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optimized generic SIMD invsqrt
2013-01-13
Michael Shirt
s
Fi
x
es for md-vv and re
r
u
n
commit
|
commitdiff
|
tree
2013-01-13
Ber
k
H
ess
fixe
d
res
e
tting
s
tates w
i
th parallel Verlet scheme
commit
|
commitdiff
|
tree
2013-01-13
Christoph Junghans
Merge "Remove
u
nuse
d
b
func
.
h
.
" into re
l
ease-4
-
6
commit
|
commitdiff
|
tree
2013-01-13
Christop
h
Jun
g
ha
n
s
Merge "Clarified so
m
e comm
e
nts & warning
s
about thread
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Christoph Junghans
M
erge "Manage BlueGene/Q configur
a
tion"
i
n
to release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph Junghan
s
M
erge "Re-organize B
l
ueGene tool
c
hain file
s
" int
o
release-4-
6
commit
|
commitdiff
|
tree
2013-01-13
C
h
ristoph Ju
n
ghans
M
e
rg
e
"Chan
g
e
d defaults for
building
s
hared librari
e
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
M
a
r
k A
b
raha
m
Clar
i
fie
d
some comments &
warni
n
g
s
about
t
h
rea
d
pi
n
ning
commit
|
commitdiff
|
tree
2013-01-13
Roland Sc
h
ulz
M
erge "prepar
e
d
t
h
e
n
bnxn code for non-x86
S
I
M
D"
into
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Mark
Abraham
Merge "Adde
d
basic CPU topology
i
n
f
ormation to cpuid
.
.
.
commit
|
commitdiff
|
tree
2013-01-12
Berk
H
e
s
s
prepared the nbnx
n
code for non-
x
86 S
I
MD
commit
|
commitdiff
|
tree
2013-01-12
Ch
r
istoph Ju
n
gha
n
s
M
e
rge "Added missing ex
p
or
t
" into release-4-6
commit
|
commitdiff
|
tree
2013-01-11
Eri
k
Linda
h
l
Merge "made S
H
AKE work a
g
ain wi
t
h
part
i
cle decompostion
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Rola
n
d S
c
hulz
Mer
g
e "
t
ime the
G
PU fo
r
ce c
l
e
aring as
y
nc launch ov
e
rhead
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Ch
r
is
t
oph Junghans
Merge "co
n
sole
a
nd log output imp
r
ovements" into release-
4
-
6
commit
|
commitdiff
|
tree
2013-01-11
Christoph Junghans
Mer
g
e
"Fix CUDA being q
u
iet and
mark all CUDA_* as
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
E
r
i
k Lindahl
A
dded b
a
sic
C
PU topology informa
t
i
o
n to cpuid
c
ode
commit
|
commitdiff
|
tree
2013-01-11
Erik Lindah
l
Merge "f
i
xe
d
nbnxn no LJ comb
.
rule AVX256 PME kernel
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
R
o
land
Schulz
M
e
r
g
e
"Handle compiler flags more
f
lexibly"
i
nto relea
s
e-4-6
commit
|
commitdiff
|
tree
2013-01-11
C
h
r
istoph J
u
nghans
M
e
rge "Remo
v
e inco
r
rect a
s
s
e
rt added by 05f9a740" i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Be
r
k Hess
fixed nbnxn no LJ comb
.
rule
A
VX256
P
ME kernel
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindahl
F
i
x
e
d
flop-accounting for periodic improper dihedrals
commit
|
commitdiff
|
tree
2013-01-10
Mark Abra
h
am
Merge "Revert def
a
ult rlist/rvdw/
r
coulomb to
v
alid
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
M
a
rk
A
braham
M
e
rge "f
i
xed
bug w
i
t
h
Verlet + DD + bonded atom
c
o
m
municatio
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Roland Schulz
Hand
l
e
c
ompi
l
er
flags more
flexibly
commit
|
commitdiff
|
tree
2013-01-10
Er
i
k Lindahl
D
i
sallow the u
s
e of Clan
g
to compi
l
e AV
X
_12
8
_FM
A
commit
|
commitdiff
|
tree
2013-01-10
R
o
land Schulz
Me
r
g
e
"M
o
ve Wind
o
ws shared/static op
t
ion
s
to
later
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Roland Schulz
Merg
e
"Remove workaround
"
into release
-
4-6
commit
|
commitdiff
|
tree
2013-01-10
R
o
land Schulz
Mov
e
Windows shared/static opt
i
o
n
s
to later
point
commit
|
commitdiff
|
tree
2013-01-10
Ro
l
and Schulz
Remove workaround
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindah
l
Remove broken g
_
dih tool
commit
|
commitdiff
|
tree
2013-01-10
Mark
Abraham
Merge
"Fixes
S
S
E/AVX compila
t
ion und
e
r Windows" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
E
r
ik Lindahl
Merge "Corrected gm
x
check output for G
r
om
o
s96
b
onds
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Roland
S
chulz
Merge "Added w
o
rk-around for gcc b
u
g
i
n
AVX intrinsincs
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Roland Schulz
Merge "Add check to remove zero Charm
m
dihedrals" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Roland Schulz
Merge
"[tools] g
_
sans - ad
d
trajectory a
v
ereging"
int
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-08
E
r
i
k Lindahl
Add check to remove z
e
r
o
C
har
m
m dihedral
s
commit
|
commitdiff
|
tree
2013-01-08
E
r
ik
L
inda
h
l
Do n
o
t alw
a
ys add -msse2
t
o
r
e
lease flags
f
or icc
commit
|
commitdiff
|
tree
2013-01-08
Ro
l
and Schulz
Merge "R
e
duce use o
f
mo
n
o
li
t
hic sets
of compil
e
r flags
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland
S
ch
u
lz
Merge
"
fixed nbnxn A
V
X-256
Ewald table pointer
a
l
ignment
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
M
ark Abraham
Redu
c
e
use
of monolithi
c
sets of compiler flags
commit
|
commitdiff
|
tree
2013-01-07
Roland Schulz
Merge "
c
m
a
k
e
: remo
v
e d
o
uble-negati
v
e quotes logic"
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
R
oland Sc
h
u
l
z
M
erge "Pr
i
nt
out atom numbers in
g
_rmsf" i
n
to releas
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
B
erk Hess
f
ixed nbnxn AVX-256
E
wal
d
tabl
e
pointe
r
alig
n
me
n
t
commit
|
commitdiff
|
tree
2013-01-07
Roland Schulz
Merge
"I
g
n
o
r
e bool cas
t
warning
f
o
r MSVC and C++" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
D
avid van der Spoel
Merge
"Removed reference t
o
nonexistent fil
e
in g_helix
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
R
o
land Sc
h
ulz
Mer
g
e "improved reporting o
f
failed affinity set
t
ing
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Ro
l
and Schulz
Mer
g
e
"
F
i
xed
format er
r
or in
on
l
i
n
e manual
.
" into re
l
ease-4-6
commit
|
commitdiff
|
tree
2013-01-07
Roland
Sc
h
ulz
Merge "Fixed
a
bu
g
that w
i
th
m
u
ltiple exchan
g
e
s
" int
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland S
c
h
ulz
Me
r
ge "Essen
t
ial dyna
m
ic
s
:
fixed restarts when ED group
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
R
oland
Schulz
M
e
r
ge "minor speed-u
p
and code clean-up in nbnxn
k
e
rnels
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Chr
i
st
o
ph Junghans
Merge "Make gmx_cpu
i
d
.
h self-s
t
anding
.
" into releas
e
-4-6
commit
|
commitdiff
|
tree
2013-01-04
T
e
e
mu Mu
r
t
o
la
Merge
"
M
inor fixes t
o
g_angl
e
h
e
lp d
e
scri
p
tion
.
" i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-04
Mark Abraham
Set CMake modu
l
e
s
earch
pa
t
h at a better time
commit
|
commitdiff
|
tree
2013-01-04
Teemu Mur
t
ol
a
Me
r
ge "add
a
n
option
to
not build the temp
l
a
te" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-04
Teemu Murtola
Merge
"
A
dd
missing defines to PKG_CF
L
AGS"
into
release-4-6
commit
|
commitdiff
|
tree
2013-01-04
Teemu Murtola
Merg
e
"Fixed
error messag
e
for zwitterion residues
.
.
.
commit
|
commitdiff
|
tree
2013-01-03
C
hris
t
oph Junghans
a
dd an option
t
o
not build the template
commit
|
commitdiff
|
tree
2013-01-03
Chris
t
o
p
h Junghan
s
Add
m
issing defines to PKG_CFLAG
S
commit
|
commitdiff
|
tree
2013-01-03
Roland Schulz
Merg
e
"Fi
x
ed GMXRC so
we are
not po
l
lutin
g
stan
d
ard
.
.
.
commit
|
commitdiff
|
tree
2013-01-03
Christoph J
u
n
g
h
ans
Mer
g
e
"Remove non-
f
unc
t
i
onal Power
P
C invsq
r
t
.
" into
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
Erik Lind
a
hl
Merge
"Thread-MPI
fixe
s
for i386 llvm
&
s
i
mplif
i
cat
i
on
.
.
.
commit
|
commitdiff
|
tree
2012-12-22
Alexey Shvetsov
[tools] g_sans
-
a
d
d tr
a
jectory av
e
reging
commit
|
commitdiff
|
tree
2012-12-22
M
a
r
k
Abraham
New bet
a
r
elease: 4
.
6-beta3
commit
|
commitdiff
|
tree
2012-12-22
Christop
h
J
u
nghans
cm
a
ke: mark FFTW_HAV
E
_{SIMD,AVX} as a
d
vanced
commit
|
commitdiff
|
tree
2012-12-22
Roland Schulz
Add mi
s
sing visibi
l
it
y
export
s
commit
|
commitdiff
|
tree
2012-12-21
Christoph Jun
g
hans
M
e
rge "Remove non-functional compiler override for
.
.
.
commit
|
commitdiff
|
tree
2012-12-21
Erik Lindahl
Fixe
d
gmx
_
cpuid not working on non-x86
commit
|
commitdiff
|
tree
2012-12-20
Erik Linda
h
l
Merg
e
"c
m
a
k
e
: added op
t
ion
t
o
disable quotes"
into
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
E
r
ik Lin
d
ahl
Merge "Small fi
x
for g_tune_pme" into release-4-6
commit
|
commitdiff
|
tree
2012-12-20
Erik Lindahl
Merge "
F
ixes
for andersen tem
p
e
rature control
"
i
n
to
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Eri
k
Lin
d
ahl
Merg
e
"Fixes for expanded
ensemble and H
R
EP
E
X"
into
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
C
h
ristoph Junghans
Me
r
ge "Fix
e
d AVX256 double-p
r
ec
i
s
i
on
kernels fo
r
gcc
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Ch
r
istoph Junghans
cmake: add
e
d opti
o
n to
disab
l
e quot
e
s
commit
|
commitdiff
|
tree
2012-12-20
M
ichae
l
Shirts
Fixes
f
or andersen te
m
p
erature c
o
ntrol
commit
|
commitdiff
|
tree
2012-12-20
M
i
chael Shirts
F
i
xes f
o
r
e
x
p
anded ensemb
l
e and HREPEX
commit
|
commitdiff
|
tree
2012-12-19
Mark Abraham
Merge "Remove the rest of the
fortra
n
/
power6 ac
c
eler
a
tion
.
.
.
commit
|
commitdiff
|
tree
2012-12-19
Mark
A
braham
Mer
g
e "Alw
a
ys build te
m
p
l
ate
p
r
ogram" into r
e
l
e
ase-4-6
commit
|
commitdiff
|
tree
2012-12-19
Mar
k
Abraham
Fix
Reference bu
i
ld type
commit
|
commitdiff
|
tree
2012-12-19
S
z
i
l
á
rd Páll
Merge "Avo
i
d using undefined CMake variables
"
into
.
.
.
commit
|
commitdiff
|
tree
2012-12-19
Szi
l
á
rd Páll
Merge "
R
e
moved
orph
a
n fil
e
" int
o
release-4-6
commit
|
commitdiff
|
tree
2012-12-19
Roland Schulz
Merge "Fix
l
icense te
x
t
p
r
inted by pr
o
grams
.
" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2012-12-19
R
o
la
n
d Sch
u
lz
Merge chang
e
s Idc
6
52236,If03c
f
569 i
n
to rele
a
s
e
-4-6
commit
|
commitdiff
|
tree
2012-12-19
Roland Sch
u
lz
Merge "issue error if
G
PU ID is
p
rovided
w
i
th GPU acc
.
.
.
commit
|
commitdiff
|
tree
2012-12-18
C
h
ristoph Junghans
Merge "Fixes r
e
dmine issue #1071"
i
nto release
-
4-6
commit
|
commitdiff
|
tree
2012-12-17
S
z
ilárd Páll
Merge "reduce
d
PLINCS
communication with H-bond
c
onst
r
ai
n
ts
.
.
.
commit
|
commitdiff
|
tree
2012-12-11
Ch
r
is
t
o
ph Junghan
s
Merg
e
"
Fix c
o
mp
i
lation
w
ith PGI"
into release-
4
-6
commit
|
commitdiff
|
tree
2012-12-10
Chris
t
oph Junghan
s
Merge "force C++ linking of
t
he gp
u
_ut
i
ls" into
r
elease-4-6
commit
|
commitdiff
|
tree
2012-12-09
Roland Schulz
Me
r
g
e
"
f
ixed GPU pair-s
e
arch
w
ith GMX_CPU_ACCELERA
T
IO
N
.
.
.
commit
|
commitdiff
|
tree
2012-12-09
Roland Schulz
Merge "Fix bui
l
d
of template
and other extern
a
l
co
d
e
.
.
.
commit
|
commitdiff
|
tree
2012-12-06
R
o
land Schulz
Make
S
SE4
.
1 warning clearer
commit
|
commitdiff
|
tree
2012-12-06
M
ark Abraham
New
b
eta
r
e
l
eas
e
:
4
.
6-beta2
commit
|
commitdiff
|
tree
2012-12-06
Sebasti
a
n Fritsch
Re-ena
b
le AdResS feature
commit
|
commitdiff
|
tree
2012-12-06
Berk Hess
r
emoved last OpenMP O(nthreads)
b
ottlene
c
k
commit
|
commitdiff
|
tree
2012-12-05
Szila
r
d Pall
firs
t
step toward moving OpenMM support to contrib
commit
|
commitdiff
|
tree
2012-12-05
Mark Abraham
Merge
"
d
o
n't
a
uto-set nvcc host co
m
piler with cmake
.
.
.
commit
|
commitdiff
|
tree
2012-12-05
Mark Abra
h
a
m
Merge "K
e
ep Find
C
UDA quiet wh
e
n
it is
n
ot
u
seful"
into
.
.
.
commit
|
commitdiff
|
tree
2012-12-05
Mark Abraham
Merge "Remo
v
e
T
EST_TMPI_ATO
M
I
CS_ONLY" i
n
to release-4-6
commit
|
commitdiff
|
tree
2012-12-05
Mark Abraham
Merge "Re
-
apply -dev version name between beta 1 and
.
.
.
commit
|
commitdiff
|
tree
2012-12-05
Roland Schulz
Merge "fixed segv in Verl
e
t
p
air
-
sea
r
c
h
w
i
t
h trili
n
ic
.
.
.
commit
|
commitdiff
|
tree
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