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Merge "Merge release-4-5-patches into release-4-6" into release-4-6
2013-03-29
Christoph Junghans
M
erge "Added install guide
sectio
n
for BLAS/LA
P
ACK
.
.
.
commit
|
commitdiff
|
tree
2013-03-19
C
h
ristoph Junghans
M
e
rge "
E
ssenti
a
l
dynamics:
f
ixed
l
egend in ED
.
xvg
.
.
.
commit
|
commitdiff
|
tree
2013-03-02
Christoph
J
unghans
Merge "Unc
r
ustifie
d
code changes
s
ince 4
.
6
" into
r
elease-4-6
commit
|
commitdiff
|
tree
2013-02-20
Christop
h
Jungh
a
ns
Bump sh
a
red
object version to 8
commit
|
commitdiff
|
tree
2013-02-12
Christoph Junghans
Upda
t
ed
FindGSL
.
cmake to version writte
n
by me
.
commit
|
commitdiff
|
tree
2013-02-05
Christoph Jungh
a
ns
Merge "
D
ocumented w
h
at GMX_CPU_ACC
E
L
E
RATION
r
eally
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Chris
t
oph Ju
n
ghans
impr
o
ve setup o
f
mult
i
ple tf tabl
e
s
commit
|
commitdiff
|
tree
2013-02-02
C
h
ristoph Junghans
Fi
x
ed flo
p
c
o
u
nting for generic
cg/
a
dress ker
n
e
l
s
commit
|
commitdiff
|
tree
2013-02-02
Chris
t
o
p
h Junghans
cmake: fixed typo in template CMakeL
i
s
ts
.
txt
commit
|
commitdiff
|
tree
2013-01-25
C
hr
i
s
toph J
u
nghans
fixed c
o
pyright of adress kernel
commit
|
commitdiff
|
tree
2013-01-25
Christoph Junghans
Merge
"
M
o
ved a
few comments back into position" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-21
Christoph Junghans
Merge "S
e
t version info
for 4
.
6
.
x release series"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2013-01-19
Christoph
J
u
ngha
n
s
Re-licenced
F
indGROMACS
.
cmake (w
a
s w
r
i
t
t
en b
y
me)
commit
|
commitdiff
|
tree
2013-01-17
Christo
p
h Ju
n
ghans
Merge "Added no
t
e
a
bo
u
t make_edi an
d
floodi
n
g in ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
C
h
r
i
stoph
J
ungha
n
s
M
e
rge
"
use
t
he co
m
p
iler
v
ersion provid
e
d by
CM
a
ke
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
M
e
rge "note
t
he reason for aut
o
-disabling GPU su
p
port
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph
Junghans
cl
e
an up
f
o
r
tran nam
e
mangling
commit
|
commitdiff
|
tree
2013-01-16
Christoph
J
unghans
Rem
o
ve debug st
a
tment
commit
|
commitdiff
|
tree
2013-01-15
Christoph Jungh
a
ns
Merge
"
Added fatal
error for constrai
n
ts + L-BFGS m
i
nim
i
zer
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Chri
s
toph Junghan
s
M
e
r
ge "d
i
sable OpenMP with all OS X
g
c
c 4
.
2-based compilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Ch
r
i
stoph Junghans
Merge "Re
m
ove unused bfunc
.
h
.
" into
r
elease-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph Jun
g
han
s
Merge "Clar
i
fied some
c
o
m
men
t
s
&
w
a
rn
i
ngs
a
b
out threa
d
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Chris
t
oph Junghans
Merg
e
"Manage Blu
e
Gene/
Q
configuratio
n
" in
t
o rel
e
ase-4-6
commit
|
commitdiff
|
tree
2013-01-13
Chri
s
toph Junghans
M
erge
"Re-organize
B
lueGene to
o
lchain files" into release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Ch
r
istoph Jun
g
hans
Merge "Changed default
s
for bu
i
ldin
g
s
hared l
i
braries
.
.
.
commit
|
commitdiff
|
tree
2013-01-12
C
hristo
p
h
Jungh
a
ns
Merge "Add
e
d m
i
ssin
g
export" into rele
a
se-4-
6
commit
|
commitdiff
|
tree
2013-01-11
Christop
h
Junghans
Merge
"co
n
sole
a
nd log output improvements" in
t
o releas
e
-4-6
commit
|
commitdiff
|
tree
2013-01-11
Christ
o
ph
J
un
g
hans
Merg
e
"Fix
CUD
A
being
q
ui
e
t and mark all CUDA_* as
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Ch
r
istop
h
J
u
n
gha
n
s
Merge "Remove incorrect a
s
sert adde
d
by 05f9a740" int
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Christ
o
ph Jungha
n
s
cmake:
remove d
o
uble-negative
q
u
o
tes
l
ogic
commit
|
commitdiff
|
tree
2013-01-07
Christoph J
u
nghans
Merge "Make gmx_cpuid
.
h self-standing
.
" i
n
to r
e
lease
-
4-6
commit
|
commitdiff
|
tree
2013-01-03
Ch
r
istoph
J
u
n
g
h
ans
add an
o
ption
to not build
t
he tem
p
late
commit
|
commitdiff
|
tree
2013-01-03
Christ
o
p
h
Junghans
Add
mi
s
sing d
e
fines
to P
K
G_CFLAGS
commit
|
commitdiff
|
tree
2013-01-03
C
h
r
istoph
Jung
h
ans
Mer
g
e "Re
m
ove non-fun
c
tio
n
al Power
P
C
invsqrt
.
" into
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
Chris
t
oph Junghans
c
mak
e
:
add option
t
o i
n
stall libmd as libgm
x
md
commit
|
commitdiff
|
tree
2012-12-22
Chr
i
stoph Junghans
c
m
ake:
mark FFTW_HAVE
_
{S
I
MD,
A
V
X
} as
a
dvanc
e
d
commit
|
commitdiff
|
tree
2012-12-21
Christoph Jun
g
h
ans
M
erge
"
Re
m
o
v
e
non-func
t
ional compiler
overri
d
e for
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Ch
r
istoph Junghans
Merge "
F
ixed AVX256 double-precision kernels
f
or
gcc
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
C
h
ri
s
toph
Junghans
c
make: added option to
dis
a
b
l
e
quotes
commit
|
commitdiff
|
tree
2012-12-18
Ch
r
istoph Jungh
a
ns
Merge "Fixes redmine issue #1071" into release
-
4-6
commit
|
commitdiff
|
tree
2012-12-17
Christop
h
Junghans
Remove
t
h
e
rest
of t
h
e for
t
ran/p
o
wer6 ac
c
elera
t
ion
commit
|
commitdiff
|
tree
2012-12-13
C
hri
s
toph
Junghans
A
l
wa
y
s bu
i
ld template program
commit
|
commitdiff
|
tree
2012-12-11
Ch
r
ist
o
ph Ju
n
ghans
Merge
"Fi
x
co
m
pi
l
ation with
PG
I
"
into re
l
ease-4-6
commit
|
commitdiff
|
tree
2012-12-10
C
hrist
o
p
h
Junghans
M
e
rge "force
C++ link
i
ng of the gpu_ut
i
ls" into release-4-
6
commit
|
commitdiff
|
tree
2012-12-05
Christoph Jun
g
han
s
fixe
d
obsolete
g
mx_f
a
t
al in OpenMM build
commit
|
commitdiff
|
tree
2012-11-29
Chri
s
toph
Junghans
Merge "Pri
n
t
e
r
r
o
r if no
thread support is
availab
l
e
.
.
.
commit
|
commitdiff
|
tree
2012-11-28
Christoph
Junghans
Merge "Fix cpack src ign
o
r
e
r
u
l
e"
i
n
to release-4-6
commit
|
commitdiff
|
tree
2012-11-28
C
hristoph
Junghans
A
dd option to internally build FFTW if selected
commit
|
commitdiff
|
tree
2012-11-22
Chr
i
s
to
p
h Junghans
i
mpro
v
e FindG
R
OMACS
.
cmake
commit
|
commitdiff
|
tree
2012-11-20
Christoph
Junghans
Merge "F
i
x g_msd -mol
"
into
r
e
lease
-
4-6
commit
|
commitdiff
|
tree
2012-11-20
Christoph
J
un
g
hans
M
e
rge "Fixes bug in g_hbond that
m
akes it produc
e
fatal
.
.
.
commit
|
commitdiff
|
tree
2012-11-16
Christop
h
Jun
g
ha
n
s
Remove
rest
of the xml suppor
t
commit
|
commitdiff
|
tree
2012-11-15
Christoph Junghans
Merge "Test tha
t
compil
i
n
g
and linking of A
V
X works
.
.
.
commit
|
commitdiff
|
tree
2012-11-08
Christoph Ju
n
ghans
Merge "auto-
s
e
t
nvcc host compi
l
er with
F
i
n
dMPI detection
.
.
.
commit
|
commitdiff
|
tree
2012-11-08
Ch
r
i
s
toph J
u
nghans
Merge "Rel
o
cated logic of simple-vs-GPU Ewald
t
a
b
le
.
.
.
commit
|
commitdiff
|
tree
2012-11-07
Ch
r
istoph Jungh
a
ns
Obey
D
SO standard
commit
|
commitdiff
|
tree
2012-11-03
C
h
ristoph Jungh
a
ns
Reworked version
of cmake FF
T
W detection
commit
|
commitdiff
|
tree
2012-11-01
Christoph Jungh
a
ns
Actually
d
isable
G
P
U w
h
en compil
i
ng in dou
b
l
e
commit
|
commitdiff
|
tree
2012-10-27
Chr
i
st
o
ph Junghans
Mer
g
e "Fix larg
e
file support" into rele
a
se-4-5
-
patches
commit
|
commitdiff
|
tree
2012-10-26
Christoph Jung
h
ans
M
e
rge "enable GMX_PREFE
R
_STATIC_L
I
BS
CMa
k
e
o
ption on
.
.
.
commit
|
commitdiff
|
tree
2012-10-26
Christoph Jun
g
han
s
Merge "fix
f
a
l
s
e
positive gcc 4
.
7 wa
r
n
ing in libxdrf
.
.
.
commit
|
commitdiff
|
tree
2012-10-10
Christoph
J
unghans
fixed header for 3rd party app
s
commit
|
commitdiff
|
tree
2012-09-27
Ch
r
istoph Jun
g
h
a
ns
Merge "F
i
xed an off-b
y
-
o
ne error in ato
m
counting
in
.
.
.
commit
|
commitdiff
|
tree
2012-09-25
C
hris
t
oph J
u
ng
h
ans
Merge "Fix REM
D
use of g
m
x_
l
arge_int
_
t for #steps
v
ariable
.
.
.
commit
|
commitdiff
|
tree
2012-09-14
Christop
h
Junghans
Mer
g
e "fixed
r
ecent bug wit
h
g
rompp c
h
eck for P-R P
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Christ
o
ph Junghans
updated references
commit
|
commitdiff
|
tree
2012-09-07
Christoph
J
unghans
Merge "Fi
x
VMD pl
u
gin
s
on Windows" i
n
to relea
s
e-4-6
commit
|
commitdiff
|
tree
2012-09-07
Christoph
Junghan
s
M
e
rge "Check tha
t
gmx_det
e
ctcpu
runs
c
orrectly" into
.
.
.
commit
|
commitdiff
|
tree
2012-09-04
Ch
r
istoph
Ju
n
ghan
s
Me
r
ge "Fixes too many bac
k
up files for *
.
n
roff
file
s
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
Chr
i
stoph
J
u
nghans
Merge "Fixi
n
g of t
h
in
g
s
a
ssociat
e
d with aminoacid
.
rtp
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
Christoph Junghans
Merge "Cle
a
n
up some vari
a
ble naming for eigenso
l
ving
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
Ch
r
istoph Junghans
Merge "Fix coordin
a
te is zero
check in g
m
xch
e
c
k" into
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
Chri
s
toph Jung
h
a
n
s
Merge
"
Explicit
l
y noted an issue with use
of genbox
.
.
.
commit
|
commitdiff
|
tree
2012-08-13
C
hristoph Junghans
fi
x
AdResS and long-range electrostat
i
cs warning
commit
|
commitdiff
|
tree
2012-08-07
Christoph
J
ung
h
ans
Merge
"fixed
incorrect T
P
I results w
i
t
h
dyn
a
mic box
.
.
.
commit
|
commitdiff
|
tree
2012-08-06
Christoph Junghans
M
e
rg
e
"
Add
e
d
comment
i
n
g
et_s
t
r
ucture abo
u
t which structures
.
.
.
commit
|
commitdiff
|
tree
2012-08-02
C
hristop
h
J
u
nghans
Add
no
t
e about
S
D integrator and t-coupling
commit
|
commitdiff
|
tree
2012-07-31
C
h
ristop
h
Ju
n
ghans
Me
r
ge
"Clarified r
e
aso
n
s for termination of EM" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2012-07-19
Christoph Junghans
cmake: a
l
low sw
i
tch between single and do
u
ble
commit
|
commitdiff
|
tree
2012-07-16
C
h
r
istoph Junghan
s
M
erge "R
e
moved c
o
mmas from gm
x
_hbond OpenMP constructs
.
.
.
commit
|
commitdiff
|
tree
2012-07-16
Christoph Ju
n
g
hans
Me
r
ge "Enforced
r
otation:
PBC/restart fi
x
"
into
r
ele
a
se-4
-
6
commit
|
commitdiff
|
tree
2012-07-09
Christoph Jungha
n
s
Merge "Fixed bug
i
n sfacto
r
.
c that mak
e
s g_rd
f
-sq
.
.
.
commit
|
commitdiff
|
tree
2012-07-05
Christoph J
u
nghans
Me
r
ge
"
D
on't re
r
un ch
e
cks a
n
d be quiet 2nd time cmake
.
.
.
commit
|
commitdiff
|
tree
2012-07-05
C
hristoph Jungha
n
s
Me
r
g
e
"Allo
w
also FindMPI for
c
make<2
.
8
.
5"
i
nto
relea
s
e-4-6
commit
|
commitdiff
|
tree
2012-07-05
Christoph Jung
h
an
s
Merge
"Fina
l
ized
a
nd extended Szilard's open
M
P
c
leanup
.
.
.
commit
|
commitdiff
|
tree
2012-07-02
Ch
r
istoph Junghans
Do not print d
i
sabl
e
d pressures
a
nd virial
s
commit
|
commitdiff
|
tree
2012-06-29
Ch
r
istoph Ju
n
ghans
Ad
d
Fi
n
dGROMACS
.
cmake to
template's CMakeList
s
.
txt
commit
|
commitdiff
|
tree
2012-06-28
C
hristoph
Junghans
F
i
x
ed adre
s
s ke
r
nel for do
u
ble pr
e
cisio
n
commit
|
commitdiff
|
tree
2012-06-28
Chr
i
stoph
Junghans
Mer
g
e
"F
i
x MPI b
u
ild
for MPI library
w
ithout mpi wrapper
.
.
.
commit
|
commitdiff
|
tree
2012-06-24
Christop
h
J
u
n
g
hans
Merge "Remove MPI define for
FAH"
into release-4-6
commit
|
commitdiff
|
tree
2012-06-22
Christoph J
u
ngha
n
s
Merge "Simple pa
t
ch for
openmm_wrapper
.
cpp" into
r
e
lease-4-
6
commit
|
commitdiff
|
tree
2012-06-19
Christoph Jungha
n
s
Merge
"Quie
t
linke
r
on B
l
ueGene" into
r
elease-4-5-
p
atches
commit
|
commitdiff
|
tree
2012-06-18
Chris
t
op
h
Junghans
Merg
e
"Fix g_l
i
e c
o
u
n
ting last frame twice"
i
n
t
o re
l
ease
.
.
.
commit
|
commitdiff
|
tree
2012-06-15
C
hristoph Jungh
a
ns
Merge "Work around
f
ailure of endi
a
n
ness testing on
.
.
.
commit
|
commitdiff
|
tree
2012-06-08
Chris
t
oph J
u
ngh
a
n
s
Merge "Ad
d
e
d
more suggested
strategies
to err
o
r message
.
.
.
commit
|
commitdiff
|
tree
2012-06-01
Christoph
J
unghans
Merg
e
"Use External BL
A
S/LA
P
AC
K
b
y
default" into relea
s
e-4-6
commit
|
commitdiff
|
tree
2012-06-01
Christoph
J
unghans
M
e
rge "Replace
our
f
ftpack version
w
ith Numpy's version
.
.
.
commit
|
commitdiff
|
tree
2012-05-29
Chr
i
s
toph J
u
nghans
Merge "Revised g_tune_
p
me" int
o
release-4-6
commit
|
commitdiff
|
tree
2012-05-28
Christoph
Ju
n
ghans
Merge "Co
n
t
i
nuing to
fix threading
o
n C
y
gwin" int
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2012-05-25
Chr
i
stoph Junghans
Merge "Fix tha
t
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igaction mask
wa
s
n't ze
r
oed"
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nto
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