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fix OpenMP detection on Mac OS broken by a6fee0b
2013-01-18
Szilárd Páll
fix OpenMP
d
etection
o
n Mac
OS broken
b
y a6fee0b
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraha
m
Merge "Remo
v
e un
n
ecess
a
ry ICC flags affe
c
ting performance
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
M
e
rg
e
"improved CUDA kernel
p
erfo
r
mance by
p
r
e-loading
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
C
h
r
istop
h
Junghans
Mer
g
e "A
d
ded note abou
t
make_edi
a
nd
f
looding in
ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
Merge "use the compiler versio
n
provided by CMake
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
R
o
l
a
nd Schul
z
M
e
r
g
e "Merge
b
ranch '
r
e
l
ease-4-5-p
a
tche
s
' in
t
o
r
el
e
ase
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Szil
á
rd Pál
l
Me
r
ge changes I930
b
316c
,
Iea428
3
e0,I103648f8 into
release-4-6
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
BlueGene
/
Q i
n
stalla
t
ion note
s
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
Merg
e
"note th
e
r
eason for a
u
to-dis
a
b
ling GPU supp
o
rt
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
M
a
r
k Ab
r
aham
Me
r
ge "Added mdp o
p
ti
o
n 'cal
c
-l
a
mbda-n
e
ighbors'
.
" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland S
c
h
ulz
Merge "clarify w
o
rding of
GPU driver-related
n
otes
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
M
ark Abraham
Fix tr
j
conv -sub
w
i
th
.
trr files
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
fi
x
ed SD+BD integration slowing down wit
h
OpenMP th
r
eads
commit
|
commitdiff
|
tree
2013-01-17
Ro
l
a
n
d
Schulz
Run
r
egressiontests from
build
commit
|
commitdiff
|
tree
2013-01-17
Sander Pronk
Added
m
d
p option '
c
alc-lambda-neighbors'
.
commit
|
commitdiff
|
tree
2013-01-17
Mar
k
Abraham
Fi
n
ally move OpenMM to contrib
commit
|
commitdiff
|
tree
2013-01-17
R
o
lan
d
Schulz
Fi
x
co
n
fusing gmx_header_config
.
h include
commit
|
commitdiff
|
tree
2013-01-17
Sz
i
lard Pal
l
don't
use
p
olling with new
d
r
i
ver
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
c
l
ean
up
f
ortran
n
ame mangling
commit
|
commitdiff
|
tree
2013-01-17
Berk
Hess
fixe
d
n
b
n
x
n
hybrid
mode
w
i
t
h
OpenMP
commit
|
commitdiff
|
tree
2013-01-17
Berk
Hess
made PME
l
o
a
d balancing
+
DD
D
L
B more efficient
commit
|
commitdiff
|
tree
2013-01-16
C
hristoph Junghans
Rem
o
ve debug st
a
tment
commit
|
commitdiff
|
tree
2013-01-15
Mark Abraham
Merge "H
i
d nbnx
n
kernel names behi
n
d
a lookup funct
i
on
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Christoph
J
ung
h
an
s
Me
r
ge
"
Add
e
d
fatal
e
rror for constraints +
L-BFG
S
m
i
ni
m
izer
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Chris
t
op
h
Jun
g
hans
Merge "di
s
abl
e
O
penMP with all OS
X gcc 4
.
2-based
compilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
San
d
er P
r
o
n
k
Mer
g
e "Co
n
tinua
t
io
n
of docu
m
entation fo
r
expanded
e
nsemble
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
M
a
rk Abrah
a
m
Velocity
-
verl
e
t integ
r
ators and v-re
s
cale are
b
roken
commit
|
commitdiff
|
tree
2013-01-14
Carsten Kut
z
ner
Essential
dynamics
output file
now in
.
xvg
format
commit
|
commitdiff
|
tree
2013-01-14
David van d
e
r
S
poel
M
erge "Fixing trjc
o
nv
-
sub" into release-4-5-patche
s
commit
|
commitdiff
|
tree
2013-01-14
David v
a
n der Spoel
Merge
"
N
oting t
h
at and why gmxdump -s
-
s
y
s
i
s
broken
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Roland Schulz
Merge "Fi
x
es for md-vv and rerun" into
release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Rola
n
d Schulz
Merge "fi
x
ed
r
esetting stat
e
s with parallel Verlet
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Ro
l
and Schu
l
z
Proper
fix f
o
r copyr
i
te cuda depende
n
ce
commit
|
commitdiff
|
tree
2013-01-13
Michael Shirts
Fixes for md-vv an
d
rerun
commit
|
commitdiff
|
tree
2013-01-13
Berk H
e
s
s
f
ixed res
e
tting
states with p
a
rallel Verlet sc
h
eme
commit
|
commitdiff
|
tree
2013-01-13
C
hristoph Junghans
Merge "R
e
move unused bfunc
.
h
.
" i
n
to release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Chris
t
oph Jun
g
hans
Merge "Clarified some
commen
t
s & wa
r
ni
n
gs abo
u
t th
r
ead
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Ch
r
i
s
toph
Jungh
a
ns
Merge "
M
anage Bl
u
eG
e
ne/Q conf
i
guratio
n
" into rele
a
s
e
-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christ
o
ph Jun
g
hans
Merge "Re-organize BlueGene toolchain files" into r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph
Junghans
M
erg
e
"Cha
n
g
ed
defaults for building sha
r
ed libraries
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
M
ark
A
b
rah
a
m
Clarified
s
ome
c
omments
& warnings a
b
out
t
hread
p
inning
commit
|
commitdiff
|
tree
2013-01-13
R
o
l
a
nd Sc
h
ulz
Merge "pr
e
p
are
d
the
n
bnxn
c
ode for
non-x86 SIMD"
into
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Ma
r
k Abrah
a
m
M
e
rge
"Added basic CP
U
topology informati
o
n
t
o cpuid
.
.
.
commit
|
commitdiff
|
tree
2013-01-12
Berk
H
ess
p
r
epared the nbnxn code for non-x86 SIM
D
commit
|
commitdiff
|
tree
2013-01-12
Christoph Junghans
M
erge "Added missi
n
g export" into release-4-6
commit
|
commitdiff
|
tree
2013-01-11
Erik Lin
d
ahl
Merge "made SHAK
E
work again with
p
arti
c
le decompost
i
on
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Roland Schu
l
z
Merge "time the
GPU f
o
r
ce clearing
a
s
ync
l
a
u
nch
o
verhea
d
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Christoph Junghans
Merge "con
s
ole an
d
l
o
g outp
u
t improvements" into
r
elease-
4
-
6
commit
|
commitdiff
|
tree
2013-01-11
Christoph Jungha
n
s
Merge "
F
ix CUDA b
e
in
g
quiet an
d
mark all CUDA_* a
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Erik Lindahl
Added basic CPU topology
i
nformat
i
o
n
t
o
cp
u
i
d
code
commit
|
commitdiff
|
tree
2013-01-11
Erik Lind
a
hl
Mer
g
e "fixed nbnxn no LJ c
o
mb
.
rule
A
VX256 PME kernel
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Roland Sch
u
lz
Merge
"
Handle com
p
ile
r
flags
more flexibly"
into release-4-6
commit
|
commitdiff
|
tree
2013-01-11
C
h
ristoph
J
unghans
Merge "Remove incor
r
e
c
t
assert
added by 05f9a740"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
B
e
rk He
s
s
fixed nbnxn no LJ
comb
.
r
ule AVX25
6
PME ker
n
el
commit
|
commitdiff
|
tree
2013-01-10
Erik L
i
n
dahl
F
i
xed f
l
op
-
accounting
for periodic
i
mproper d
i
hedra
l
s
commit
|
commitdiff
|
tree
2013-01-10
Mark A
b
r
a
h
am
Merge "Revert
defaul
t
rlist/rvdw/rcoulomb to v
a
lid
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Mark Abraham
Merge "fixed
b
u
g
w
ith Verlet + D
D
+ bonded atom com
m
unicatio
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Roland
Sch
u
lz
Handle compiler fla
g
s more flex
i
bly
commit
|
commitdiff
|
tree
2013-01-10
Erik
Lindahl
Disallow the
use
o
f Clang to compile AVX
_
128_FMA
commit
|
commitdiff
|
tree
2013-01-10
Roland Schulz
Merge
"
Move W
i
n
dows
s
hared/static options to later
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Ro
l
and Schulz
Mer
g
e "
R
emove workar
o
und" int
o
r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-01-10
R
o
la
n
d Sc
h
u
l
z
Move
Windows shared/static
o
p
t
i
ons to l
a
ter poi
n
t
commit
|
commitdiff
|
tree
2013-01-10
Roland Schu
l
z
Remove
workaround
commit
|
commitdiff
|
tree
2013-01-10
Eri
k
Lin
d
ahl
Remo
v
e broken g_dih
t
ool
commit
|
commitdiff
|
tree
2013-01-10
Mar
k
Abraham
Mer
g
e "Fixes
S
S
E/AVX compi
l
ation under Win
d
ows" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Erik Lin
d
ahl
Merge "Cor
r
ected gmxc
h
eck
output for Gromos96 bon
d
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Roland Sc
h
u
l
z
M
e
r
g
e "Added work-around for gc
c
bug in AVX intr
i
nsinc
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Ro
l
an
d
Schu
l
z
Merg
e
"Add check to
remove zero Charmm
d
i
h
e
drals" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
R
oland Schulz
Merge "[tools] g_sans - add trajector
y
ave
r
e
ging" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-08
Erik Lindahl
Add c
h
e
c
k to remove zero Cha
r
mm
d
i
h
edrals
commit
|
commitdiff
|
tree
2013-01-08
Erik Lindahl
Do not always add
-
msse2 to release fl
a
gs for
i
cc
commit
|
commitdiff
|
tree
2013-01-08
Roland Schulz
M
erge "R
e
duce
u
s
e of m
o
n
olith
i
c set
s
o
f compiler
f
l
ags
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland Schu
l
z
Merg
e
"fixed n
b
nx
n
AVX-256 Ew
a
l
d
tabl
e
pointe
r
a
lignment
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
M
ark Abraham
Redu
c
e use of mo
n
o
l
ithic sets of
c
omp
i
ler fla
g
s
commit
|
commitdiff
|
tree
2013-01-07
Roland
Sch
u
lz
Merge "c
m
ake: remove double-negat
i
ve qu
o
t
e
s logic"
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Ro
l
and Sc
h
ulz
Mer
g
e "Print out atom n
u
mbers
i
n g_rmsf"
into r
e
l
ease
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Berk Hess
fixed nbnxn AVX
-
256 E
w
a
l
d
t
able pointer
a
lignm
e
nt
commit
|
commitdiff
|
tree
2013-01-07
Roland Schulz
Merge "Ignore bool
c
ast warning for MSVC
a
nd C+
+
" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
David van der S
p
oel
Me
r
ge
"
Removed
r
eference to no
n
e
xistent file
in g_heli
x
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland
S
chulz
Mer
g
e
"
im
p
roved r
e
portin
g
of failed affinity setting
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
R
o
l
a
nd Schul
z
Merge "Fi
x
ed format error in online manual
.
"
into rele
a
se-4
-
6
commit
|
commitdiff
|
tree
2013-01-07
Roland
S
chulz
Merg
e
"Fixed a bug that
with mul
t
iple e
x
c
hange
s
" int
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland Schulz
Merge "Essential dynamics: fixed restarts
w
hen ED gr
o
u
p
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland Schulz
M
e
rge "minor speed-up a
n
d code clean-up in nbn
x
n kernels
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
C
hrist
o
ph
J
ungha
n
s
Merge "Make
g
mx
_
cpui
d
.
h self-sta
n
di
n
g
.
" into release-4
-
6
commit
|
commitdiff
|
tree
2013-01-04
Teem
u
Murtola
Merge "Minor fix
e
s to g_angl
e
help descript
i
on
.
" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-01-04
Mark
A
b
raham
Set CMa
k
e module search path at a better time
commit
|
commitdiff
|
tree
2013-01-04
Teemu Murt
o
la
Merge "add an
o
pti
o
n to not
bu
i
l
d
the
t
emplate" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-04
Teemu Mur
t
o
l
a
Merge "
A
d
d
missing defines
to PKG_CFLA
G
S" into r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-01-04
T
e
e
mu Murtol
a
Merge "Fix
e
d
error
m
essag
e
for zwitteri
o
n residues
.
.
.
commit
|
commitdiff
|
tree
2013-01-03
Christoph Junghans
add
a
n
option t
o
not build the template
commit
|
commitdiff
|
tree
2013-01-03
C
hristoph Junghans
Add
m
i
ss
i
n
g
defines to PKG_C
F
LAGS
commit
|
commitdiff
|
tree
2013-01-03
Rol
a
nd Schulz
Merge "Fixed GMXR
C
so we are not polluting standa
r
d
.
.
.
commit
|
commitdiff
|
tree
2013-01-03
Christoph Ju
n
ghans
Mer
g
e "Rem
o
v
e
non-funct
i
onal Po
w
e
r
PC invsqr
t
.
" into
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
Erik
L
indahl
Merge "Thread-MPI fixes for i
3
86 llvm & simplifi
c
a
tion
.
.
.
commit
|
commitdiff
|
tree
2012-12-22
Alexey
Shvet
s
ov
[t
o
ols] g_sans - ad
d
trajecto
r
y ave
r
egin
g
commit
|
commitdiff
|
tree
2012-12-22
Mark Abraham
New beta release:
4
.
6-beta3
commit
|
commitdiff
|
tree
2012-12-22
Christoph J
u
nghans
cma
k
e: mark
F
FTW_H
A
VE
_
{SIMD,AVX
}
as adva
n
ced
commit
|
commitdiff
|
tree
2012-12-22
Roland Sc
h
ul
z
Add missing
v
is
i
bility exports
commit
|
commitdiff
|
tree
2012-12-21
Christoph Junghans
Merge "Remove
non-
f
u
nction
a
l
c
o
mpiler overr
i
de for
.
.
.
commit
|
commitdiff
|
tree
next