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Optimized the vsite threading
2016-05-10
Berk Hess
Optimized the v
s
ite thread
i
ng
commit
|
commitdiff
|
tree
2016-05-10
Roland
S
c
hu
l
z
Add
O
penMP for functions l
i
miting s
c
al
i
ng
commit
|
commitdiff
|
tree
2016-05-08
M
a
rk Abraham
Fixes for clang 3
.
7
on Powe
r
P
C
commit
|
commitdiff
|
tree
2016-05-08
Jam
e
s
W
.
B
a
rne
t
t
Correct and clarify outp
u
t unit
s
fo
r
fluct_pro
p
s
commit
|
commitdiff
|
tree
2016-05-08
Eri
k
L
i
n
dahl
Fix Luz
a
r/Cha
n
der
l
iteratur
e
r
eference
i
n g
_
hbond
commit
|
commitdiff
|
tree
2016-05-08
David van der Spoel
Mod
i
fy
l
m
f
i
t
library to avo
i
d clashes
w
ith o
t
her
v
ersions
.
commit
|
commitdiff
|
tree
2016-04-28
Teemu M
u
rtola
Use
H
a
r
dwareTopol
o
gy to set nthrea
d
s_hw
_
avail
commit
|
commitdiff
|
tree
2016-04-28
Teem
u
Murtola
Rem
o
ve gm
x
_hw_in
f
o_t::ncor
e
commit
|
commitdiff
|
tree
2016-04-28
Szi
l
árd P
á
ll
Work
a
round f
o
r
gc
c
false
positi
v
e
w
arning
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murt
o
la
Improve re
l
ease workflow testing
commit
|
commitdiff
|
tree
2016-04-27
Tee
m
u M
u
rtola
Disable
m
ultip
l
e ranks for n
o
n-MPI u
n
it
test
s
commit
|
commitdiff
|
tree
2016-04-27
Mark Abraham
Merge
branch
relea
s
e
-
5-1
commit
|
commitdiff
|
tree
2016-04-27
Szilárd Páll
Fix mul
t
i
p
le MPI ranks per node with OpenCL
commit
|
commitdiff
|
tree
2016-04-27
T
ee
m
u Mu
r
tola
Fix
issues with fa
i
l
ing thread
affinit
y
setting
commit
|
commitdiff
|
tree
2016-04-19
Roland S
c
hulz
Fix
n
umerically un
s
ta
b
le select
i
on
t
es
t
commit
|
commitdiff
|
tree
2016-04-19
Szi
l
árd Páll
Move out
C
U
D
A profiler t
r
igger
s
f
rom N
B
NXN
commit
|
commitdiff
|
tree
2016-04-19
B
erk He
s
s
A
l
low rcoulomb>rvdw wit
h
PME
commit
|
commitdiff
|
tree
2016-04-19
M
a
r
k
Abra
h
am
R
e
place libx
m
l2 with tinyxml2
f
or use in tes
t
code
commit
|
commitdiff
|
tree
2016-04-19
Roland Schulz
Tune nstlist i
n
c
r
ease
f
or KNL
commit
|
commitdiff
|
tree
2016-04-19
Mark Abra
h
am
Fix pars
e
_
d
ig
i
ts
_
from
_
string
commit
|
commitdiff
|
tree
2016-04-19
Ber
k
Hess
B
roadcast pull extern
a
l
p
o
tential provider stri
n
g
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Fix m
d
p label generati
o
n
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Fix gmx hbond group overl
a
p check
commit
|
commitdiff
|
tree
2016-04-14
Mark Abraham
Merge
branch release
-
5
-1
commit
|
commitdiff
|
tree
2016-04-14
C
a
rsten K
u
t
zner
Corrected
v
alue
of ele
c
tr
i
c
conversion factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
Rol
a
nd Sc
h
u
lz
AVX512 transposeS
c
atterIncr
/
De
c
rU with load/
s
tore
commit
|
commitdiff
|
tree
2016-04-04
Erik Lindahl
F
i
x compile err
o
r for
I
BM VM
X
on ppc64
commit
|
commitdiff
|
tree
2016-04-04
E
rik
Lindahl
F
i
x SIMD detectio
n
on new AMD AVX
CPUs w/o fma
commit
|
commitdiff
|
tree
2016-04-03
Erik Lindah
l
Fix unit test se
g
faults with gcc-
6
.
0
commit
|
commitdiff
|
tree
2016-04-03
Erik Linda
h
l
Fix inc
o
rrect r
e
turn type for scalar
v
ersion of simd
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Semen Yesy
l
evskyy
Adde
d
refer
e
nces to Pro
t
Squeeze
and g_membed to the
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
Rol
a
n
d
S
chulz
Fix c
o
o
lquotes
commit
|
commitdiff
|
tree
2016-04-01
Mark A
b
raha
m
R
e
vert to t
r
eati
n
g
-1
as "genera
t
e
a seed" in
.
m
dp
commit
|
commitdiff
|
tree
2016-03-31
B
erk Hess
Add o
p
t
ion for exte
r
nal pull p
o
t
e
ntia
l
commit
|
commitdiff
|
tree
2016-03-31
J
a
mes
W
.
Barne
t
t
Revert behavior for handl
i
ng SETTLE errors
commit
|
commitdiff
|
tree
2016-03-31
Szilárd Pá
l
l
r
efactor CUDA t
e
xture-b
a
se
d
table
initial
i
z
a
t
ion
commit
|
commitdiff
|
tree
2016-03-31
Szi
l
ard
Pall
avoid C
P
U
oversub
s
cription with GPUs
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
L
J com
b
i
n
ation rule k
e
rne
l
s for OpenCL
commit
|
commitdiff
|
tree
2016-03-30
Szilárd P
á
ll
Re-
e
n
ab
l
e i-atom ty
p
e
l
ocal mem
prefetch in OpenCL
commit
|
commitdiff
|
tree
2016-03-30
Berk He
s
s
Correct mdrun
t
MP
I
(non-)
p
ar
a
llel er
r
or message
commit
|
commitdiff
|
tree
2016-03-30
T
eemu Murtola
Ma
k
e
include
s
o
r
ter
.
py work with Doxygen 1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
Des
c
ri
b
e AMD AP
P
SDK 3
.
0 issues in the guide
commit
|
commitdiff
|
tree
2016-03-30
Teemu M
u
rto
l
a
Fix e
r
ror rep
o
r
t
i
ng
f
or doc
u
mentati
o
n
build
commit
|
commitdiff
|
tree
2016-03-30
Mark A
b
r
aha
m
Cl
e
an up vsite
cod
e
commit
|
commitdiff
|
tree
2016-03-22
Carst
e
n
K
utzner
C
l
e
an-up code for swa
p
coords
.
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ co
m
bination rule kernels for CU
D
A
commit
|
commitdiff
|
tree
2016-03-19
M
ark Abraham
Add more const correctness
commit
|
commitdiff
|
tree
2016-03-19
M
ark
A
braham
Improv
e
d s
o
me
m
d
r
u
n int
e
gratio
n
test
s
commit
|
commitdiff
|
tree
2016-03-18
Ma
r
k
Abraham
Warn ab
o
u
t OpenM
P
I 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Berk He
s
s
Fix non-normalization o
f
FF
T
autocorr
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
Fix
t
ypo
in Fourier dihe
d
ral eq
u
ation
commit
|
commitdiff
|
tree
2016-03-18
Vive
c
a Lind
a
hl
Ad
d
ed p
u
ll coordinate geom
e
tr
y
angle
.
commit
|
commitdiff
|
tree
2016-03-18
David van de
r
Spo
e
l
F
ixed division by zero in polarize
.
commit
|
commitdiff
|
tree
2016-03-18
Nicholas Br
e
en
Va
r
ious minor spell
i
ng fixes - messages and
c
o
de comments
.
.
.
commit
|
commitdiff
|
tree
2016-03-17
Ca
r
sten
Kutzner
Fix
membed ini
t
i
a
l
i
za
t
ion
commit
|
commitdiff
|
tree
2016-03-15
Mark Abra
h
am
Merge
b
ranch release-5-0 into r
e
lease-5-1
commit
|
commitdiff
|
tree
2016-03-11
Ma
r
k Abra
h
am
Me
r
ge branc
h
relea
s
e-5-0 into relea
s
e-5-1
commit
|
commitdiff
|
tree
2016-03-10
Mark A
b
raham
Require
20
1
5 version for MS
V
C
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Remove eps
f
ac from
G
P
U
ker
n
el
inne
r
-loops
commit
|
commitdiff
|
tree
2016-02-23
Mark Ab
r
ah
a
m
R
e
pl
a
ce cp
p
check
suppr
e
ssio
n
in che
c
kpoin
t
code
commit
|
commitdiff
|
tree
2016-02-16
Mark Abraham
Merge branch release-5-0 into
release-5-1
commit
|
commitdiff
|
tree
2016-02-14
Mark Abrah
a
m
Re-generate
d
eps fo
r
fig
u
re
4
.
8
commit
|
commitdiff
|
tree
2016-02-10
Mar
k
Abrah
a
m
Re-
r
emove *_stochd_state fu
n
ction declarations
commit
|
commitdiff
|
tree
2016-02-10
Erik Lindahl
Scalar functions mim
i
c
king
the SIMD interface
commit
|
commitdiff
|
tree
2016-02-08
Mark Abraham
Me
r
ge branch re
l
ease-5-0 int
o
r
e
lease-5-
1
commit
|
commitdiff
|
tree
2016-02-06
Mark
Abr
a
ham
M
e
r
g
e
b
ranch rel
e
a
se-5-1
commit
|
commitdiff
|
tree
2016-02-03
M
a
rk
A
braham
Bumped patch number
t
o
prepare for future
5
.
1
.
3 release
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Version 5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mar
k
Abraham
Merge release-5-0 into relea
s
e
-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mar
k
A
b
raham
Merge b
r
anch release
-
5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Avoid FP exception
commit
|
commitdiff
|
tree
2016-01-27
Mark Abra
h
a
m
M
erge branch release-5-1
commit
|
commitdiff
|
tree
2016-01-27
Mark Abra
h
a
m
Remove bNotLastFrame
commit
|
commitdiff
|
tree
2016-01-26
Mark
Abraham
Fix d
e
f
ault for GMX_US
E
_NVML
commit
|
commitdiff
|
tree
2016-01-25
M
ark
Ab
r
a
ham
Merge branch release-5-1
commit
|
commitdiff
|
tree
2016-01-12
Mark Abraham
Merge bran
c
h rele
a
se
-
5-0
i
nto rele
a
se-
5
-1
commit
|
commitdiff
|
tree
2016-01-08
Mark Abraham
M
e
rge branch rele
a
se-5-1
commit
|
commitdiff
|
tree
2016-01-07
Ma
r
k
A
braham
Fix
s
ome mdrun h
e
ader dependen
c
ies
commit
|
commitdiff
|
tree
2016-01-07
Mark Abrah
a
m
Avoi
d
more
C
+
+
bindings for MPI
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Sto
p
u
s
ing UNDEFINED
a
s name
of
a symbol
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Re
m
ove fields used only for SD2
commit
|
commitdiff
|
tree
2016-01-07
Ma
r
k Abraham
Backport md-vv fixes
commit
|
commitdiff
|
tree
2016-01-06
Mar
k
Abraham
Fix spurious gcc wa
r
ning
commit
|
commitdiff
|
tree
2015-12-29
Berk Hes
s
Correct vector check of gmx
c
heck
commit
|
commitdiff
|
tree
2015-12-29
T
e
emu Mu
r
tola
Pack
a
ging build scr
i
pt
f
or web site
commit
|
commitdiff
|
tree
2015-12-28
Mark Abra
h
am
M
erge b
r
anch
release-5-1
commit
|
commitdiff
|
tree
2015-12-27
Mark Abrah
a
m
F
ix so
m
e Open
C
L
i
ssues
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
Reorganized domdec
i
nitialization
commit
|
commitdiff
|
tree
2015-12-24
Mark Abraham
Shell code cleanup
commit
|
commitdiff
|
tree
2015-12-24
Erik
L
i
n
d
ahl
IBM Power6
VMX
e
xtended SIMD
commit
|
commitdiff
|
tree
2015-12-17
Mark
Abraha
m
Sim
p
lified
e
nergy-summation cod
e
commit
|
commitdiff
|
tree
2015-12-16
Be
r
k Hes
s
Add one element to sta
t
e
rvec arra
y
s
commit
|
commitdiff
|
tree
2015-12-15
E
ri
k
Lindahl
C++ mat
h
function cleanup
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murto
l
a
M
o
ve main
.
*, s
p
litter
.
*, g
m
x
_om
p
_
nthreads
.
* to
m
dli
b
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
M
o
v
e readinp
.
*
and
w
arnin
p
.
*
to fileio/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
M
ove hardware detection to h
a
r
dware/
commit
|
commitdiff
|
tree
2015-12-15
T
e
e
m
u Mur
t
o
la
M
ove so
m
e
mdrun code out of gmxlib/
commit
|
commitdiff
|
tree
2015-12-12
T
eem
u
Murtola
Move disre
.
* and orires
.
*
to listed-
f
or
c
es/
commit
|
commitdiff
|
tree
2015-12-12
Teemu Murtola
Mov
e
put_atoms_in_box_o
m
p
(
) to sim_uti
l
.
*
commit
|
commitdiff
|
tree
2015-12-12
T
e
emu Murtola
Remove topolog
y
-
> fil
e
io dep
e
nden
c
y
commit
|
commitdiff
|
tree
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