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Merge branch release-5-1 into release-2016
2016-07-08
Mark Abraham
Merge br
a
nch release-5-1 into release
-
2
016
commit
|
commitdiff
|
tree
2016-07-08
Mark
A
braham
S
i
mplify SIMD com
p
iler flag
c
onstruction
commit
|
commitdiff
|
tree
2016-07-07
Mar
k
A
braham
Move consi
s
tency check for number of th
r
eads
commit
|
commitdiff
|
tree
2016-07-07
Mark
A
bra
h
am
Fix build
if
lib
c
uda
i
s
f
ound but nvcc is
n
ot
commit
|
commitdiff
|
tree
2016-07-04
Mark Abraham
F
i
x
es for Po
w
er7 bi
g
-end
i
an
commit
|
commitdiff
|
tree
2016-07-01
Mark Ab
r
aham
Fi
x
use of _PO
S
IX_THREAD*
commit
|
commitdiff
|
tree
2016-06-30
Mar
k
Abraham
Merge
b
r
a
nch r
e
lease-5-1
i
nto release-2016
commit
|
commitdiff
|
tree
2016-06-29
Mark Abraham
Refact
o
r sysconf checking
commit
|
commitdiff
|
tree
2016-06-29
Mark Abraham
Wor
k
a
r
o
u
nd glibc
2
.
23
w
ith C
U
DA
commit
|
commitdiff
|
tree
2016-06-28
Mark Abra
h
a
m
Up
d
ate to
includ
e
a gc
c
6
.
1 config
u
rat
i
on
commit
|
commitdiff
|
tree
2016-06-28
Mark Abraham
Fix
SIMD
c
onfigurati
o
n manageme
n
t
commit
|
commitdiff
|
tree
2016-06-27
Ma
r
k Abraham
R
e
moved unnecess
a
ry
i
n
ter-simulatio
n
signalli
n
g
commit
|
commitdiff
|
tree
2016-06-27
M
a
rk A
b
raham
M
e
rge br
a
n
ch release-5-1 i
n
to release-2
0
16
commit
|
commitdiff
|
tree
2016-06-23
Mark Abraham
Allow use
of
e
x
t
ernal lmf
i
t package
commit
|
commitdiff
|
tree
2016-06-23
Mark
Abraham
Prev
e
nt use
of
m
dr
u
n -maxh -multi
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
F
i
x
configuratio
n
-
t
i
me cpuinfo code
commit
|
commitdiff
|
tree
2016-06-22
Mark
A
braham
Merge branch rele
a
se-5-1 into
release-20
1
6
commit
|
commitdiff
|
tree
2016-06-22
Mark A
b
raham
Adju
s
t and docum
e
nt
C++1
1
comp
i
ler test
s
commit
|
commitdiff
|
tree
2016-06-20
Mar
k
Abraham
U
p
date pre
-
submit matrix c
o
n
tents
commit
|
commitdiff
|
tree
2016-06-19
Ma
r
k Abraham
I
m
prove docs for linking stdlibc++ ne
e
ded by
i
cc
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Mer
g
e br
a
nch
relea
s
e-5
-
1
into re
l
ease-2
0
16
commit
|
commitdiff
|
tree
2016-06-17
M
ark Abra
h
am
Fix multi-sim + DD + simple distance restraint
s
commit
|
commitdiff
|
tree
2016-06-10
Mark Abra
h
am
Find python fo
r
d
o
cs build
q
uietly
commit
|
commitdiff
|
tree
2016-06-08
Mark Ab
r
aham
Merge branch rel
e
ase-5-1 in
t
o r
e
lease-2016
commit
|
commitdiff
|
tree
2016-06-07
M
a
rk Abraham
Re
-
ad
d
support for l
i
nking
a
gainst external TinyXML-2
commit
|
commitdiff
|
tree
2016-06-07
Mark Abraham
Up
d
ates to do
c
umentation
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Fix c
o
mpatibility with
o
l
d
er
C
Make
commit
|
commitdiff
|
tree
2016-06-02
M
ark Abraham
M
a
ke more CMa
k
e
v
ariables ad
v
anced
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Ig
n
o
re std
e
rr when detecting SIMD
and
b
uild info
commit
|
commitdiff
|
tree
2016-05-31
Mark Abr
a
ham
Fix reference to vmdio
.
c to be vmdio
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mar
k
Ab
r
aham
S
e
cond
2016 beta release
commit
|
commitdiff
|
tree
2016-05-29
Mark Abraham
Simplified and u
p
dated OpenCL compi
l
ation
commit
|
commitdiff
|
tree
2016-05-27
Mark Abr
a
ham
Fix readin
g
o
f
b
o
n
ded
t
a
bles
commit
|
commitdiff
|
tree
2016-05-26
Mark Abraham
N
e
w quote
commit
|
commitdiff
|
tree
2016-05-12
M
ark Abraham
Merge b
r
anch release-5
-
1 into release-2016
commit
|
commitdiff
|
tree
2016-05-12
Mark
Abraham
GROM
A
CS
2
016 beta1 rel
e
ase
commit
|
commitdiff
|
tree
2016-05-10
Mark
A
braham
Bump
cl
a
ng static anal
y
zer to version 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Minor update
t
o
sphi
n
x
dependency
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Facilitate l
i
nking with lib
c
xx
commit
|
commitdiff
|
tree
2016-05-08
Mark
Abraham
Fixes for clang 3
.
7 on PowerPC
commit
|
commitdiff
|
tree
2016-05-08
M
ark Abraham
Fix constants, units and convers
i
o
n factors
commit
|
commitdiff
|
tree
2016-04-27
Mark Ab
r
aham
Merge branch re
l
eas
e
-
5
-
1
commit
|
commitdiff
|
tree
2016-04-19
M
a
rk Abraham
Replace
libxml2 with tinyxml2 for use in test cod
e
commit
|
commitdiff
|
tree
2016-04-19
Mark Abrah
a
m
Fix
parse_digits_fr
o
m_string
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraha
m
Fix m
d
p
labe
l
generatio
n
commit
|
commitdiff
|
tree
2016-04-18
Mar
k
Abraham
Reduce compilation coupling of
S
IMD module
commit
|
commitdiff
|
tree
2016-04-14
Mark
Ab
r
aham
Merge
branc
h
release-
5
-1
commit
|
commitdiff
|
tree
2016-04-01
M
a
r
k A
b
raham
Revert to treating -
1
as "g
e
n
erate a see
d
" i
n
.
md
p
commit
|
commitdiff
|
tree
2016-03-31
Mark Abraham
Add t
e
st a
n
d
improved docs fo
r
custom che
c
kSequen
c
e
commit
|
commitdiff
|
tree
2016-03-30
M
a
rk Abra
h
am
Clean up
v
site
code
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Add more
const correctness
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Fix
w
arning from
GCC 6
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
I
m
proved
s
o
me mdrun
int
e
gr
a
tion tests
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
W
a
rn about O
p
e
n
MPI 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
M
a
rk Abraham
Fix typo in Fourier dihedral equat
i
on
commit
|
commitdiff
|
tree
2016-03-15
Mark Abrah
a
m
M
e
rge branch r
e
lease-5-0 in
t
o rel
e
ase-5-1
commit
|
commitdiff
|
tree
2016-03-12
Mark Ab
r
aham
Update use
o
f isnan
i
n line
a
r
a
lgebra
commit
|
commitdiff
|
tree
2016-03-12
Mark
A
braham
Find
hw
l
oc qu
i
etl
y
if
it's al
r
eady
been found
commit
|
commitdiff
|
tree
2016-03-11
Mark Abraha
m
Add
i
nfrastructure for tests to compare m
d
runs
commit
|
commitdiff
|
tree
2016-03-11
Mark Abrah
a
m
Merge branch release-5-0 i
n
to release-5-1
commit
|
commitdiff
|
tree
2016-03-10
Mark Abr
a
ham
Require
2
015 version
for
MSVC
commit
|
commitdiff
|
tree
2016-03-05
Ma
r
k A
b
raham
Add SETTLE
u
nit te
s
ts
commit
|
commitdiff
|
tree
2016-02-26
Mark Abraham
Separa
t
ed test of CDATA end tag
handling from others
commit
|
commitdiff
|
tree
2016-02-23
Mark Abraham
Replac
e
cppcheck suppression in
c
heckpoint
code
commit
|
commitdiff
|
tree
2016-02-22
Mark Abraham
Move init
of
s
p
e
c
ialized
d
ynamical algorithms t
o
do_md
commit
|
commitdiff
|
tree
2016-02-21
Mark Abra
h
am
Separ
a
t
e table const
r
uction
commit
|
commitdiff
|
tree
2016-02-19
M
a
r
k Abrah
a
m
Merge branc
h
release-5-1
commit
|
commitdiff
|
tree
2016-02-19
Mar
k
Abr
a
ha
m
Make both ftp and http links
for source download
commit
|
commitdiff
|
tree
2016-02-18
Ma
r
k
A
bra
h
am
Updated referenc
e
manual text about P
M
E
tuni
n
g
commit
|
commitdiff
|
tree
2016-02-16
Mark Abraham
Merge
branch r
e
l
e
ase-5-0 into release-5-1
commit
|
commitdiff
|
tree
2016-02-14
Mark Abraham
Re-ge
n
e
r
ated e
p
s for
f
igure 4
.
8
commit
|
commitdiff
|
tree
2016-02-10
Mark Abr
a
h
am
R
e
-
r
emove *_stochd_state function declarations
commit
|
commitdiff
|
tree
2016-02-10
M
ark
A
br
a
ha
m
Improved up
d
ate_coord
s
ha
n
dling of xprime
commit
|
commitdiff
|
tree
2016-02-10
Mark Abr
a
ham
Fix issues
t
o update
cppcheck
suppor
t
to
1
.
72
commit
|
commitdiff
|
tree
2016-02-08
M
ark Abrah
a
m
Me
r
g
e branch release-5-0
into release-
5
-1
commit
|
commitdiff
|
tree
2016-02-06
Mark
A
braha
m
Me
r
ge
b
ranch re
l
ease-5-1
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraha
m
Bumped patch number to prepare for f
u
t
u
re 5
.
1
.
3 releas
e
commit
|
commitdiff
|
tree
2016-02-03
M
ark Abra
h
a
m
Version 5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mar
k
Abraham
Fix gr
o
mpp not wa
r
ning when
.
mdp values hav
e
w
r
o
ng
.
.
.
commit
|
commitdiff
|
tree
2016-02-03
Ma
r
k A
b
r
aham
M
e
r
ge relea
s
e-5-
0
in
t
o
release
-
5-1
commit
|
commitdiff
|
tree
2016-02-03
Mark Ab
r
a
ham
F
ix d
E
kin/dl handling with multiple
r
ank
s
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Merg
e
branch release-5-
1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Fix use of __APPLE__
i
n Open
C
L code
commit
|
commitdiff
|
tree
2016-01-28
M
a
rk Abraha
m
Add OpenCL sourc
e
file types to copyright checker
commit
|
commitdiff
|
tree
2016-01-28
M
ark
A
braham
Avoid FP exception
commit
|
commitdiff
|
tree
2016-01-27
Mark Abraham
Merge branch
r
ele
a
se
-
5-1
commit
|
commitdiff
|
tree
2016-01-27
Mark Abraham
Remov
e
bNotLastFrame
commit
|
commitdiff
|
tree
2016-01-27
Mark
Abraham
Add s
u
gge
s
tion
s
for updating binutils
commit
|
commitdiff
|
tree
2016-01-26
Mar
k
Abra
h
am
F
i
x
d
efault
for
G
M
X_U
S
E_NVML
commit
|
commitdiff
|
tree
2016-01-25
Mark Abraham
Merge
b
ranch
r
e
l
ease
-
5-1
commit
|
commitdiff
|
tree
2016-01-24
Mark A
b
raha
m
Fix duplic
a
te LaTeX equatio
n
label
commit
|
commitdiff
|
tree
2016-01-24
Mark Abraham
Up
d
ate
references to
HTML and o
n
line documentation
commit
|
commitdiff
|
tree
2016-01-14
Mark Abraham
Pe
r
mit
cus
t
omized testing
o
f grompp a
n
d mdrun
commit
|
commitdiff
|
tree
2016-01-13
Mark
A
braham
A
l
l
o
w
e
d NVML sup
p
ort to be
to
g
gl
e
d
commit
|
commitdiff
|
tree
2016-01-12
Mark Abr
a
ham
Merge
branch release
-
5
-
0 into
release-5-1
commit
|
commitdiff
|
tree
2016-01-11
Ma
r
k Abraham
Improved
u
pdate_co
o
r
d
s
commit
|
commitdiff
|
tree
2016-01-08
Mark Abra
h
am
Improve tpr header version han
d
li
n
g
commit
|
commitdiff
|
tree
2016-01-08
Mark
A
braham
Merge branch release-5
-
1
commit
|
commitdiff
|
tree
2016-01-07
M
ar
k
Abraham
Fix some mdrun header de
p
end
e
n
c
ies
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Avoid more
C++
bindings
f
or
M
PI
commit
|
commitdiff
|
tree
next