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Merge branch release-5-0 into release-5-1
2016-02-08
M
a
rk Abraham
Merge b
r
a
nch rel
e
ase-5-0 into release
-
5-1
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Bum
p
ed patch number t
o
p
r
epare fo
r
future 5
.
1
.
3 release
commit
|
commitdiff
|
tree
2016-02-03
Mark Ab
r
a
ha
m
Version
5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mark Abra
h
a
m
Fix grompp n
o
t warn
i
ng w
h
en
.
m
dp values have w
r
ong
.
.
.
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Merge
r
elease-5-0
into release
-
5-
1
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Fix dEk
i
n
/
dl handli
n
g w
i
th multip
l
e rank
s
commit
|
commitdiff
|
tree
2016-01-28
Mark
A
b
raham
Add OpenCL s
o
urce fil
e
types t
o
copyright checker
commit
|
commitdiff
|
tree
2016-01-27
M
a
rk Abraham
Ad
d
sugg
e
stions for
updatin
g
binutils
commit
|
commitdiff
|
tree
2016-01-26
Ma
r
k Abraham
Fix default fo
r
GMX
_
USE_NVML
commit
|
commitdiff
|
tree
2016-01-24
Mark Abra
h
am
Fix dup
l
ic
a
te LaTeX equation label
commit
|
commitdiff
|
tree
2016-01-24
Mark Ab
r
aham
Update references to HT
M
L and o
n
line documenta
t
ion
commit
|
commitdiff
|
tree
2016-01-13
Mar
k
Abrah
a
m
Allowed NVML support to be
t
oggled
commit
|
commitdiff
|
tree
2016-01-12
Mark
A
braham
Merge
b
ranch rel
e
ase-5-0 int
o
release-5-1
commit
|
commitdiff
|
tree
2016-01-07
M
a
rk
A
b
r
aham
Avoid
more C++
b
indings f
o
r MPI
commit
|
commitdiff
|
tree
2016-01-07
Mark Abrah
a
m
Document how potential-switch
w
orks
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraha
m
Stop
u
sing
U
NDEFINED as name of a symbo
l
commit
|
commitdiff
|
tree
2016-01-07
M
ark A
b
raham
Backport md-vv fixes
commit
|
commitdiff
|
tree
2015-12-27
Mark Abraha
m
Fix some OpenCL issues
commit
|
commitdiff
|
tree
2015-12-12
Mar
k
A
b
r
aham
R
equire Nose-Hoover with MTTK
commit
|
commitdiff
|
tree
2015-12-11
Mar
k
A
b
r
a
ham
Stop global com
m
u
n
ication depending on integrator
commit
|
commitdiff
|
tree
2015-12-08
Ma
r
k Abra
h
am
Merge bran
c
h 'release-5-0' in
t
o release-5-1
commit
|
commitdiff
|
tree
2015-12-08
M
a
rk
Abraham
Fix Trotter integration
commit
|
commitdiff
|
tree
2015-11-24
Mark Abraham
Fix error in m
u
lti-sim
com
m
u
nication
commit
|
commitdiff
|
tree
2015-11-14
Mark Abra
h
am
F
i
x
wall
t
ime
mea
s
uremen
t
with bgclang
commit
|
commitdiff
|
tree
2015-11-11
M
ark Abrah
a
m
M
e
rge rel
e
ase-5-0 into re
l
e
a
se-5-
1
commit
|
commitdiff
|
tree
2015-11-10
Mark Abraham
Bump pa
t
ch versi
o
n to prepare for 5
.
1
.
2
commit
|
commitdiff
|
tree
2015-11-04
Mark Abr
a
h
am
Version 5
.
1
.
1
commit
|
commitdiff
|
tree
2015-10-28
Mark Abraham
Suppress warnings
w
h
en we have OpenCL 2
.
0 suppor
t
commit
|
commitdiff
|
tree
2015-10-19
Mark Abraham
Fix
c
ycle subcounters
commit
|
commitdiff
|
tree
2015-10-14
Mark Abraham
Merge
re
l
ea
s
e-5-0
i
n
to
r
elea
s
e-5-1
commit
|
commitdiff
|
tree
2015-10-14
Mar
k
Abraham
Versi
o
n bumps a
f
ter
r
elease
commit
|
commitdiff
|
tree
2015-10-14
M
ar
k
Abraham
Version 5
.
0
.
7
commit
|
commitdiff
|
tree
2015-10-13
Mark
A
braham
M
erge
b
ranch releas
e
-4-
6
into relea
s
e
-5-0
commit
|
commitdiff
|
tree
2015-10-07
Ma
r
k A
b
r
a
ham
Fixed
F
FTW
detection status message lo
c
ation
commit
|
commitdiff
|
tree
2015-10-05
Mark Abraha
m
Merge releas
e
-
5
-0
into release
-
5-1
commit
|
commitdiff
|
tree
2015-10-03
Mark Abraham
Fix
F
indFFTW behaviou
r
commit
|
commitdiff
|
tree
2015-10-03
Mark Abraham
Fix mdrun -nb
a
uto -r
e
r
u
n
with GPU
a
nd energy groups
commit
|
commitdiff
|
tree
2015-09-26
Mark Abraha
m
F
i
x react
i
on-field warning message
commit
|
commitdiff
|
tree
2015-09-06
Mark Abraham
Add GROMACS 5
paper
to pa
p
er lists
commit
|
commitdiff
|
tree
2015-08-19
Mark
Abraham
Harden
F
indSphin
x
.
cmake
commit
|
commitdiff
|
tree
2015-08-14
Mark Abrah
a
m
Bump pa
t
ch version
t
o prepare for
5
.
1
.
1
commit
|
commitdiff
|
tree
2015-08-14
Ma
r
k
Abr
a
ham
Ve
r
sion 5
.
1
commit
|
commitdiff
|
tree
2015-08-13
M
ark
Abraham
M
a
ke it eas
i
e
r
to find selectio
n
help
commit
|
commitdiff
|
tree
2015-08-13
M
a
rk Abrah
a
m
Make
i
t e
a
sier to f
i
n
d
sele
c
tion
h
elp
commit
|
commitdiff
|
tree
2015-08-13
Mark
Abraham
R
e-en
a
ble
multi-
G
P
U s
u
pp
o
rt in OpenCL
for thread MPI
commit
|
commitdiff
|
tree
2015-08-13
Mar
k
Abrah
a
m
Do
c
u
m
e
n
t
a
tion fixes
commit
|
commitdiff
|
tree
2015-08-13
Mark
A
b
raham
Avoid FP e
x
ce
p
t
ion with
em
p
t
y
.
mdp file
commit
|
commitdiff
|
tree
2015-08-12
Mark Abraham
Add documen
t
a
t
io
n
for energygrps
with GPUs
commit
|
commitdiff
|
tree
2015-08-12
Mar
k
Abr
a
h
a
m
A
d
d to author lists
commit
|
commitdiff
|
tree
2015-08-11
M
a
rk Abr
a
ham
Abort if PME tuning is ac
t
i
v
e and count
e
rs res
e
t
commit
|
commitdiff
|
tree
2015-08-10
Mark Abraham
Require tune_pme
t
o
t
a
ke
-mdrun
p
arameter
commit
|
commitdiff
|
tree
2015-08-08
Mark A
b
raham
Merge branch
r
el
e
ase-5-
0
in
t
o r
e
le
a
se-
5
-1
commit
|
commitdiff
|
tree
2015-08-08
Mar
k
A
b
raham
F
ix do
c
s of ftypes o
f
dihe
d
r
als
commit
|
commitdiff
|
tree
2015-08-06
Mark Abraham
Fix
F
indNVML
.
cmake
commit
|
commitdiff
|
tree
2015-08-06
Mark Abraham
Fix thre
a
d-af
f
inity checking
commit
|
commitdiff
|
tree
2015-08-05
M
a
rk Abr
a
ham
F
ix em da
s
h in new ref
e
re
n
ce
commit
|
commitdiff
|
tree
2015-08-04
Mark
A
braham
Merge rele
a
se-5-0 into rel
e
ase-5-1
commit
|
commitdiff
|
tree
2015-08-03
M
a
rk Abrah
a
m
Fix use
of w
r
ongly-
n
amed GCC mi
n
o
r
-version variable
commit
|
commitdiff
|
tree
2015-08-03
Ma
r
k
A
braham
Fix possibl
e
linking of libxml2
t
o
zlib
commit
|
commitdiff
|
tree
2015-07-26
Mark Abra
h
am
Merge branch
r
elease-5-0 in
t
o release
-
5-
1
commit
|
commitdiff
|
tree
2015-07-26
Mark
A
braham
Stop
m
drun printing
p
otentiall
y
undefined value
commit
|
commitdiff
|
tree
2015-07-26
Ma
r
k
Abraham
V
e
rsion bumps after new
release
commit
|
commitdiff
|
tree
2015-07-24
Mark Abraham
Version
5
.
0
.
6
commit
|
commitdiff
|
tree
2015-07-19
Mark Abraham
Update advice about grompp -t
commit
|
commitdiff
|
tree
2015-07-08
Mark Abraham
Give bT
y
peP
e
rturbed a va
l
id ini
t
i
al value
commit
|
commitdiff
|
tree
2015-07-08
Mark
A
braham
F
ix gro
m
pp
.
edr IO estimate for
free
-
e
n
ergy
c
a
l
cs
commit
|
commitdiff
|
tree
2015-07-06
Mark Abraham
First 5
.
1
r
el
e
ase cand
i
da
t
e
commit
|
commitdiff
|
tree
2015-07-03
Mark Abraham
Fix ThreadMPI GPU assump
t
io
n
s
commit
|
commitdiff
|
tree
2015-06-30
Mark Ab
r
aham
D
ocument
how
to
a
dd and use NVM
L
s
u
p
p
ort
commit
|
commitdiff
|
tree
2015-06-30
Mark Abraham
Avoid
G
PU da
t
a
r
a
ce
also
w
ith OpenC
L
commit
|
commitdiff
|
tree
2015-06-30
Mark Abra
h
am
Add support for flushing WDDM qu
e
ue
commit
|
commitdiff
|
tree
2015-06-29
Mark Abraham
Merge "Merge branch rele
a
s
e
-
5
-
0"
commit
|
commitdiff
|
tree
2015-06-29
Mark Abraham
Merge
b
ranch
release-5-0
commit
|
commitdiff
|
tree
2015-06-29
Mark
A
bra
h
a
m
D
ocumented bu
i
ld types i
n
developer guide
commit
|
commitdiff
|
tree
2015-06-29
Mark Ab
r
aha
m
Me
r
ge
rel
e
ase-4-6 in
t
o
r
e
lease
-
5-0
commit
|
commitdiff
|
tree
2015-06-29
Mark Abr
a
ham
Ad
d
MSAN buil
d
typ
e
commit
|
commitdiff
|
tree
2015-06-29
Ma
r
k A
b
raham
Fix all
u
s
e
of nbnxn
_
s
imd
.
h
commit
|
commitdiff
|
tree
2015-06-27
Mar
k
Abraha
m
Merge rele
a
se-5-
0
into m
a
ster
commit
|
commitdiff
|
tree
2015-06-26
M
a
rk Ab
r
aham
Merg
e
re
l
ease-4-
6
into
release-5-0
commit
|
commitdiff
|
tree
2015-06-26
M
ark Abraham
F
ix mdrun -c
o
n
fout sometimes affecting final
.
edr fra
m
e
commit
|
commitdiff
|
tree
2015-06-25
Mark Abraham
M
e
rge "Merge release-5-0 into maste
r
"
commit
|
commitdiff
|
tree
2015-06-25
Mark Abraham
M
e
rge relea
s
e-5-0 into ma
s
ter
commit
|
commitdiff
|
tree
2015-06-24
Mark Abraha
m
Merge rele
a
se-4-6 into release-5-
0
commit
|
commitdiff
|
tree
2015-06-18
Mark Abraham
Fix typo in
G
MX_BUILD_OWN_FFTW me
s
sage
commit
|
commitdiff
|
tree
2015-06-16
Mark Abraham
Stop people
installing into the buil
d
t
r
e
e
commit
|
commitdiff
|
tree
2015-06-16
Mark
A
braham
M
ove code for m
a
n
a
ging mdrun -cpi and -a
p
pend
commit
|
commitdiff
|
tree
2015-06-16
M
ark Abraham
Fix p
a
i
rs_nb not recognize
d
as part
o
f
m
o
l
eculetype
commit
|
commitdiff
|
tree
2015-06-16
Mark
A
braham
Add unit tests for ArrayRe
f
commit
|
commitdiff
|
tree
2015-06-12
Mark Abraham
Fix
commandline test d
a
ta
commit
|
commitdiff
|
tree
2015-06-11
Ma
r
k
Abraham
M
erg
e
"
M
erge
b
r
a
nch release-4-6 int
o
r
eleas
e
-5-0" into
.
.
.
commit
|
commitdiff
|
tree
2015-06-11
Mark Abraha
m
Han
d
l
e
timi
n
g better in Je
n
k
i
ns
commit
|
commitdiff
|
tree
2015-06-11
Mark Ab
r
aham
Cl
e
an up vsite
i
nteraction c
l
e
a
n-up code
commit
|
commitdiff
|
tree
2015-06-09
Mark Abrah
a
m
Document limit
a
tions of trjconv -dump
commit
|
commitdiff
|
tree
2015-06-09
Mark
Abraham
Me
r
g
e branch
release-4-6 in
t
o release-5-0
commit
|
commitdiff
|
tree
2015-06-05
Mark Abraham
Remove gmx_simd_check_and_rese
t
_overflow
commit
|
commitdiff
|
tree
2015-06-04
M
a
rk Abr
a
h
am
Fix namin
g
from
"
Gromac
s
" to "GROMAC
S
"
commit
|
commitdiff
|
tree
2015-05-27
Mark Abraham
Fix war
n
ing
s
from GCC 5
commit
|
commitdiff
|
tree
2015-05-26
Mark
A
braham
Avoid possible floating-poi
n
t exception
commit
|
commitdiff
|
tree
2015-05-26
M
a
rk Abra
h
am
C
o
nvert ewald
m
odule to C++
commit
|
commitdiff
|
tree
2015-05-26
M
ark Abra
h
am
Fi
x
use
of hard-code
d
tempor
a
ry
f
ilen
a
m
e
commit
|
commitdiff
|
tree
next