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Merge "Merge branch release-4-6 into release-5-0" into release-5-0
2014-03-11
Christoph Junghans
Inst
a
ll e
n
um
s
.
h
commit
|
commitdiff
|
tree
2014-03-01
Chris
t
oph Jungha
n
s
switch ld
_
seed from int to gmx_i
n
t64_t
commit
|
commitdiff
|
tree
2014-02-20
C
h
r
i
sto
p
h Junghans
added gmx_i
s
_
{
single,double}_precisi
o
n
commit
|
commitdiff
|
tree
2014-02-03
Christo
p
h Junghan
s
c
m
ake eats s
l
ashes
commit
|
commitdiff
|
tree
2014-01-28
C
h
ristoph J
u
nghans
cmake:
added FFTW_URL to
a
ll
o
w e
a
sy offline build
commit
|
commitdiff
|
tree
2013-12-29
Chri
s
toph Jung
h
ans
cmake: m
a
ke
G
MX_
B
UIL
D
_OWN_FFTW work withou
t
fortran
.
.
.
commit
|
commitdiff
|
tree
2013-12-20
Chr
i
st
o
ph Jun
g
h
a
ns
re-add Carste
n
& me to the copyrit
e
commit
|
commitdiff
|
tree
2013-10-03
C
hris
t
oph
J
u
n
ghans
F
ix parallel build for
GMX_BUILD_OWN
_
F
F
TW
commit
|
commitdiff
|
tree
2013-09-26
Chri
s
toph Junghans
Drop md5
s
um check f
o
r GMX_BUILD_OWN_FFT
W
commit
|
commitdiff
|
tree
2013-07-30
Christoph
J
unghans
cmak
e
: I
m
prove so
m
e error messag
e
s
commit
|
commitdiff
|
tree
2013-07-06
C
hristo
p
h Junghans
more pkg-con
f
ig fixes
commit
|
commitdiff
|
tree
2013-07-04
Chri
s
toph Junghans
Fixed so
m
e in
c
onsistencies
in
p
kg-config files
commit
|
commitdiff
|
tree
2013-05-15
C
hristoph
J
unghans
Merge "
f
ixed inc
o
rrec
t
scaling of cos
-
a
ccele
r
a
tion
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Christoph Junghans
improve
b
uild with Ope
n
M
M
,
still not 100%
f
ixed
commit
|
commitdiff
|
tree
2013-04-29
Chri
s
toph J
u
n
gh
a
n
s
Merge "Fix
a
nother bug in select
i
on subexpression handling
.
"
commit
|
commitdiff
|
tree
2013-04-29
C
hristoph Junghans
Merge "Fix bug in s
e
lection subexpre
s
s
ion han
d
l
i
ng
.
"
commit
|
commitdiff
|
tree
2013-04-26
Christoph J
u
nghan
s
Merge "v-rescale works with tau-t >= 0
"
into
r
elease-4-6
commit
|
commitdiff
|
tree
2013-04-16
Christoph Ju
n
ghans
Use
git snapshots of
t
he tes
t
s
if
are on git
commit
|
commitdiff
|
tree
2013-03-29
Chr
i
stoph Ju
n
g
hans
Merge "Added install guide section for BL
A
S/LAPACK
.
.
.
commit
|
commitdiff
|
tree
2013-03-19
C
h
ristoph
Junghans
Merge "Ess
e
n
t
i
a
l dynamics
:
fixed le
g
en
d
in ED
.
xvg
.
.
.
commit
|
commitdiff
|
tree
2013-03-02
Chr
i
sto
p
h
J
unghans
Merge "Uncru
s
ti
f
i
e
d code chan
g
es since 4
.
6" into release-4
-
6
commit
|
commitdiff
|
tree
2013-02-26
Christoph
Junghans
Merge "M
e
r
g
e rel
e
ase
-
4-6 into mas
t
er"
commit
|
commitdiff
|
tree
2013-02-20
Christoph Jungh
a
ns
Bump shar
e
d
obj
e
ct version t
o
8
commit
|
commitdiff
|
tree
2013-02-12
Christop
h
J
unghans
Up
d
ated F
i
n
d
G
S
L
.
cmake to ver
s
ion writt
e
n
by
me
.
commit
|
commitdiff
|
tree
2013-02-05
Christ
o
ph Junghans
Merge "Docum
e
n
t
ed wha
t
GM
X
_C
P
U
_A
C
CELERATION rea
l
ly
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Christoph J
u
ng
h
ans
improve setup of mul
t
iple tf t
a
bles
commit
|
commitdiff
|
tree
2013-02-02
Christop
h
Junghans
Fixed
f
lop counting
f
or generic cg/adre
s
s k
e
rnels
commit
|
commitdiff
|
tree
2013-02-02
Christ
o
p
h
Jungha
n
s
cmake: fixed typ
o
i
n
template CMa
k
eL
i
sts
.
txt
commit
|
commitdiff
|
tree
2013-01-25
Christ
o
p
h
J
unghan
s
fixed copyr
i
g
ht of adress kernel
commit
|
commitdiff
|
tree
2013-01-25
Christoph Junghans
Merge "Moved a few comments b
a
ck into
pos
i
tion" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-01-21
Chri
s
toph Junghans
Merge "Set
version info f
o
r 4
.
6
.
x releas
e
series" i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-19
Christo
p
h Jung
h
ans
Re-licence
d
FindGROMACS
.
cmake (was written by me)
commit
|
commitdiff
|
tree
2013-01-17
Christop
h
Junghans
Merge "Added note about make_edi and flooding in ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
Merg
e
"use the compiler ver
s
ion p
r
ovided by CMake
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Chr
i
stoph J
u
nghans
Merg
e
"no
t
e the reason
for a
u
t
o
-disa
b
ling GPU suppo
r
t
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghan
s
clean up fort
r
an na
m
e mangling
commit
|
commitdiff
|
tree
2013-01-16
Chris
t
oph
Junghans
Remove debug
stat
m
ent
commit
|
commitdiff
|
tree
2013-01-15
C
h
ristoph J
u
nghans
Merge "Added fatal error for cons
t
raints + L-BFGS minimiz
e
r
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Christoph J
u
ngha
n
s
Merge
"
disable
O
penMP with
a
ll OS X gcc 4
.
2-based compilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Chri
s
to
p
h
J
u
ngha
n
s
Merge "Remove unused bfunc
.
h
.
" int
o
release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christ
o
ph Junghans
Merge "Clarifi
e
d so
m
e com
m
e
n
ts & warnings abou
t
t
h
read
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Christ
o
ph
Junghan
s
Me
r
ge
"
Man
a
ge Bl
u
eGene/Q configura
t
ion" into
r
eleas
e
-4-6
commit
|
commitdiff
|
tree
2013-01-13
C
hristo
p
h Junghans
Merge "Re-organize BlueGene toolcha
i
n
file
s
"
into rel
e
ase-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph Jungha
n
s
Me
r
ge "Ch
a
nged default
s
for building
s
hared libra
r
ie
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-12
Chri
s
toph Junghans
Merge "Added m
i
ssi
n
g
e
xport" into release-4-6
commit
|
commitdiff
|
tree
2013-01-11
Christoph Ju
n
gh
a
ns
Merge "
c
onsole an
d
log output im
p
r
ovements" into release-4-6
commit
|
commitdiff
|
tree
2013-01-11
Christoph Junghans
Merge
"
Fix C
U
DA
b
e
i
ng q
u
iet and mark all
C
UDA_*
as
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Christo
p
h Junghans
Merge "Remove incorrect assert added by 05f9a740" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Chri
s
toph Jun
g
hans
c
m
ake: remove double-negativ
e
quotes log
i
c
commit
|
commitdiff
|
tree
2013-01-07
Chr
i
stop
h
J
un
g
h
ans
M
e
rg
e
"Make
g
mx_cpuid
.
h
self-standing
.
" i
n
to re
l
ease
-
4-6
commit
|
commitdiff
|
tree
2013-01-03
Ch
r
isto
p
h Junghans
add an opt
i
on to not buil
d
the templ
a
te
commit
|
commitdiff
|
tree
2013-01-03
C
hristoph Jungha
n
s
Add
m
issi
n
g defines
to PKG_CFL
A
GS
commit
|
commitdiff
|
tree
2013-01-03
Chri
s
t
o
p
h Junghans
Me
r
ge "Remove non-funct
i
o
n
al PowerPC invsqrt
.
" into
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
C
h
ris
t
o
p
h Junghans
cmake: add o
p
tion to install libmd as libgmxmd
commit
|
commitdiff
|
tree
2012-12-22
Christoph Jung
h
ans
c
make: ma
r
k FFTW_HA
V
E_{
S
IMD,A
V
X}
a
s advance
d
commit
|
commitdiff
|
tree
2012-12-21
Chri
s
toph Junghans
Merge "Remove non-fun
c
tional compi
l
er ov
e
rrid
e
for
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
C
hristoph Junghans
Merge
"
Fixed AVX256
d
o
ub
l
e
-preci
s
ion kernels
f
o
r
gcc
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Chri
s
toph
J
unghans
cmake: added opt
i
on to d
i
s
able
quotes
commit
|
commitdiff
|
tree
2012-12-18
Chri
s
toph Junghans
M
er
g
e
"
F
ixes redmine issue #1071" int
o
release-4-
6
commit
|
commitdiff
|
tree
2012-12-17
Christ
o
ph
J
unghans
R
e
move the re
s
t of
the fortran
/
p
o
wer6 acceleration
commit
|
commitdiff
|
tree
2012-12-13
C
h
ristoph Junghans
M
e
rge
"
E
x
t
ended ge
n
bo
x
t
o
i
nsert m
o
lecu
l
es at gi
v
en
.
.
.
commit
|
commitdiff
|
tree
2012-12-13
Chr
i
stop
h
Junghans
Always build template program
commit
|
commitdiff
|
tree
2012-12-11
Christoph Junghans
Merge "Fix compil
a
t
i
on
w
i
th PGI" i
n
to relea
s
e
-
4-6
commit
|
commitdiff
|
tree
2012-12-10
Chris
t
oph
Jung
h
ans
Me
r
ge "force C+
+
linking of
the gpu_utils" into
r
eleas
e
-4-6
commit
|
commitdiff
|
tree
2012-12-05
Ch
r
i
s
t
oph Junghans
fixed obsole
t
e gmx
_
fatal in O
p
enMM build
commit
|
commitdiff
|
tree
2012-11-29
C
h
ris
t
oph
J
u
ngha
n
s
Merge "Pr
i
nt
e
r
r
o
r if no
thread support i
s
avail
a
ble
.
.
.
commit
|
commitdiff
|
tree
2012-11-28
Christoph Jung
h
a
n
s
Me
r
ge
"Fix cpack s
r
c igno
r
e rule" into release-4-6
commit
|
commitdiff
|
tree
2012-11-28
Christoph
J
un
g
hans
Add op
t
i
o
n to internally
b
uil
d
FFTW if
s
elected
commit
|
commitdiff
|
tree
2012-11-22
Ch
r
isto
p
h Jungha
n
s
improve FindGROMACS
.
cmake
commit
|
commitdiff
|
tree
2012-11-20
Chris
t
o
ph Junghan
s
Mer
g
e "F
i
x g_m
s
d -mol"
i
nto release-4-6
commit
|
commitdiff
|
tree
2012-11-20
Chris
t
o
p
h Junghans
Merge "Fi
x
es
b
u
g in g_hbond that m
a
kes it produce fatal
.
.
.
commit
|
commitdiff
|
tree
2012-11-16
Chr
i
stoph Jung
h
ans
Remo
v
e rest of
t
he
x
ml support
commit
|
commitdiff
|
tree
2012-11-15
Chr
i
s
t
oph Ju
n
ghans
Merg
e
"Test that
c
omp
i
ling
a
nd linking of AVX wo
r
ks
.
.
.
commit
|
commitdiff
|
tree
2012-11-12
Christoph
Junghans
M
e
r
g
e "O
p
ti
o
n to creat
e
symlinks t
o
g_ana
.
"
commit
|
commitdiff
|
tree
2012-11-12
Christoph Jun
g
h
a
ns
Merge "Al
w
ay
s
u
s
e relative
install
p
aths
.
"
commit
|
commitdiff
|
tree
2012-11-08
Christo
p
h Ju
n
ghans
Merge
"
auto-set nvcc host compiler wit
h
FindMPI det
e
c
tion
.
.
.
commit
|
commitdiff
|
tree
2012-11-08
Christoph Jungha
n
s
Merge "Relocated logic of simple-v
s
-GPU Ewa
l
d ta
b
le
.
.
.
commit
|
commitdiff
|
tree
2012-11-07
Christoph Jungha
n
s
Obey DSO
s
t
andard
commit
|
commitdiff
|
tree
2012-11-03
Christoph
Junghans
Rewo
r
k
ed version of c
m
ake FFTW d
e
tection
commit
|
commitdiff
|
tree
2012-11-01
Christoph Junghans
Actually disable GPU when c
o
mpil
i
n
g in d
o
uble
commit
|
commitdiff
|
tree
2012-10-27
Chri
s
toph Jun
g
h
ans
M
erge "
F
ix
l
arge file
s
upport" into
r
elease-4-5-pat
c
hes
commit
|
commitdiff
|
tree
2012-10-26
Christoph Jung
h
ans
Merg
e
"enable GM
X
_
PREFER_STATIC_LIBS CMake
o
ption on
.
.
.
commit
|
commitdiff
|
tree
2012-10-26
Christoph
Junghans
Merge "fix
f
alse p
o
si
t
i
ve gcc 4
.
7 warni
n
g in li
b
xdrf
.
.
.
commit
|
commitdiff
|
tree
2012-10-10
Christop
h
Junghan
s
fixed hea
d
er for
3
rd party app
s
commit
|
commitdiff
|
tree
2012-10-02
Christoph
Junghans
Merge "M
e
r
ge release-4-6
i
n
t
o
m
a
s
ter"
commit
|
commitdiff
|
tree
2012-09-27
C
h
ristoph Jung
h
a
n
s
Me
r
ge
"Fixed an off-by-one
e
r
ro
r
in atom counting in
.
.
.
commit
|
commitdiff
|
tree
2012-09-25
Christoph Junghans
Merg
e
"Fix
R
E
MD us
e
of gmx_l
a
rg
e
_
i
nt_
t
for #step
s
vari
a
ble
.
.
.
commit
|
commitdiff
|
tree
2012-09-14
Christoph Jungh
a
ns
Merge "fixed recent bug
w
ith grompp
check
for P-R P
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
C
hristoph Jun
g
hans
up
d
ated
r
e
ferences
commit
|
commitdiff
|
tree
2012-09-10
Christoph Jungh
a
n
s
Merge
"
Allo
w
'atomname' and 'atomtype'
i
n
sel
e
cti
o
ns
.
"
commit
|
commitdiff
|
tree
2012-09-07
Christoph Junghans
Merg
e
"Fix VMD plugi
n
s o
n
Window
s
"
i
n
t
o rel
e
ase-
4
-6
commit
|
commitdiff
|
tree
2012-09-07
C
h
ris
t
o
p
h J
u
n
gh
a
ns
Merg
e
"Check t
h
at
g
mx_detectc
p
u runs
cor
r
ectly" into
.
.
.
commit
|
commitdiff
|
tree
2012-09-04
Ch
r
i
s
t
o
ph J
u
n
g
hans
M
erge
"
Fixes
too many b
a
ck
u
p
f
iles for *
.
nroff fi
l
es
.
.
.
commit
|
commitdiff
|
tree
2012-09-04
Chris
t
op
h
Jun
g
hans
Merge "Reorganize CommandLineHelpWriter
i
mplementatio
n
.
"
commit
|
commitdiff
|
tree
2012-09-04
Chri
s
toph Jung
h
a
ns
Me
r
ge "Fix Selection
P
ars
e
rParameter move constructor
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
Christoph Junghans
M
erge "
F
ixing of thi
n
gs associated
w
ith aminoacid
.
rtp
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
C
hristoph Junghans
Merge "Clean
u
p
some varia
b
le na
m
i
ng for
e
igen
s
olving
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
Christoph Junghans
Merg
e
"F
i
x
c
oordinate is zero c
h
eck in gmx
c
heck"
into
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
Chr
i
sto
p
h Jun
g
han
s
Merge
"Explicitly noted
a
n i
s
su
e
wit
h
use of genbox
.
.
.
commit
|
commitdiff
|
tree
2012-08-13
Christoph Jungh
a
ns
fix
A
d
ResS a
n
d long-
r
an
g
e electrostatics w
a
rni
n
g
commit
|
commitdiff
|
tree
next