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Merge branch release-5-1 into release-2016
2016-06-30
Ma
r
k Ab
r
a
h
am
M
erge branch release-5
-
1 into
r
e
le
a
s
e
-2016
commit
|
commitdiff
|
tree
2016-06-29
Mark A
b
rah
a
m
Refacto
r
s
ysc
o
nf chec
k
ing
commit
|
commitdiff
|
tree
2016-06-29
Mark Abraham
Work around glibc 2
.
2
3
w
ith CUDA
commit
|
commitdiff
|
tree
2016-06-28
M
ark Abraham
U
pdate to in
c
lude a gcc 6
.
1 con
f
iguration
commit
|
commitdiff
|
tree
2016-06-28
M
a
rk Abraham
Fix SIMD configuration
m
a
nagem
e
n
t
commit
|
commitdiff
|
tree
2016-06-27
Mark
A
braham
Removed unnecessary i
n
t
e
r-simulation signalling
commit
|
commitdiff
|
tree
2016-06-27
Mark
Ab
r
aham
Me
r
ge branch release-5-1 into relea
s
e
-
2016
commit
|
commitdiff
|
tree
2016-06-23
Mark
Abraham
Allow use o
f
externa
l
lmfit
p
ackage
commit
|
commitdiff
|
tree
2016-06-23
Mark
A
braham
P
revent us
e
of mdrun -maxh -mu
l
ti
commit
|
commitdiff
|
tree
2016-06-22
Mark
A
braham
Fix configuration-time
cpuinfo code
commit
|
commitdiff
|
tree
2016-06-22
Mark
A
braham
Merge branch re
l
ease-5-1
i
nto release-
2
016
commit
|
commitdiff
|
tree
2016-06-22
M
a
r
k Abraha
m
A
d
just and do
c
um
e
nt C++11 compiler
tes
t
s
commit
|
commitdiff
|
tree
2016-06-20
Mark Abraha
m
Update
pre-su
b
mit matrix
contents
commit
|
commitdiff
|
tree
2016-06-19
Ma
r
k Ab
r
aham
Improve do
c
s for linking stdlibc++ needed by
icc
commit
|
commitdiff
|
tree
2016-06-17
Mark Abra
h
am
Merge
branch r
e
lease-5-1 into releas
e
-
2
016
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Fix mul
t
i-sim
+ DD
+ sim
p
le dis
t
ance re
s
traints
commit
|
commitdiff
|
tree
2016-06-10
Mark Abraha
m
Find python f
o
r docs build qui
e
tly
commit
|
commitdiff
|
tree
2016-06-08
Mark
Abrah
a
m
Merge br
a
nch release-5
-
1 into release-2
0
16
commit
|
commitdiff
|
tree
2016-06-07
Mark
A
braham
Re
-
add
s
up
p
ort f
o
r linking again
s
t ex
t
erna
l
T
inyXM
L
-2
commit
|
commitdiff
|
tree
2016-06-07
Mark Abra
h
a
m
Updat
e
s to document
a
t
ion
commit
|
commitdiff
|
tree
2016-06-02
Mar
k
Abraham
F
i
x co
m
pa
t
ibility with older CMake
commit
|
commitdiff
|
tree
2016-06-02
M
a
rk Ab
r
aha
m
Make more CM
a
ke variable
s
advanced
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
I
gnore s
t
d
e
r
r
w
h
en de
t
ec
t
ing
S
IMD and build info
commit
|
commitdiff
|
tree
2016-05-31
Mark Ab
r
aham
F
i
x
r
eference
t
o vmdio
.
c to
be
v
mdio
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mar
k
Abraham
Second 20
1
6
b
eta
re
l
e
a
se
commit
|
commitdiff
|
tree
2016-05-29
Mark Abr
a
ham
Si
m
plified and updated O
p
enCL com
p
ilation
commit
|
commitdiff
|
tree
2016-05-27
M
a
rk Abraham
Fix re
a
ding of
b
onded ta
b
les
commit
|
commitdiff
|
tree
2016-05-26
M
ark Abraham
New
q
uote
commit
|
commitdiff
|
tree
2016-05-12
Mark Ab
r
aham
Merge
b
ranch
re
l
ease
-
5
-1 into rel
e
a
se
-
201
6
commit
|
commitdiff
|
tree
2016-05-12
Ma
r
k Abr
a
ham
GROMACS 2016 beta1 release
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Bump clang static an
a
l
yzer to version
3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
M
inor update to sphinx d
e
pendency
commit
|
commitdiff
|
tree
2016-05-10
M
a
r
k
Abraham
Facilitate linking
w
it
h
libcxx
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
F
i
x
e
s
f
or clang 3
.
7 on Po
w
erPC
commit
|
commitdiff
|
tree
2016-05-08
Ma
r
k Ab
r
aham
Fix constants,
u
nits and conversion fa
c
tors
commit
|
commitdiff
|
tree
2016-04-27
M
a
rk Abraham
Merge branch release-5-1
commit
|
commitdiff
|
tree
2016-04-19
Mark Abrah
a
m
Replace
lib
x
m
l2
w
ith
t
inyxm
l
2 for us
e
in test code
commit
|
commitdiff
|
tree
2016-04-19
Mark Ab
r
aham
Fix parse_dig
i
ts_from_string
commit
|
commitdiff
|
tree
2016-04-19
Ma
r
k Abra
h
a
m
Fi
x
m
dp label generation
commit
|
commitdiff
|
tree
2016-04-18
Mark Abraham
Reduc
e
compilation coupli
n
g
o
f
S
IMD module
commit
|
commitdiff
|
tree
2016-04-14
Mark Abr
a
ham
Me
r
ge branch
r
elease-5-1
commit
|
commitdiff
|
tree
2016-04-01
Mark Abra
h
am
Revert to
tre
a
ting -1 as "generate a seed" in
.
m
d
p
commit
|
commitdiff
|
tree
2016-03-31
Mark Abraham
A
d
d
t
est
a
n
d
im
p
roved
d
ocs for
c
ustom checkSequence
commit
|
commitdiff
|
tree
2016-03-30
Mark Abraham
C
lean up vsite cod
e
commit
|
commitdiff
|
tree
2016-03-19
M
ark Abraham
Add
more
c
o
ns
t
c
orrectness
commit
|
commitdiff
|
tree
2016-03-19
M
a
rk Ab
r
aham
Fix
war
n
in
g
f
r
om GCC
6
commit
|
commitdiff
|
tree
2016-03-19
Ma
r
k
A
braham
Improved
some mdr
u
n integration t
e
sts
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
Warn about OpenMPI 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Mark Abrah
a
m
Fi
x
t
ypo in Fourier dihedral e
q
ua
t
ion
commit
|
commitdiff
|
tree
2016-03-15
Mark Abrah
a
m
M
erge branch
r
e
lease-
5
-0 i
n
to release-5-
1
commit
|
commitdiff
|
tree
2016-03-12
Mark Abraham
Update
u
se of isnan in linearalgebra
commit
|
commitdiff
|
tree
2016-03-12
Mark Abraham
F
i
n
d
hw
l
oc qu
i
etly if it's already been fo
u
nd
commit
|
commitdiff
|
tree
2016-03-11
Mark Abraham
Add infrastruc
t
ure fo
r
t
ests to compa
r
e mdruns
commit
|
commitdiff
|
tree
2016-03-11
M
a
rk Ab
r
aham
Merge
branch release-5-0 into rel
e
a
se-5-1
commit
|
commitdiff
|
tree
2016-03-10
M
a
r
k Abrah
a
m
Req
u
ire
2015 version for
MSVC
commit
|
commitdiff
|
tree
2016-03-05
Mark A
b
r
aham
Add SET
T
L
E
unit te
s
ts
commit
|
commitdiff
|
tree
2016-02-26
Mar
k
Abrah
a
m
Sep
a
rated test of CDATA end
tag handl
i
n
g
from others
commit
|
commitdiff
|
tree
2016-02-23
Ma
r
k Abraham
Rep
l
ac
e
cppcheck su
p
p
r
ession in checkpoint
c
ode
commit
|
commitdiff
|
tree
2016-02-22
Mar
k
Abrah
a
m
Move in
i
t
of
specialized
d
ynamical algori
t
hms to do_md
commit
|
commitdiff
|
tree
2016-02-21
Mark Abraham
Separate t
a
ble
c
ons
t
ruction
commit
|
commitdiff
|
tree
2016-02-19
Mark Abraham
Merge br
a
nch release-5-1
commit
|
commitdiff
|
tree
2016-02-19
Mark Ab
r
aham
Make both ftp
a
n
d http li
n
ks for sour
c
e download
commit
|
commitdiff
|
tree
2016-02-18
Mark Abrah
a
m
Updated
r
efe
r
ence manual text ab
o
ut PME tuning
commit
|
commitdiff
|
tree
2016-02-16
Mark
A
braham
Mer
g
e branch rel
e
ase-5-0 in
t
o
release-5-
1
commit
|
commitdiff
|
tree
2016-02-14
M
a
r
k Abraham
Re-gene
r
ated
e
ps f
o
r figure 4
.
8
commit
|
commitdiff
|
tree
2016-02-10
Mark
A
brah
a
m
R
e-remove *_stoc
h
d_state
funct
i
on
dec
l
arations
commit
|
commitdiff
|
tree
2016-02-10
Mark A
b
raham
Impr
o
v
ed
u
pdate_c
o
ords
h
andlin
g
of xpr
i
me
commit
|
commitdiff
|
tree
2016-02-10
Mark Abraham
Fix i
s
sues to u
p
date cppcheck sup
p
or
t
to 1
.
72
commit
|
commitdiff
|
tree
2016-02-08
Mark A
b
raham
Merge branc
h
relea
s
e-
5
-
0 into release-5-1
commit
|
commitdiff
|
tree
2016-02-06
Mark A
b
raham
Merge branch releas
e
-5-1
commit
|
commitdiff
|
tree
2016-02-03
M
a
rk A
b
raham
Bumped patch number to prepare for future 5
.
1
.
3 r
e
le
a
se
commit
|
commitdiff
|
tree
2016-02-03
Mark A
b
raha
m
Version
5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mark Abrah
a
m
Fix gr
o
m
p
p not warning when
.
mdp values have wrong
.
.
.
commit
|
commitdiff
|
tree
2016-02-03
Mar
k
A
br
a
ham
Merge
relea
s
e
-
5-0
i
n
t
o
release-5-1
commit
|
commitdiff
|
tree
2016-02-03
Ma
r
k Abraham
Fix dEkin/d
l
ha
n
dling
w
ith multiple ranks
commit
|
commitdiff
|
tree
2016-01-28
Mark
A
braham
Merge
branch relea
s
e-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mar
k
Ab
r
aham
Fix u
s
e
o
f __APPLE__ in OpenCL code
commit
|
commitdiff
|
tree
2016-01-28
Ma
r
k Abraha
m
Add OpenCL source file type
s
t
o co
p
yrigh
t
checker
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
A
v
o
id FP exception
commit
|
commitdiff
|
tree
2016-01-27
Mark Abraham
Me
r
ge branch r
e
le
a
se-5-1
commit
|
commitdiff
|
tree
2016-01-27
Mark
A
br
a
ham
Remove bNotLastFrame
commit
|
commitdiff
|
tree
2016-01-27
Mark Abr
a
ham
Add suggestions for upda
t
ing binutils
commit
|
commitdiff
|
tree
2016-01-26
Mark Abraham
Fix default f
o
r GM
X
_US
E
_N
V
ML
commit
|
commitdiff
|
tree
2016-01-25
Mark Abraham
Merge branch
release-5-1
commit
|
commitdiff
|
tree
2016-01-24
Mark Abrah
a
m
F
ix dup
l
ic
a
t
e
LaTe
X
equatio
n
label
commit
|
commitdiff
|
tree
2016-01-24
Mark
A
bra
h
am
Update references to
HTML and
online do
c
ume
n
t
ation
commit
|
commitdiff
|
tree
2016-01-14
Mark Abra
h
am
Per
m
it customized tes
t
i
n
g of grompp a
n
d mdrun
commit
|
commitdiff
|
tree
2016-01-13
Ma
r
k Abraham
Allow
e
d NVML support to be t
o
g
g
led
commit
|
commitdiff
|
tree
2016-01-12
Ma
r
k Abraham
M
erge branch
r
elease-5-0
int
o
release
-
5
-
1
commit
|
commitdiff
|
tree
2016-01-11
Mar
k
A
brah
a
m
I
m
p
roved update_c
o
ords
commit
|
commitdiff
|
tree
2016-01-08
Mark Abraham
Improve tpr header
v
ersion
h
andling
commit
|
commitdiff
|
tree
2016-01-08
Mar
k
Abraham
Merge bra
n
c
h
r
e
lease-5-1
commit
|
commitdiff
|
tree
2016-01-07
M
ar
k
Abraham
Fi
x
some
mdrun he
a
der dependencies
commit
|
commitdiff
|
tree
2016-01-07
M
ark Ab
r
aham
Avoid
more C+
+
bindings for MPI
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Document
h
ow potential-
s
w
i
tch works
commit
|
commitdiff
|
tree
2016-01-07
M
ar
k
A
braha
m
Stop u
s
ing UNDEFI
N
ED
a
s name of
a symbol
commit
|
commitdiff
|
tree
2016-01-07
Mark
Abr
a
ham
Remove fiel
d
s used only for SD2
commit
|
commitdiff
|
tree
2016-01-07
Mark Abra
h
am
Backport
md-vv fixes
commit
|
commitdiff
|
tree
2016-01-07
Mar
k
Abraham
Remove SD
2
integr
a
tor
commit
|
commitdiff
|
tree
2016-01-06
Ma
r
k
A
br
a
ham
Fix spuri
o
u
s
gcc warning
commit
|
commitdiff
|
tree
next