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Merge branch release-5-1 into release-2016
2017-02-05
Mark Abrah
a
m
Merge branch re
l
e
a
se-5-1 into release
-
201
6
commit
|
commitdiff
|
tree
2017-02-02
Mark A
b
raham
Clarify use of ta
u
-
p and pcoupltype
commit
|
commitdiff
|
tree
2017-01-31
Mar
k
Abr
a
ham
Merge bran
c
h re
l
ease-5-1 into
release-2016
commit
|
commitdiff
|
tree
2017-01-30
Mark Abraha
m
Fix m
u
lti-d
o
main reru
n
s
commit
|
commitdiff
|
tree
2017-01-30
M
a
rk Abraham
Don't
print
i
nv
a
l
id
performan
c
e
d
ata
commit
|
commitdiff
|
tree
2017-01-22
Mark Abraham
F
ix
e
d gmx rmsf -q -
o
q
.
commit
|
commitdiff
|
tree
2017-01-04
Mark Abraham
S
t
op trying to use objdump --
r
eloc
o
n Mac
commit
|
commitdiff
|
tree
2017-01-03
Mark Abraham
Merge branch rele
a
se-5-1 into relea
s
e-20
1
6
commit
|
commitdiff
|
tree
2016-12-20
M
ark Abraham
Corre
c
ted docu
m
ent
a
ti
o
n
a
bout ei
g
e
nvalue handling
commit
|
commitdiff
|
tree
2016-12-20
Mark A
b
r
aham
Impr
o
ve bu
i
ld system for
plug
i
n suppo
r
t
commit
|
commitdiff
|
tree
2016-12-15
Mark Abraham
Handle warn
i
np
correctl
y
in
xpm
2
ps and
membed
commit
|
commitdiff
|
tree
2016-12-14
Mark Abraham
F
i
x misl
e
ading parallelizat
i
on d
o
c
s for gmx w
h
am
commit
|
commitdiff
|
tree
2016-12-09
Mark
A
braha
m
Fix logi
c
of TRR reading
commit
|
commitdiff
|
tree
2016-12-07
Mark
A
braham
Fix memory
h
andling in
gm
x
dump of TNG
files
commit
|
commitdiff
|
tree
2016-12-05
Mark Abraham
Re
m
ove undue n
a
rrowing of
integer in T
N
G r
e
ading
commit
|
commitdiff
|
tree
2016-12-01
Mark Abraham
Fix minor tr
j
con
v
bug
commit
|
commitdiff
|
tree
2016-10-28
Mark Abraham
Bumped ve
r
sio
n
to p
r
e
pare for
next
p
atc
h
rel
e
a
s
e
commit
|
commitdiff
|
tree
2016-10-28
Mark
A
br
a
ham
Versio
n
2016
.
1
commit
|
commitdiff
|
tree
2016-10-21
Mark Abr
a
ham
Update install guide
commit
|
commitdiff
|
tree
2016-10-18
Mark Abraham
F
i
x
SIMD suggestion for VMX
commit
|
commitdiff
|
tree
2016-10-11
Mark Abraham
U
pdate for FFTW 3
.
3
.
5
commit
|
commitdiff
|
tree
2016-10-07
Mar
k
Abraham
Add
s
cript for Jenkins re
g
ressiontest
update job
commit
|
commitdiff
|
tree
2016-10-03
Ma
r
k Abrah
a
m
Merge branch
r
elease-5-1 into release-
2
016
commit
|
commitdiff
|
tree
2016-10-03
Mark Abraham
R
e
p
lace use
o
f deprecat
e
d readdir_r
commit
|
commitdiff
|
tree
2016-09-08
Mark
Ab
r
aham
Merge branch re
l
ease-5-1 into
release-2016
commit
|
commitdiff
|
tree
2016-09-08
Mark
Abraham
Bumped patch n
u
mber to prepar
e
for future
5
.
1
.
5 release
commit
|
commitdiff
|
tree
2016-09-07
Mark Abraham
V
e
rsion 5
.
1
.
4
commit
|
commitdiff
|
tree
2016-09-07
Mark Abraham
Remove
d
HIS1 from op
l
s
a
a a
n
d c
h
armm definitions
commit
|
commitdiff
|
tree
2016-09-07
Mark Abrah
a
m
Fix LYN charges i
n
amber03
commit
|
commitdiff
|
tree
2016-09-07
Mark
A
braham
Fix amber03 HIP cha
r
ges
commit
|
commitdiff
|
tree
2016-09-06
Mark Abraham
Work around gli
b
c
2
.
23 with CUDA
commit
|
commitdiff
|
tree
2016-08-27
Ma
r
k Abraham
Stop
u
s
ing
g
mx_fatal in
gr
o
mpp
commit
|
commitdiff
|
tree
2016-08-15
Mark Abraha
m
Fixes fo
r
BG/Q
platform files and instal
l
guide
commit
|
commitdiff
|
tree
2016-08-12
Mark Abrah
a
m
Bump
n
u
mber to prepare fo
r
fi
r
st
patch release
commit
|
commitdiff
|
tree
2016-08-04
Ma
r
k Abraham
Ver
s
ion
2
0
1
6
commit
|
commitdiff
|
tree
2016-07-29
Mar
k
Abraham
I
m
p
rove h
a
ndlin
g
of gmock and
g
cc6
commit
|
commitdiff
|
tree
2016-07-29
Mark
Abr
a
h
am
Merge
b
ran
c
h release-
5
-1 into release
-
2016
commit
|
commitdiff
|
tree
2016-07-28
Mar
k
Abraham
Add toolchain flags
f
or SSE2 compilation
commit
|
commitdiff
|
tree
2016-07-21
Ma
r
k Ab
r
aham
Bumped patch numb
e
r to
p
r
epare for futu
r
e 5
.
1
.
4 releas
e
commit
|
commitdiff
|
tree
2016-07-14
M
a
rk Abraham
Fix issues
w
ith
using int for number of
s
teps
commit
|
commitdiff
|
tree
2016-07-13
Mark Abraham
Version 5
.
1
.
3
commit
|
commitdiff
|
tree
2016-07-12
Mark Abr
a
ham
Fix trr mag
i
c
n
umber read
i
n
g
commit
|
commitdiff
|
tree
2016-07-11
M
ark Abraham
F
ix gmx mdrun -membed -n
t
mpi
-
1
commit
|
commitdiff
|
tree
2016-07-11
M
ark
Abra
h
am
Fix regr
e
s
siontest
d
ownload md5
s
um
commit
|
commitdiff
|
tree
2016-07-09
Mark Abraham
First 2016 release
cand
i
date
commit
|
commitdiff
|
tree
2016-07-08
Ma
r
k
Abr
a
h
am
Merge branch rel
e
ase-5
-
1 into release-2016
commit
|
commitdiff
|
tree
2016-07-08
Mar
k
A
b
raham
Simplify SIMD compiler flag construc
t
ion
commit
|
commitdiff
|
tree
2016-07-07
M
a
rk Abraham
Move cons
i
stency check for number of threads
commit
|
commitdiff
|
tree
2016-07-07
M
a
rk Abra
h
am
Fix build
if lib
c
uda is found but nvcc is n
o
t
commit
|
commitdiff
|
tree
2016-07-04
M
ark A
b
raham
Fi
x
es for
P
ower7 big-endian
commit
|
commitdiff
|
tree
2016-07-01
M
ark Abr
a
h
a
m
Fi
x
us
e
of _P
O
SIX_THRE
A
D*
commit
|
commitdiff
|
tree
2016-06-30
M
a
rk Abraham
Merge branch rel
e
ase
-
5-1 into release
-
2016
commit
|
commitdiff
|
tree
2016-06-29
Mark
A
b
r
aham
R
efacto
r
s
ysc
o
nf ch
e
cki
n
g
commit
|
commitdiff
|
tree
2016-06-29
Mark Abra
h
am
Work aro
u
nd glibc 2
.
2
3 with CUDA
commit
|
commitdiff
|
tree
2016-06-28
Mark Abraham
Update to include a gcc 6
.
1 configuration
commit
|
commitdiff
|
tree
2016-06-28
Mark
A
braham
F
i
x
S
IMD confi
g
ura
t
i
o
n man
a
gement
commit
|
commitdiff
|
tree
2016-06-27
Mark
A
braha
m
Remo
v
ed
u
nnec
e
ssar
y
i
nter
-
s
i
mulation signalling
commit
|
commitdiff
|
tree
2016-06-27
Mar
k
Abra
h
am
M
e
rge branch release-5-1 into release-20
1
6
commit
|
commitdiff
|
tree
2016-06-23
Mark
A
braham
Allow
u
se of exter
n
al l
m
fit
p
a
c
kage
commit
|
commitdiff
|
tree
2016-06-23
Mark Abraham
Prevent use of mdrun -maxh -multi
commit
|
commitdiff
|
tree
2016-06-22
Ma
r
k Abr
a
ham
Fi
x
co
n
fig
u
ratio
n
-ti
m
e cpuinfo
co
d
e
commit
|
commitdiff
|
tree
2016-06-22
Mark Abra
h
am
Me
r
ge br
a
nch
release-5-1 into
releas
e
-2016
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
Adjust and
d
ocume
n
t
C
++11 compiler
t
est
s
commit
|
commitdiff
|
tree
2016-06-20
Mark
A
br
a
ham
Update
p
re-submit matrix contents
commit
|
commitdiff
|
tree
2016-06-19
Mark
A
brah
a
m
I
mprove docs for linking stdlibc++
n
eeded by icc
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Merge branc
h
rele
a
se-5
-
1 in
t
o release-2016
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Fix
m
ulti-si
m
+
D
D +
simple
d
istance restraints
commit
|
commitdiff
|
tree
2016-06-10
Ma
r
k
A
braham
Find pyth
o
n
f
or docs build quietl
y
commit
|
commitdiff
|
tree
2016-06-08
M
a
rk Abraham
Merg
e
bra
n
ch rele
a
se-5-1 into release-201
6
commit
|
commitdiff
|
tree
2016-06-07
Ma
r
k Ab
r
aham
Re-add support for linking
against
e
x
ternal
TinyX
M
L-2
commit
|
commitdiff
|
tree
2016-06-07
Mark Abraha
m
U
p
dates to documentati
o
n
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Fix com
p
ati
b
i
lity
w
ith older CMake
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Make more
C
M
a
ke vari
a
bles advanced
commit
|
commitdiff
|
tree
2016-06-02
Mark Abr
a
ham
Ignore stderr whe
n
d
etecting SIMD and build in
f
o
commit
|
commitdiff
|
tree
2016-05-31
M
a
r
k Abr
a
ham
Fix
r
efe
r
ence to
v
md
i
o
.
c
t
o
b
e vmdio
.
c
pp
commit
|
commitdiff
|
tree
2016-05-31
M
ark
Abraham
Second 20
1
6 beta rel
e
ase
commit
|
commitdiff
|
tree
2016-05-29
Mark Ab
r
aha
m
S
i
mplified and updated OpenCL c
o
m
pilation
commit
|
commitdiff
|
tree
2016-05-27
Ma
r
k
Ab
r
aham
Fi
x
r
e
a
ding
of bonded tables
commit
|
commitdiff
|
tree
2016-05-26
Ma
r
k Abraham
New quot
e
commit
|
commitdiff
|
tree
2016-05-12
Mark Ab
r
aham
Merge branch re
l
e
ase-5-1 into release-2016
commit
|
commitdiff
|
tree
2016-05-12
Ma
r
k Abraham
GROMACS
2
016
beta1 release
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Bump clan
g
st
a
tic analyzer to ver
s
i
on
3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mar
k
Abraham
Minor update to sphinx dependency
commit
|
commitdiff
|
tree
2016-05-10
Mar
k
Abraham
F
acilitate linking with libcxx
commit
|
commitdiff
|
tree
2016-05-08
Mark
A
br
a
ham
Fi
x
es for clan
g
3
.
7
on PowerPC
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraha
m
Fix con
s
tants, units and conve
r
si
o
n
factors
commit
|
commitdiff
|
tree
2016-04-27
M
a
r
k
A
braham
Mer
g
e branch release-5
-
1
commit
|
commitdiff
|
tree
2016-04-19
Mark Abr
a
ham
Replace libxml2 with
t
i
n
y
xml2 for use in test code
commit
|
commitdiff
|
tree
2016-04-19
M
ark Abraham
F
ix parse
_
digits_from_string
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Fix mdp label generatio
n
commit
|
commitdiff
|
tree
2016-04-18
Mark
A
br
a
ha
m
Redu
c
e compilation
co
u
pling
of SIMD module
commit
|
commitdiff
|
tree
2016-04-14
Mark Abraham
Merge bra
n
ch re
l
ease-5-1
commit
|
commitdiff
|
tree
2016-04-01
Mark A
b
raham
Revert t
o
tre
a
ting -1 as "generate a seed" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Mark Abraham
Add test and improved
docs f
o
r custom chec
k
Se
q
uence
commit
|
commitdiff
|
tree
2016-03-30
Mark Abraham
Cl
e
an up vsite code
commit
|
commitdiff
|
tree
2016-03-19
Ma
r
k Abra
h
am
Add more
c
onst correctne
s
s
commit
|
commitdiff
|
tree
2016-03-19
Mark
Abraham
Fix warning
f
r
om GCC 6
commit
|
commitdiff
|
tree
2016-03-19
Mar
k
Abraham
Improve
d
some mdrun int
e
gration tests
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
Warn about Op
e
nMP
I
1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Mark Ab
r
aham
F
i
x typo in F
o
urie
r
dihedral e
q
u
at
i
on
commit
|
commitdiff
|
tree
next