
Berk Hess
R
emove warnings o
n
chec
k
p
oint mismatch
commit
|
commitdiff
|
tree
2016-06-19
Mark
A
braham
I
m
p
rove docs
f
or linking
s
tdlibc++ needed b
y
icc
commit
|
commitdiff
|
tree
2016-06-17
Berk Hess
R
e
m
ove std::threa
d
:
:
h
a
rdware_concurrency()
commit
|
commitdiff
|
tree
2016-06-17
Vedran Miletić
R
e
port the
filename an
d
the lin
e
n
umber on fai
l
u
r
e
commit
|
commitdiff
|
tree
2016-06-17
Ma
r
k Abraham
M
e
rge branch re
l
ease-5-1 in
t
o release-2016
commit
|
commitdiff
|
tree
2016-06-17
Mar
k
A
braham
Fix mu
l
ti-sim
+
D
D + simple dis
t
a
nce r
e
straint
s
commit
|
commitdiff
|
tree
2016-06-13
B
erk Hess
Handle co
n
straint errors with EM
commit
|
commitdiff
|
tree
2016-06-10
Mark Abraham
Find p
y
thon
for docs build
quietly
commit
|
commitdiff
|
tree
2016-06-08
Erik Lindahl
Dis
a
ble
s
tatic libcu
d
art
on OS X
commit
|
commitdiff
|
tree
2016-06-07
M
ark Abraham
Re-
a
dd su
p
port for linking a
g
ainst e
x
ternal TinyXML-2
commit
|
commitdiff
|
tree
2016-06-07
Ma
r
k Ab
r
a
h
am
Upd
a
tes to documentation
commit
|
commitdiff
|
tree
2016-06-07
B
erk
H
e
ss
Fix
d
ata race in hw
i
nfo with thr
e
a
d
-MPI
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
F
ix compatibili
t
y with
o
lder CMake
commit
|
commitdiff
|
tree
2016-06-02
Mark Ab
r
aham
Make more
C
Make v
a
ri
a
bles ad
v
anced
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Ignore std
e
rr when
detecting S
I
MD and build
i
nfo
commit
|
commitdiff
|
tree
2016-05-31
M
a
rk Ab
r
a
h
a
m
F
i
x
r
ef
e
re
n
ce to vmdio
.
c to be vmdio
.
c
p
p
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
Second 2016
b
eta release
commit
|
commitdiff
|
tree
2016-05-31
Berk H
e
ss
Reposition
nbnxn
f
ill
e
r parti
c
les
commit
|
commitdiff
|
tree
2016-05-31
Ber
k
Hes
s
Avoid num
e
r
i
c
al o
v
erflow
with overlapping atoms
commit
|
commitdiff
|
tree
2016-05-31
B
e
rk H
e
ss
Add check
fo
r
f
inite energies
commit
|
commitdiff
|
tree
2016-05-28
Roland Sch
u
lz
Fix b
u
ild with c
l
ang
3
.
1+3
.
2
commit
|
commitdiff
|
tree
2016-05-27
Mark Ab
r
a
ham
Fix reading of bonde
d
ta
b
l
e
s
commit
|
commitdiff
|
tree
2016-05-26
Ma
r
k Abraham
N
e
w
q
u
o
te
commit
|
commitdiff
|
tree
2016-05-26
Mark Abraham
Merge branch re
l
ease-2016
commit
|
commitdiff
|
tree
2016-05-25
Teemu Murt
o
la
Su
p
p
o
rt
for rea
l
MP
I
uni
t
t
es
t
s
commit
|
commitdiff
|
tree
2016-05-21
Erik Lindahl
Disable automated
F
FTW3 b
u
i
lds on Windows
commit
|
commitdiff
|
tree
2016-05-17
Roland Schulz
Add referenc
e
to TopoTools 1
.
6
commit
|
commitdiff
|
tree
2016-05-17
Teemu
M
u
r
tola
Fix
some thread af
f
inity cases
commit
|
commitdiff
|
tree
2016-05-13
Rola
n
d Schulz
Don't use
abort for fata
l
error
s
commit
|
commitdiff
|
tree
2016-05-12
Mark Abr
a
ham
Me
r
ge bra
n
c
h
r
e
lease-5
-
1 into r
e
lease-
2
016
commit
|
commitdiff
|
tree
2016-05-12
Mark A
b
raha
m
GROMACS
2016 be
t
a1 release
commit
|
commitdiff
|
tree
2016-05-12
V
e
d
r
an Miletić
Remove static function
q
u
a
li
f
ier
i
n Open
C
L
ke
r
nel utils
commit
|
commitdiff
|
tree
2016-05-10
Teemu
Murtola
Additional
Jen
k
i
n
s d
o
cumentat
i
on
commit
|
commitdiff
|
tree
2016-05-10
Mark
A
br
a
ham
Bump clang st
a
tic analyzer to versi
o
n 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mark Ab
r
a
h
a
m
Minor u
p
date t
o
sp
h
inx
d
e
p
e
n
dency
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
Includ
e
releng docum
e
nta
t
ion
t
o deve
l
op
e
r guid
e
commit
|
commitdiff
|
tree
2016-05-10
E
r
ik Li
n
dahl
Fix precision loss in tabulated normal d
i
stributi
o
n
commit
|
commitdiff
|
tree
2016-05-10
Mar
k
Abraham
Facili
t
ate li
n
king with li
b
cxx
commit
|
commitdiff
|
tree
2016-05-10
Erik L
i
ndahl
Flush st
r
ea
m
s when not writing newline character
commit
|
commitdiff
|
tree
2016-05-10
Ber
k
He
s
s
Optimized the vsite
t
hreading
commit
|
commitdiff
|
tree
2016-05-10
Ro
l
and Schulz
Add
OpenMP for functio
n
s limiting
scaling
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
F
i
xes
fo
r
clang 3
.
7 on Powe
r
PC
commit
|
commitdiff
|
tree
2016-05-08
James W
.
Barnett
Correct and clarify outpu
t
units for flu
c
t_pr
o
p
s
commit
|
commitdiff
|
tree
2016-05-08
Erik Lindahl
Fi
x
Lu
z
ar/Chander literature r
e
ference in
g
_hbo
n
d
commit
|
commitdiff
|
tree
2016-05-08
Da
v
i
d
va
n
der
S
poel
Modify lm
f
i
t library to avoid clashes with othe
r
ve
r
sion
s
.
commit
|
commitdiff
|
tree
2016-04-28
T
e
em
u
Mu
r
t
o
la
Use HardwareTopolo
g
y to set
nth
r
eads_hw_ava
i
l
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtola
Remov
e
gmx_
h
w
_info_t::ncore
commit
|
commitdiff
|
tree
2016-04-28
Szilárd Páll
Workaro
u
n
d for
g
cc false
positive warni
n
g
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
I
mprove release wor
k
flow te
s
t
ing
commit
|
commitdiff
|
tree
2016-04-27
Teemu
Murtola
D
i
sable multiple ranks for non-MPI unit t
e
sts
commit
|
commitdiff
|
tree
2016-04-27
M
a
rk
A
braham
Merge
branch rel
e
ase-
5
-1
commit
|
commitdiff
|
tree
2016-04-27
Szilár
d
Páll
Fix mult
i
ple
M
PI
r
a
n
ks per
n
o
de with Ope
n
CL
commit
|
commitdiff
|
tree
2016-04-27
Teem
u
M
urtola
Fix issues with f
a
i
l
i
n
g
thread a
f
f
i
nity se
t
ting
commit
|
commitdiff
|
tree
2016-04-19
R
oland
S
chulz
Fix numerically unstable sele
c
t
i
on
test
commit
|
commitdiff
|
tree
2016-04-19
Sz
i
l
á
rd Pál
l
Move out CUDA profiler triggers from NBNXN
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
A
l
low rcoulomb>rvdw with PME
commit
|
commitdiff
|
tree
2016-04-19
Mark A
b
raham
Replac
e
libxml2 with
t
in
y
x
ml2 for
u
se in test code
commit
|
commitdiff
|
tree
2016-04-19
Ro
l
and Sch
u
lz
Tune n
s
tlis
t
incre
a
se for
K
NL
commit
|
commitdiff
|
tree
2016-04-19
M
a
rk Abraham
Fi
x
parse_digits_from_string
commit
|
commitdiff
|
tree
2016-04-19
B
erk Hess
Broadc
a
st pull externa
l
p
ote
n
tial provider string
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Fix m
d
p la
b
el
generation
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Fix g
m
x
hbond group overlap
check
commit
|
commitdiff
|
tree
2016-04-14
Mark
A
bra
h
am
Merg
e
b
r
anch
r
elease
-
5-1
commit
|
commitdiff
|
tree
2016-04-14
Carsten Kutzner
Cor
r
ected valu
e
of electric conversion factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
Roland
S
chulz
AVX512 trans
p
oseScatterIncr/DecrU with
l
oad/store
commit
|
commitdiff
|
tree
2016-04-04
E
r
ik Lindahl
Fix compile err
o
r fo
r
IBM V
M
X on ppc64
commit
|
commitdiff
|
tree
2016-04-04
Erik Lindahl
Fix
S
I
MD detec
t
ion on new AM
D
AV
X
CPUs w/o fma
commit
|
commitdiff
|
tree
2016-04-03
Erik Lindahl
Fix unit test
s
egfaults wit
h
gcc
-
6
.
0
commit
|
commitdiff
|
tree
2016-04-03
E
rik
L
indahl
Fix incorr
e
c
t
r
e
turn type for scalar versio
n
of simd
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Sem
e
n
Yesylevskyy
Added
r
ef
e
ren
c
es to ProtSqu
e
eze and g_me
m
bed to
t
h
e
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
R
o
l
and Schu
l
z
Fix coo
l
quotes
commit
|
commitdiff
|
tree
2016-04-01
Mark
Abraham
R
e
vert to trea
t
ing -1 as
"gener
a
te a seed" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Add option for extern
a
l pull potential
commit
|
commitdiff
|
tree
2016-03-31
James
W
.
B
arnett
R
evert behavior f
o
r han
d
ling S
E
T
T
L
E
e
r
r
o
rs
commit
|
commitdiff
|
tree
2016-03-31
Szilárd P
á
l
l
refactor CUDA texture-based tab
l
e ini
t
ialization
commit
|
commitdiff
|
tree
2016-03-31
S
z
ilar
d
Pall
avoid CPU overs
u
bscription w
i
t
h G
P
Us
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
LJ combinatio
n
rule
kernels
f
o
r
Ope
n
CL
commit
|
commitdiff
|
tree
2016-03-30
Szilárd
P
áll
Re-
e
nable
i
-atom ty
p
e
local mem prefetch in OpenC
L
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
Cor
r
ect mdrun tMPI
(
n
on-)parallel
error message
commit
|
commitdiff
|
tree
2016-03-30
Teem
u
Mu
r
to
l
a
Make includesorter
.
py wo
r
k with Doxygen 1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
Szilá
r
d Páll
Descr
i
b
e
A
MD APPSDK
3
.
0 issues in the guide
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtola
Fix error repo
r
ting for d
o
c
umenta
t
ion buil
d
commit
|
commitdiff
|
tree
2016-03-30
M
a
r
k Abrah
a
m
Clean
up
v
sit
e
code
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutzner
C
le
a
n-up code for
swapcoords
.
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ comb
i
n
ation ru
l
e kernels fo
r
CU
D
A
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Add
more const corr
e
ctnes
s
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Imp
r
oved some mdrun integrat
i
o
n
tests
commit
|
commitdiff
|
tree
2016-03-18
Mark
A
braham
W
ar
n
abo
u
t
OpenMP
I
1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fix n
o
n-normalization of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-18
M
ark Abraham
Fi
x
t
ypo in F
o
urier dihe
d
ral
equation
commit
|
commitdiff
|
tree
2016-03-18
Vivec
a
Lindahl
Added p
u
ll c
o
ordinate geomet
r
y angle
.
commit
|
commitdiff
|
tree
2016-03-18
David van der S
p
oel
Fixed division
by z
e
ro in polarize
.
commit
|
commitdiff
|
tree
2016-03-18
Nic
h
ol
a
s
Br
e
en
V
a
rious minor spelling fixes - messages
an
d
c
ode
comm
e
nts
.
.
.
commit
|
commitdiff
|
tree
2016-03-17
Car
s
ten
K
utz
n
er
Fix
mem
b
ed i
n
itiali
z
a
tion
commit
|
commitdiff
|
tree
2016-03-15
Mark
Abrah
a
m
Merge
b
ranch r
e
lease-5-0 int
o
r
ele
a
se-5-1
commit
|
commitdiff
|
tree
2016-03-11
Mark Abraham
Merge bra
n
c
h
relea
s
e
-5-0 into
rele
a
se-5-1
commit
|
commitdiff
|
tree
next