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Merge "Fixes "Function type U-B not implemented in ip_pert."" into release-4-6
2013-05-10
Mar
k
Abraham
Merge
"F
i
x
e
s
"F
u
nc
t
ion t
y
pe U-B not implemented
i
n
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
M
a
rk Abraham
M
e
rge "improve b
u
ild with OpenMM, st
i
ll n
o
t
100% fixed
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Mark Ab
r
aha
m
Merge "fix
i
ng rerun with free energy +
.
xtc
o
r
.
gro
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Christ
o
ph Junghans
improve
build w
i
t
h
O
penMM, s
t
ill not 1
0
0% f
i
xed
commit
|
commitdiff
|
tree
2013-04-29
C
arsten Kutzner
Evaluate enfo
r
c
ed rota
t
ion
p
otenial w
i
t
h Verlet, fi
x
es
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Mark Abraham
M
er
g
e "Update linkin
g
to MKL and
d
ocument same" into
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Mark Abraham
M
erge "general SIMD acceler
a
tion for angles+
d
ihedrals
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Mark Abra
h
am
Merge
"PME
loa
d
balancing now checks f
o
r PME grid r
e
stricti
o
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Be
r
k Hess
gene
r
al SIM
D
acceleration for angles+dihedrals
commit
|
commitdiff
|
tree
2013-04-29
M
a
rk Abra
h
am
Merge
"Fixing a proble
m
with dh/dl 1-4 in
t
eractions
.
.
.
commit
|
commitdiff
|
tree
2013-04-26
M
ark Ab
r
aham
M
erge "CUDA PME kernels with
analytical Ewal
d
correction
.
.
.
commit
|
commitdiff
|
tree
2013-04-26
M
ark Abraham
M
e
r
g
e "improved load balancing with
Verlet
cut-off
.
.
.
commit
|
commitdiff
|
tree
2013-04-26
Christop
h
Ju
n
g
hans
Merge "
v
-
res
c
ale
w
orks with
t
a
u-t
>= 0"
into release
-
4-6
commit
|
commitdiff
|
tree
2013-04-25
Mark Abraham
M
erge "M
e
rge bran
c
h
'r
e
leas
e
-4
-
5-pa
t
ches'
"
i
nto release-4-6
commit
|
commitdiff
|
tree
2013-04-22
Mark Abraha
m
Merge "Use
git snapshots of th
e
tests if are on
git
.
.
.
commit
|
commitdiff
|
tree
2013-04-16
C
h
rist
o
ph Junghans
Use git snapshots of th
e
t
e
st
s
if
a
re o
n
git
commit
|
commitdiff
|
tree
2013-04-16
David van de
r
S
p
oel
Merge "corrected grompp
r
vd
w
charge-group radii c
h
eck
.
.
.
commit
|
commitdiff
|
tree
2013-04-13
David v
a
n d
e
r
Spo
e
l
Merge
"
added mdrun check for V
e
rlet+perturbed
a
t
oms
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
Mark Abr
a
ham
Merge "remo
v
e
d
x86 specif
i
cs f
r
om nb
n
xn SI
M
D
kernels
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
Mark A
b
r
a
ham
Me
r
g
e
"corrected log file wall t
i
me
breakdow
n
" into
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
Mar
k
Abraham
Merge "made PME
w
ork wit
h
a mix of 1 and
m
ore thre
a
ds
.
.
.
commit
|
commitdiff
|
tree
2013-04-10
Teem
u
M
urt
o
la
Merge "Merge
r
e
lease-4-5-patch
e
s
into re
l
ease-4-6"
.
.
.
commit
|
commitdiff
|
tree
2013-03-29
Chr
i
stoph Jun
g
hans
Mer
g
e "Ad
d
ed
i
nstall
guide s
e
ction for BLAS/LAPACK
.
.
.
commit
|
commitdiff
|
tree
2013-03-19
Christoph J
u
nghans
Merge "Es
s
ential
d
ynamics
:
fixed legend in ED
.
xvg
.
.
.
commit
|
commitdiff
|
tree
2013-03-12
Mark
Ab
r
a
ham
M
erge
"
f
i
x bro
k
en things
in mkhtml" into rel
e
ase-4-6
commit
|
commitdiff
|
tree
2013-03-11
M
ark Abraham
Merge "
F
ixes linkage with F
F
TW + MK
L
for B
L
A
S
/LAPACK
.
.
.
commit
|
commitdiff
|
tree
2013-03-06
Rolan
d
Schulz
Me
r
ge "fix
e
d PME
t
ime print with -ntomp_pme
!= -ntomp
.
.
.
commit
|
commitdiff
|
tree
2013-03-05
Mark Abr
a
ham
New p
a
tch release 4
.
6
.
1
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
F
i
x automat
e
d re
g
ression testi
n
g
G
MXLIB value
commit
|
commitdiff
|
tree
2013-03-05
Berk Hess
fixed bug with DD cut-off check and PME DLB
commit
|
commitdiff
|
tree
2013-03-05
Mark Abra
h
am
F
i
x
regressi
o
ntests
automated download
commit
|
commitdiff
|
tree
2013-03-05
B
e
rk Hess
fixed re
c
ent bug
w
ith s
o
rting a
t
oms fo
r
G
PUs
commit
|
commitdiff
|
tree
2013-03-05
Mark A
b
raham
U
pdat
e
sh
e
ll completions
commit
|
commitdiff
|
tree
2013-03-05
Mark A
b
raham
Update outdated a
d
m
in things
commit
|
commitdiff
|
tree
2013-03-05
Justin Lemkul
Fixes for install
g
uide page
.
commit
|
commitdiff
|
tree
2013-03-05
Ma
r
k
Abra
h
am
U
p
d
a
t
ed in
s
tall
g
uid
e
commit
|
commitdiff
|
tree
2013-03-02
Christo
p
h
Junghans
Merg
e
"Uncrust
i
fied
cod
e
c
ha
n
g
es
s
inc
e
4
.
6
"
into releas
e
-
4
-6
commit
|
commitdiff
|
tree
2013-02-20
Chris
t
op
h
J
unghans
Bump s
h
ared object version to
8
commit
|
commitdiff
|
tree
2013-02-20
B
erk Hess
fixed is
s
ues with FEP soft
-
cor
e
and c
u
t-off's
commit
|
commitdiff
|
tree
2013-02-18
Berk Hess
fixed
G
PU particle griddi
n
g performa
n
ce
issue
commit
|
commitdiff
|
tree
2013-02-18
Carsten Kutzne
r
Made g_tune_pme work with 4
.
6
if user sets "-p
"
c
o
mma
n
d
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Mark Abraham
Fix CMake namespace
p
ollu
t
ion
commit
|
commitdiff
|
tree
2013-02-15
M
ark
A
b
raham
Merge "Mino
r
fixes
to
Verlet kernels"
into release-4-6
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraha
m
M
erge
"improved PME
l
oad bal
a
ncing repo
r
ting"
into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Merge "Re-gene
r
a
t
ed group ker
n
els" into releas
e
-4-6
commit
|
commitdiff
|
tree
2013-02-15
M
a
rk A
b
raham
Merge "Un
w
ind
s
f
lag
d
ependenci
e
s in g
_
order
.
" into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
D
avid van der Spo
e
l
Merge
"Fix
e
d an initialization iss
u
e in gmx_dipoles
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Ma
r
k
A
braha
m
Merge "
u
s
e leg
a
c
y
CUDA
non-bonded k
e
r
n
els only on
F
ermi
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraha
m
Merge "More
descriptive V
e
rlet kern
e
l
macr
o
p
a
rameter
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
B
erk Hess
impro
v
ed PME load
b
ala
n
c
ing repor
t
ing
commit
|
commitdiff
|
tree
2013-02-15
Mar
k
Abraha
m
M
inor fixes to
Verlet kernels
commit
|
commitdiff
|
tree
2013-02-15
Ma
r
k
Abraham
M
e
r
g
e "Fix and add Verle
t
kernel
e
rror mes
s
ages"
into
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
San
d
e
r Pro
n
k
Merge "Fix
c
o
de bug with t
h
read
-
MPI on Pow
e
rP
C
w
i
th
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Rola
n
d
Sch
u
lz
Merge "Fixed the MP
I
r
e
cognition string i
n
g_t
u
ne
_
pme
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Roland Schulz
Merge "i
m
pr
o
ve setup
o
f mult
i
p
l
e
tf tables" into release-4-6
commit
|
commitdiff
|
tree
2013-02-13
Ro
l
a
nd Schulz
M
e
rge
"Updated FindGSL
.
cmake
to
v
e
rsi
o
n
written by
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Mark Ab
r
aham
Me
r
ge "PME-only count
e
r
s
are now reset
wi
t
h -maxh
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
C
hrist
o
ph
Junghans
Updat
e
d Fin
d
GSL
.
cmak
e
to version writte
n
by m
e
.
commit
|
commitdiff
|
tree
2013-02-12
Mark
A
braham
Merge "fixed bug w
i
th sd inte
g
ra
t
or and OpenMP threading
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Mark Abraham
Merge
"Fix CUDA_HO
S
T_COMPI
L
ER fla
g
name" into release-4-6
commit
|
commitdiff
|
tree
2013-02-09
Roland Schulz
Merge
"
Typo fi
x
" i
n
to
relea
s
e-4-6
commit
|
commitdiff
|
tree
2013-02-08
Mark Abraham
Merge
"ad
d
e
d
back cuda
.
h includes to fix missi
n
g CUDA_VERSI
O
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark
Abraham
Merge "Fi
x
ed
flop counting for generic cg
/
adress
k
ernel
s
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark Abr
a
ham
Merge
"
cmake:
f
ixed
typo in template CMake
L
is
t
s
.
txt
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Christoph J
u
ng
h
ans
M
e
rge
"Documented
w
hat GMX_
C
PU_ACCELERATION re
a
lly
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Ma
r
k A
b
raham
Merge
"
improved load
b
a
la
n
cing o
n
the
GP
U
" int
o
release-4-6
commit
|
commitdiff
|
tree
2013-02-01
Berk Hess
PM
E
-only counters ar
e
now res
e
t
w
ith -maxh -resethway
commit
|
commitdiff
|
tree
2013-01-25
Christ
o
ph Jungh
a
ns
Me
r
ge "Moved a few
comments back i
n
to positio
n
" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark
Abraha
m
M
erge "Illegal acce
l
eration defau
l
ted t
o
QP
X
" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark Abr
a
h
am
Merge "Re-licenced F
i
ndG
R
OMACS
.
c
m
ake
(was written by
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Roland Sch
u
l
z
Illeg
a
l acceleration defaulted
to
QPX
commit
|
commitdiff
|
tree
2013-01-22
M
a
rk Abraham
Me
r
ge "Fix TOUPPER usage" into re
l
ease-4-6
commit
|
commitdiff
|
tree
2013-01-22
Mark Abraham
Merg
e
"
U
pdated
h
tml
manual to 4
.
6
" into release-4-6
commit
|
commitdiff
|
tree
2013-01-22
M
a
r
k
A
bra
h
am
Merge "add
e
d m
i
ssing cleanup
o
f
som
e
nbnxn_cuda data
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
R
o
lan
d
Schulz
Fix TOUPPER usage
commit
|
commitdiff
|
tree
2013-01-22
Rolan
d
Schulz
U
pdated html
man
u
al to 4
.
6
commit
|
commitdiff
|
tree
2013-01-21
Christoph Jungh
a
ns
Merge "Set version info for 4
.
6
.
x release seri
e
s"
into
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Mark
Ab
r
aha
m
Set version
info for 4
.
6
.
x rel
e
a
s
e series
commit
|
commitdiff
|
tree
2013-01-18
Mark Abraha
m
New major
r
elease: 4
.
6
commit
|
commitdiff
|
tree
2013-01-18
Michael Shirts
Addendum for exp
a
nded ensemble op
t
ions plus formatting
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Ro
l
a
n
d Schulz
Fix typo
commit
|
commitdiff
|
tree
2013-01-18
Roland Schulz
C
o
de beau
t
if
i
cation w
i
th uncrustify
commit
|
commitdiff
|
tree
2013-01-18
Rolan
d
S
c
hulz
Add co
l
on
a
fter ma
c
ro to help uncrustify
commit
|
commitdiff
|
tree
2013-01-18
B
e
rk Hess
thre
a
d affinity
n
ow uses
s
ome
t
opology informatio
n
commit
|
commitdiff
|
tree
2013-01-18
Mark A
b
r
a
ha
m
F
i
x
i
ng co
p
yright issues and c
o
de contribu
t
ors
commit
|
commitdiff
|
tree
2013-01-18
Erik
L
indahl
Merge "re
m
ove u
n
nec
e
ssary cmake
m
essages" in
t
o release-4-6
commit
|
commitdiff
|
tree
2013-01-18
Erik Lindahl
Merge "fix
Op
e
nMP
d
e
t
ection on Mac OS brok
e
n by
a
6fee0b
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Szilárd Páll
fix OpenMP d
e
tection on M
a
c
O
S brok
e
n by a6fee0b
commit
|
commitdiff
|
tree
2013-01-17
Szilárd Pá
l
l
ad
d
ed missing
c
le
a
n
u
p of some
n
bnxn_cu
d
a data
commit
|
commitdiff
|
tree
2013-01-17
Mark A
b
raham
Merge "Remove unnecessary
I
CC flags affecting
p
erformance
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abr
a
h
a
m
Me
r
g
e
"imp
r
oved CUDA kernel perfor
m
ance
by pre-loa
d
ing
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph J
u
nghans
Merge "
A
d
ded note
a
b
out make_edi and
f
looding in ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
C
h
ristoph Ju
n
gh
a
ns
Merg
e
"use t
h
e
compi
l
er
v
ersion pr
o
vided b
y
CMake
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Rola
n
d
Schul
z
Merge
"Merge bra
n
ch
'
releas
e
-
4-5-patche
s
'
into r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Szilárd P
á
ll
Merge ch
a
n
g
e
s
I930b316c,Iea4283
e
0,
I
103648f8 into release-4-6
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Me
r
ge "Fix trj
c
o
n
v -sub with
.
trr files" into release
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abra
h
am
BlueG
e
ne/Q ins
t
al
l
ation
notes
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
Merge "note the reason for auto-disab
l
i
n
g GPU support
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark A
b
raham
Merge "A
d
ded
m
dp optio
n
'calc-l
a
mbda-n
e
i
ghbors'
.
"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
M
e
rge "clarif
y
wording
o
f GPU dri
v
e
r
-rel
a
te
d
notes
.
.
.
commit
|
commitdiff
|
tree
next