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Merge "Merge release-4-5-patches into release-4-6" into release-4-6
2013-04-10
Teemu Murtol
a
Me
r
g
e
"Merge rel
e
a
s
e
-4-5-
p
a
tches
i
nt
o
release-4
-
6"
.
.
.
commit
|
commitdiff
|
tree
2013-03-29
C
h
r
i
stoph Jungh
a
ns
Merge "Added install guide se
c
t
ion for BLAS
/
LAPACK
.
.
.
commit
|
commitdiff
|
tree
2013-03-19
Christoph Junghans
Me
r
ge "Essent
i
al d
y
namics
:
fixed le
g
end in ED
.
xvg
.
.
.
commit
|
commitdiff
|
tree
2013-03-12
Mark Abraham
Merge "
f
ix broken
things in mkht
m
l
"
into relea
s
e
-4
-
6
commit
|
commitdiff
|
tree
2013-03-11
Mark
Abraham
Merge "Fixes li
n
kage
w
ith FFTW +
M
KL for
B
LAS/LAP
A
CK
.
.
.
commit
|
commitdiff
|
tree
2013-03-06
Roland Schu
l
z
Merge "fixe
d
PME t
i
me print wi
t
h -ntomp_p
m
e
!
= -n
t
omp
.
.
.
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
New p
a
t
c
h release 4
.
6
.
1
commit
|
commitdiff
|
tree
2013-03-05
Mark
Abraham
Fix aut
o
m
ated regress
i
on testing GMXLIB
v
alue
commit
|
commitdiff
|
tree
2013-03-05
B
erk Hes
s
fi
x
e
d bug
w
ith D
D
cut-off check and PME DL
B
commit
|
commitdiff
|
tree
2013-03-05
Mark A
b
r
a
ham
Fix r
e
gre
s
sio
n
tests
a
utomated download
commit
|
commitdiff
|
tree
2013-03-05
Berk
H
ess
fixed recent
b
ug wit
h
sorting atoms for GPUs
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
Upd
a
te shell c
o
mpletions
commit
|
commitdiff
|
tree
2013-03-05
Mar
k
Abr
a
h
am
Upda
t
e outdated admin
things
commit
|
commitdiff
|
tree
2013-03-05
Ju
s
t
i
n L
e
mkul
Fixes fo
r
install guide
p
a
ge
.
commit
|
commitdiff
|
tree
2013-03-05
M
ark A
b
raham
U
p
dated install
guide
commit
|
commitdiff
|
tree
2013-03-02
Christop
h
Junghans
Merg
e
"U
n
c
r
ustified
code changes s
i
n
c
e 4
.
6"
i
nto rele
a
s
e
-4-6
commit
|
commitdiff
|
tree
2013-02-20
Christoph Jun
g
hans
Bump shared object
v
ersion to 8
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
fixed
i
s
sues wit
h
FEP s
o
f
t-core
an
d
cut
-
o
f
f's
commit
|
commitdiff
|
tree
2013-02-18
B
e
rk H
e
ss
f
i
xed GPU particle gridding p
e
rformance issue
commit
|
commitdiff
|
tree
2013-02-18
C
arste
n
Kutzne
r
Made g_tune_pme work with 4
.
6 if us
e
r sets "-p" command
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Mark Abraham
Fix CMake names
p
ace po
l
lution
commit
|
commitdiff
|
tree
2013-02-15
Mark
Abraham
Merge "Minor fixes to Verlet kernels" into rel
e
ase-4-6
commit
|
commitdiff
|
tree
2013-02-15
Mark
A
b
rah
a
m
Merge "i
m
pr
o
ved
PME load balancing reporting" into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abr
a
ha
m
Me
r
ge
"Re-gene
r
ated grou
p
k
e
rnels" into release-4-6
commit
|
commitdiff
|
tree
2013-02-15
Mar
k
Ab
r
aham
M
erge "Unwinds flag dependenc
i
e
s
in g_or
d
er
.
"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
David van der Spo
e
l
M
e
rge
"
F
i
xe
d
a
n
initialization issue
i
n gmx_dipoles
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Ab
r
aham
Merge
"
u
se legacy CUDA non-bonded kernel
s
o
n
ly on F
e
rmi
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
M
ark Abr
a
h
a
m
Merge "More
des
c
riptiv
e
Verl
e
t kernel macro parameter
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Berk Hess
improved PME load balancing reporting
commit
|
commitdiff
|
tree
2013-02-15
M
ark Ab
r
aham
Minor fix
e
s to Ve
r
let kernels
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Me
r
ge "Fix an
d
a
dd Verl
e
t
kernel e
r
ror me
s
s
ages"
in
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Sand
e
r Pronk
Merg
e
"Fix
co
d
e bug with
thread-MPI o
n
PowerPC
w
ith
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Roland
Schulz
Merge "
F
ixed t
h
e MPI recog
n
ition string
i
n
g_tune_pme
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
R
o
land Sch
u
l
z
M
e
rge "improve setup of m
u
ltiple tf tables" into re
l
ease
-
4-6
commit
|
commitdiff
|
tree
2013-02-13
R
o
l
a
n
d Sc
h
ulz
Merge "Updat
e
d FindGSL
.
cma
k
e
to versio
n
written
b
y
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Mar
k
Abra
h
am
Merge "PME-only c
o
unter
s
are now re
s
e
t with -
m
axh
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
C
h
risto
p
h Junghans
Updated F
i
ndGSL
.
cm
a
ke to
v
ersi
o
n written by
me
.
commit
|
commitdiff
|
tree
2013-02-12
Mark Abra
h
am
Me
r
g
e "fixed bug wi
t
h sd inte
g
rator and OpenMP threadi
n
g
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Ma
r
k
A
b
raham
Mer
g
e
"
Fix CUDA_HO
S
T_COMPILER flag name" int
o
relea
s
e-4
-
6
commit
|
commitdiff
|
tree
2013-02-09
Rola
n
d Sch
u
lz
Merge
"
Typo
f
ix" into
r
elease-4-6
commit
|
commitdiff
|
tree
2013-02-08
M
ark Abraham
Merg
e
"added back
cuda
.
h inc
l
udes to fix missing
C
UDA_VE
R
SIO
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Ma
r
k Abraham
Merge "Fixe
d
flop co
u
ntin
g
for ge
n
eric cg
/
adress kernels
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark Abraham
Merge "cmake: fixed typo in templat
e
CMakeLi
s
t
s
.
txt
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Ch
r
ist
o
ph J
u
nghans
Merge "Documented
w
hat
G
MX_CPU_ACCELERATION really
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Mark Ab
r
aham
Merge "improved
load bal
a
n
c
ing on the GPU" in
t
o r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-02-01
Ber
k
Hess
PME-only coun
t
ers are
n
ow reset with -maxh -re
s
et
h
w
a
y
commit
|
commitdiff
|
tree
2013-01-25
C
h
ristoph Ju
n
ghans
Merge
"Mo
v
ed
a
few commen
t
s back int
o
positio
n
" i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark
A
braham
Merge "Illegal acceleration d
e
faulted
to QPX" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark
A
br
a
ham
Mer
g
e "Re-licenced FindGR
O
MA
C
S
.
cmake (w
a
s
writ
t
e
n by
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Roland
Schu
l
z
Illegal a
c
celeration defaul
t
e
d
to QPX
commit
|
commitdiff
|
tree
2013-01-22
Ma
r
k Ab
r
aham
Merge "F
i
x TOUP
P
ER
usage" into release
-
4-
6
commit
|
commitdiff
|
tree
2013-01-22
M
ark Abraham
M
e
rg
e
"Updat
e
d html manual
t
o 4
.
6" in
t
o r
e
l
e
ase-4-6
commit
|
commitdiff
|
tree
2013-01-22
Ma
r
k Abrah
a
m
Merge "added missing cleanup of some nbnxn_cuda
data
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Roland
S
chulz
Fix TOUPPER usage
commit
|
commitdiff
|
tree
2013-01-22
Roland
S
chulz
Updated htm
l
manual to 4
.
6
commit
|
commitdiff
|
tree
2013-01-21
C
h
ristoph J
u
nghans
Merge "Set v
e
rsion inf
o
f
o
r 4
.
6
.
x
relea
s
e se
r
i
es" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Mark
A
braham
Set v
e
rs
i
on in
f
o for 4
.
6
.
x release serie
s
commit
|
commitdiff
|
tree
2013-01-18
Mark Abraham
New ma
j
or rele
a
se: 4
.
6
commit
|
commitdiff
|
tree
2013-01-18
Mic
h
a
e
l
Shirts
Adde
n
dum
for e
x
panded e
n
sem
b
le options plu
s
format
t
ing
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Roland
S
c
h
ul
z
Fix typo
commit
|
commitdiff
|
tree
2013-01-18
R
oland Schulz
Cod
e
beautifica
t
ion wi
t
h
uncrustify
commit
|
commitdiff
|
tree
2013-01-18
R
oland Sch
u
lz
Add colon after mac
r
o to he
l
p
uncrustify
commit
|
commitdiff
|
tree
2013-01-18
B
erk H
e
ss
thread af
f
inity now u
s
e
s some to
p
ology inform
a
tion
commit
|
commitdiff
|
tree
2013-01-18
Mark Abraham
Fixing copyr
i
ght
is
s
u
es and code contributors
commit
|
commitdiff
|
tree
2013-01-18
Erik
L
i
ndahl
Merge "remove unn
e
c
es
s
ary cmak
e
me
s
s
a
ges" into release-4-6
commit
|
commitdiff
|
tree
2013-01-18
Erik
L
indahl
Merge "fix OpenMP detec
t
ion on
Mac OS br
o
ken
b
y a
6
fee0b
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Szilárd P
á
l
l
fix OpenMP
detection on Mac
O
S broken by
a6fee0b
commit
|
commitdiff
|
tree
2013-01-17
Szilárd Páll
adde
d
m
i
ssing c
l
e
anup of some nbnxn_cuda
d
ata
commit
|
commitdiff
|
tree
2013-01-17
Mark A
b
r
a
ham
Merge "Remove unnecessary ICC flags affecting performanc
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Merge "i
m
pro
v
e
d CU
D
A
k
ernel performance by pre-
l
oading
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Ch
r
i
stoph Junghans
Me
r
ge "Added note about m
a
ke_edi and floodi
n
g
i
n
ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph
Jungh
a
ns
Merge "use t
h
e
c
omp
i
l
er version
provide
d
by CMake
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Rol
a
n
d Schulz
Merge "M
e
rge branch 'release-4-
5
-p
a
tches' i
n
to release
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Szilárd Páll
Mer
g
e ch
a
n
ges I930b316c,Iea4
2
83e0,I103
6
48f8 into rel
e
ase-4-6
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Merge "
F
i
x trjconv -sub w
i
t
h
.
t
rr files" into release
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Bl
u
eG
e
ne/Q installation
notes
commit
|
commitdiff
|
tree
2013-01-17
C
h
ristoph Junghan
s
M
erge "note
the
reas
o
n for auto-disa
b
ling GPU support
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Me
r
ge "Adde
d
md
p
option 'calc-
l
ambda
-
neighbors'
.
" int
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Rola
n
d Schulz
Merge "clarify wording of G
P
U drive
r
-related notes
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland
S
chulz
Mer
g
e "Added check for
valid wall_atomtype in
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
M
ark Abraham
Fix t
r
jcon
v
-sub with
.
trr
f
il
e
s
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
fixed
S
D+BD i
n
tegration slowing do
w
n with OpenMP threads
commit
|
commitdiff
|
tree
2013-01-17
Rola
n
d Schulz
Run regressiontests
from build
commit
|
commitdiff
|
tree
2013-01-17
Sander Pr
o
nk
Added mdp option 'ca
l
c-lamb
d
a
-n
e
i
g
h
bors'
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Finally move OpenMM to contrib
commit
|
commitdiff
|
tree
2013-01-17
R
oland Schulz
Fix
c
o
n
fusing gmx_heade
r
_config
.
h include
commit
|
commitdiff
|
tree
2013-01-17
Szilard Pall
don't use
po
l
ling with new
driver
commit
|
commitdiff
|
tree
2013-01-17
C
h
ristoph Jun
g
hans
clean up fortr
a
n name mangling
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
f
ixed nbnx
n
h
y
brid m
o
de with OpenM
P
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
made
PME loa
d
balanc
i
n
g + DD
DLB more effic
i
ent
commit
|
commitdiff
|
tree
2013-01-16
Christoph Jungh
a
ns
R
e
m
ove debug statment
commit
|
commitdiff
|
tree
2013-01-15
Mark Abraham
Merge "
H
id nbnxn ke
r
nel na
m
e
s
b
ehin
d
a lookup function
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Ch
r
i
s
top
h
J
u
nghans
M
e
r
g
e
"Added
fat
a
l
er
r
or f
o
r
constraints
+
L-BFGS minim
i
zer
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
C
hris
t
op
h
Junghans
Me
r
ge
"
disable O
p
e
n
M
P
w
i
t
h
all OS X g
c
c 4
.
2
-ba
s
ed compil
e
rs
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Sand
e
r Pronk
Me
r
ge "Continuat
i
o
n o
f
d
ocu
m
entation for e
x
panded ensemble
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Mar
k
Abraham
Veloc
i
ty-verle
t
inte
g
rators
a
nd v-rescale a
r
e bro
k
e
n
commit
|
commitdiff
|
tree
2013-01-14
Carsten
K
u
t
zne
r
Essential dynamics output
file n
o
w in
.
xvg format
commit
|
commitdiff
|
tree
2013-01-14
David
van
d
er
Spoel
Merge "Fixing trjco
n
v
-sub" into
r
ele
a
se-4-
5
-patc
h
e
s
commit
|
commitdiff
|
tree
2013-01-14
David van d
e
r
S
poel
Merge "No
t
ing t
h
at
and why gmxdump -s
-
sy
s
is
b
r
oke
n
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Rolan
d
Schulz
Merge "
F
ixes f
o
r md-vv and rerun" into release-4-6
commit
|
commitdiff
|
tree
next