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First 2016 release candidate
2016-07-09
Mark Abraham
Fir
s
t 2
0
16 release can
d
idate
commit
|
commitdiff
|
tree
2016-07-08
Mark Abraham
Merge br
a
nch release-5-1 into release-2016
commit
|
commitdiff
|
tree
2016-07-08
Mark
Abrah
a
m
Simp
l
i
f
y SIMD co
m
pile
r
flag cons
t
ruction
commit
|
commitdiff
|
tree
2016-07-07
Mark
Ab
r
aham
Move
consistency check f
o
r
number of threads
commit
|
commitdiff
|
tree
2016-07-07
M
ark Abraham
Fix build i
f
libcuda
i
s
f
ound but nvcc is n
o
t
commit
|
commitdiff
|
tree
2016-07-04
M
a
rk A
b
ra
h
am
Fixes for Power7 big-endian
commit
|
commitdiff
|
tree
2016-07-01
Mark Abr
a
ham
F
i
x
use of _PO
S
IX_THR
E
AD*
commit
|
commitdiff
|
tree
2016-06-30
Mark Abraha
m
Merge branch
rele
a
se-5-1
i
nto release-2016
commit
|
commitdiff
|
tree
2016-06-29
Mark A
b
raham
R
efactor sysconf checking
commit
|
commitdiff
|
tree
2016-06-29
M
a
r
k Abraham
W
ork around glibc 2
.
23 with CUDA
commit
|
commitdiff
|
tree
2016-06-28
Mark Ab
r
aha
m
Update to include a gcc 6
.
1 con
f
i
g
u
r
ation
commit
|
commitdiff
|
tree
2016-06-28
M
a
rk Abraham
Fix SIMD co
n
figuration
m
a
nagement
commit
|
commitdiff
|
tree
2016-06-27
Mark Abraham
Rem
o
ved unnecessary
i
nter-simulation
signalli
n
g
commit
|
commitdiff
|
tree
2016-06-27
Mark
A
braha
m
Me
r
g
e branch
r
e
lease-5-1 into
rel
e
ase-201
6
commit
|
commitdiff
|
tree
2016-06-23
Mar
k
A
b
rah
a
m
A
ll
o
w use
o
f
e
x
te
r
n
al l
m
fit
p
ackage
commit
|
commitdiff
|
tree
2016-06-23
Mark Abrah
a
m
Prevent use of mdru
n
-m
a
xh -multi
commit
|
commitdiff
|
tree
2016-06-22
Mark Abrah
a
m
Fix con
f
iguration-time cp
u
info code
commit
|
commitdiff
|
tree
2016-06-22
Ma
r
k Abraham
Me
r
ge branch release-5-1 int
o
rele
a
se-2016
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
Adjust
a
nd document C++11 compiler tes
t
s
commit
|
commitdiff
|
tree
2016-06-20
Ma
r
k Abra
h
am
Update pre-submit matrix
c
ontents
commit
|
commitdiff
|
tree
2016-06-19
M
ar
k
Abra
h
am
Improve
d
ocs fo
r
l
inking stdli
b
c
++ needed by icc
commit
|
commitdiff
|
tree
2016-06-17
M
ark Abraham
Me
r
ge br
a
nc
h
release-5
-
1 into r
e
lease-2016
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Fix multi-sim +
D
D + simple
d
is
t
an
c
e restr
a
i
n
t
s
commit
|
commitdiff
|
tree
2016-06-10
Mark A
b
r
a
ha
m
Find python for docs
b
uild quietly
commit
|
commitdiff
|
tree
2016-06-08
Mark Abrah
a
m
Merge b
r
anc
h
release-5-1
i
nto release-20
1
6
commit
|
commitdiff
|
tree
2016-06-07
Mark
Ab
r
aham
Re-add support for linking against external Tin
y
XML-2
commit
|
commitdiff
|
tree
2016-06-07
Mar
k
Abraham
U
pdate
s
t
o
documenta
t
ion
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraha
m
Fix
compatibi
l
ity with older C
M
ake
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Make m
o
re CMake vari
a
bles ad
v
anced
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Ignore
s
tderr when det
e
cting SIMD and build
i
nfo
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
Fi
x
reference
t
o
vmdio
.
c
t
o be v
m
dio
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
Second 2016 beta release
commit
|
commitdiff
|
tree
2016-05-29
Ma
r
k Abr
a
ha
m
Simplified
an
d
updated OpenCL co
m
pilation
commit
|
commitdiff
|
tree
2016-05-27
Mark
Abraham
Fix
reading of
b
onded tables
commit
|
commitdiff
|
tree
2016-05-26
Mark Abraham
New qu
o
te
commit
|
commitdiff
|
tree
2016-05-12
Mark Abraham
M
e
r
ge branch
release-5-1 into re
l
ease-2
0
16
commit
|
commitdiff
|
tree
2016-05-12
Mark Abraham
GROMAC
S
2016 beta
1
r
e
lease
commit
|
commitdiff
|
tree
2016-05-10
M
ark Abraham
Bum
p
clan
g
static
a
nalyzer to version 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Mino
r
update
t
o sphinx dependency
commit
|
commitdiff
|
tree
2016-05-10
M
a
rk Abraham
Facil
i
tate linking w
i
t
h
l
ibcxx
commit
|
commitdiff
|
tree
2016-05-08
M
ark Abraham
Fixes f
o
r clang 3
.
7 on PowerPC
commit
|
commitdiff
|
tree
2016-05-08
M
a
rk Abraha
m
Fix constants, unit
s
a
n
d conver
s
i
o
n factors
commit
|
commitdiff
|
tree
2016-04-27
M
a
r
k
Abraham
Merge
branch release-5-1
commit
|
commitdiff
|
tree
2016-04-19
Mark A
b
raham
Re
p
lace libxml2 with ti
n
yxm
l
2
f
or use in t
e
s
t
code
commit
|
commitdiff
|
tree
2016-04-19
M
ark Abra
h
am
Fix
p
a
r
s
e_digits_fr
o
m_string
commit
|
commitdiff
|
tree
2016-04-19
Mark Ab
r
aham
Fix
mdp label generation
commit
|
commitdiff
|
tree
2016-04-18
Mark Abraham
Reduce comp
i
lati
o
n
c
oupl
i
ng of SIMD module
commit
|
commitdiff
|
tree
2016-04-14
Mark Abrah
a
m
M
e
rg
e
branch
releas
e
-5-1
commit
|
commitdiff
|
tree
2016-04-01
Mark Abraham
Revert to treatin
g
-1 as "gen
e
rate
a seed" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Ma
r
k
A
braham
Add te
s
t an
d
i
m
proved doc
s
for custom checkS
e
quence
commit
|
commitdiff
|
tree
2016-03-30
Mar
k
Abraham
Clean up vsit
e
co
d
e
commit
|
commitdiff
|
tree
2016-03-19
M
a
r
k Abrah
a
m
Add
m
ore const corre
c
tness
commit
|
commitdiff
|
tree
2016-03-19
Ma
r
k Ab
r
aham
Fix
warning from GC
C
6
commit
|
commitdiff
|
tree
2016-03-19
Mark A
b
raham
Impr
o
ved
s
o
me mdrun i
n
tegrat
i
on tests
commit
|
commitdiff
|
tree
2016-03-18
Mark Abra
h
am
Warn ab
o
ut Ope
n
M
P
I 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
Fix typo in Fou
r
ier dihe
d
ral equation
commit
|
commitdiff
|
tree
2016-03-15
Mark
A
bra
h
am
Merge
branch
release-5-0
into
r
e
lease-5-1
commit
|
commitdiff
|
tree
2016-03-12
Mark Abraham
Update
u
se o
f
isnan
i
n linearalgebr
a
commit
|
commitdiff
|
tree
2016-03-12
Ma
r
k Abraham
Fin
d
hwloc quietly
if it's a
l
r
e
ady been
fou
n
d
commit
|
commitdiff
|
tree
2016-03-11
Mark
A
braham
Add infrastructure for t
e
sts to compare m
d
runs
commit
|
commitdiff
|
tree
2016-03-11
M
a
r
k Abraham
M
erge branch release-5-0
into release
-
5-1
commit
|
commitdiff
|
tree
2016-03-10
M
a
rk
Abraham
Require 2015 v
e
rsio
n
for MSV
C
commit
|
commitdiff
|
tree
2016-03-05
Mark Ab
r
aham
Add SETTLE
uni
t
tests
commit
|
commitdiff
|
tree
2016-02-26
Ma
r
k Abraham
S
e
p
arated te
s
t of
C
DATA e
n
d
tag handling from others
commit
|
commitdiff
|
tree
2016-02-23
Ma
r
k Abraham
Replace c
p
pcheck s
u
p
p
res
s
i
o
n
in checkpoint
code
commit
|
commitdiff
|
tree
2016-02-22
Mar
k
Abrah
a
m
M
ove
i
n
i
t of sp
e
cialized d
y
namical a
l
gorithm
s
t
o do_md
commit
|
commitdiff
|
tree
2016-02-21
Mark Ab
r
aham
Se
p
arate tab
l
e constru
c
tion
commit
|
commitdiff
|
tree
2016-02-19
Mark Abraham
Merg
e
branch rele
a
s
e
-
5
-
1
commit
|
commitdiff
|
tree
2016-02-19
Mark Abraham
Make b
o
th
ftp
a
nd http links
f
or source download
commit
|
commitdiff
|
tree
2016-02-18
Mark Abraham
Up
d
ated reference manual t
e
xt
about PME tun
i
ng
commit
|
commitdiff
|
tree
2016-02-16
M
ark Ab
r
aham
Mer
g
e branch re
l
ease-5-0
i
nto release
-
5-1
commit
|
commitdiff
|
tree
2016-02-14
Mark Abraham
R
e-gener
a
ted
ep
s
f
or fi
g
ure 4
.
8
commit
|
commitdiff
|
tree
2016-02-10
Mark
A
braham
Re-
r
emove *_stochd_state function declara
t
ions
commit
|
commitdiff
|
tree
2016-02-10
Mark Abraham
Improved update_coords handling of xprime
commit
|
commitdiff
|
tree
2016-02-10
Ma
r
k Abraham
Fix issues to update c
p
pc
h
eck suppo
r
t
to 1
.
72
commit
|
commitdiff
|
tree
2016-02-08
M
a
rk
A
br
a
ham
Merge branch relea
s
e-5-0
i
nt
o
release-
5
-1
commit
|
commitdiff
|
tree
2016-02-06
Mark
Abraham
Merge bra
n
c
h
r
el
e
ase-5-1
commit
|
commitdiff
|
tree
2016-02-03
Mark Abr
a
ham
Bu
m
pe
d
pat
c
h numb
e
r to
p
repa
r
e for future 5
.
1
.
3 release
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Version 5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Fix grom
p
p not warning when
.
mdp v
a
lues hav
e
wrong
.
.
.
commit
|
commitdiff
|
tree
2016-02-03
M
a
r
k Ab
r
aham
Merg
e
r
e
lease-5-0 into
release-5-1
commit
|
commitdiff
|
tree
2016-02-03
Mark
A
bra
h
am
Fix dEkin/dl han
d
ling with
m
ultipl
e
ran
k
s
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Mer
g
e
b
r
anc
h
release
-
5
-1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraha
m
Fix use of _
_
APPLE__
in
OpenCL co
d
e
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Add OpenCL
sourc
e
f
ile ty
p
es to copyright checke
r
commit
|
commitdiff
|
tree
2016-01-28
M
a
r
k
Ab
r
ah
a
m
Avoid FP exception
commit
|
commitdiff
|
tree
2016-01-27
Mark Ab
r
aha
m
Mer
g
e bra
n
c
h release-5-1
commit
|
commitdiff
|
tree
2016-01-27
Mark Abraham
Remove
bNotLastFrame
commit
|
commitdiff
|
tree
2016-01-27
Ma
r
k Abraham
Add suggestions for
u
pdating binutils
commit
|
commitdiff
|
tree
2016-01-26
Mark
Abraham
Fix default fo
r
GMX_USE_NVML
commit
|
commitdiff
|
tree
2016-01-25
Mar
k
Ab
r
aham
Merge b
r
anch release-5-1
commit
|
commitdiff
|
tree
2016-01-24
Mark
A
braham
Fix duplicate LaTeX
e
q
uation l
a
b
e
l
commit
|
commitdiff
|
tree
2016-01-24
Mark Abraham
U
p
d
ate references to HTML and online documentat
i
on
commit
|
commitdiff
|
tree
2016-01-14
Mark A
b
r
a
ham
Pe
r
mit cu
s
tomized testi
n
g
o
f gro
m
pp
and mdrun
commit
|
commitdiff
|
tree
2016-01-13
M
a
r
k Abraham
A
l
low
e
d NVM
L
support to
be
to
g
gl
e
d
commit
|
commitdiff
|
tree
2016-01-12
M
a
rk Abraham
M
erge branch
release-5-
0
i
nto rele
a
se-5-1
commit
|
commitdiff
|
tree
2016-01-11
Mark Abrah
a
m
Im
p
roved upd
a
te_coo
r
ds
commit
|
commitdiff
|
tree
2016-01-08
M
a
rk A
b
raham
I
m
prove tpr header vers
i
on
handl
i
ng
commit
|
commitdiff
|
tree
2016-01-08
Mark Abraham
Merge branch release-5-1
commit
|
commitdiff
|
tree
2016-01-07
M
ark A
b
raha
m
Fix som
e
m
d
run h
e
ad
e
r dependenc
i
es
commit
|
commitdiff
|
tree
next