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Merge branch release-5-1 into release-2016
2016-07-08
M
ark Abraham
M
e
rge branch re
l
ease-5-1 into release
-
2016
commit
|
commitdiff
|
tree
2016-07-08
Mark Ab
r
a
h
a
m
Simplify SIM
D
c
ompiler fl
a
g con
s
truc
t
ion
commit
|
commitdiff
|
tree
2016-07-07
Mark Abraham
Move c
o
ns
i
stency check for number of threads
commit
|
commitdiff
|
tree
2016-07-07
Mark Abrah
a
m
F
ix build if libcuda is found b
u
t nvcc i
s
n
ot
commit
|
commitdiff
|
tree
2016-07-04
Mark
A
braham
Fixes f
o
r Power7 bi
g
-en
d
ian
commit
|
commitdiff
|
tree
2016-07-01
Mark Ab
r
aham
Fix
u
s
e
of
_POSIX_THREAD*
commit
|
commitdiff
|
tree
2016-06-30
Ma
r
k
Abraham
Mer
g
e branch re
l
ease-5-1 into rele
a
se-201
6
commit
|
commitdiff
|
tree
2016-06-29
Mark Abr
a
ha
m
R
e
factor sysconf checking
commit
|
commitdiff
|
tree
2016-06-29
M
a
rk A
b
raha
m
Work around glib
c
2
.
23 with C
U
DA
commit
|
commitdiff
|
tree
2016-06-28
Mark
A
braham
U
p
date to include a gcc 6
.
1
configu
r
ation
commit
|
commitdiff
|
tree
2016-06-28
M
ark Abraham
Fix SIMD co
n
fi
g
uration m
a
nagement
commit
|
commitdiff
|
tree
2016-06-27
Mark Abraham
Removed
u
n
n
ecessary
i
nter-simulation sign
a
lling
commit
|
commitdiff
|
tree
2016-06-27
Mark
Abraham
Merge branch
r
elease-5
-
1 into rele
a
se
-
2
016
commit
|
commitdiff
|
tree
2016-06-23
Mark Abraham
Allow use of externa
l
lmf
i
t packa
g
e
commit
|
commitdiff
|
tree
2016-06-23
Mar
k
Abraham
Prevent use o
f
m
d
r
un -maxh -multi
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
Fix conf
i
guration
-
time cp
u
info
c
o
de
commit
|
commitdiff
|
tree
2016-06-22
Mark
Abraham
Merge bran
c
h release-5-1 into
relea
s
e
-
2016
commit
|
commitdiff
|
tree
2016-06-22
Ma
r
k Abra
h
am
Adjust and
document C
+
+
11 compi
l
e
r
tests
commit
|
commitdiff
|
tree
2016-06-20
Mark
Abraham
U
pdate p
r
e-
s
ubmit matrix contents
commit
|
commitdiff
|
tree
2016-06-19
Mark Abraham
Improv
e
docs for linki
n
g stdlibc++ needed by icc
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
M
e
r
ge branch releas
e
-5-1
i
n
to releas
e
-
2
016
commit
|
commitdiff
|
tree
2016-06-17
Mark Ab
r
aham
Fix multi
-
si
m
+ DD + simpl
e
distance restra
i
nts
commit
|
commitdiff
|
tree
2016-06-10
Mar
k
Abraham
Fin
d
python fo
r
docs bui
l
d
qui
e
tly
commit
|
commitdiff
|
tree
2016-06-08
Mark
Abraham
Merg
e
bran
c
h
release-5-
1
int
o
release
-
2
0
16
commit
|
commitdiff
|
tree
2016-06-07
M
ark Abr
a
ham
Re-add supp
o
rt for linkin
g
agai
n
st external T
i
nyXML
-
2
commit
|
commitdiff
|
tree
2016-06-07
Mark
A
b
ra
h
am
U
p
d
ates to
d
ocument
a
tion
commit
|
commitdiff
|
tree
2016-06-02
M
ark Abraham
F
ix compatibilit
y
with
o
l
d
e
r
C
M
ake
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Make more CMake
var
i
ables advanced
commit
|
commitdiff
|
tree
2016-06-02
Mark
A
braham
Ignore s
t
derr when
detect
i
ng
SIMD and b
u
ild info
commit
|
commitdiff
|
tree
2016-05-31
Mar
k
Abraham
Fix reference
to vm
d
io
.
c to be vmdio
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mar
k
A
b
raham
Second 2016 beta rel
e
ase
commit
|
commitdiff
|
tree
2016-05-29
Mark Abraham
Simplifi
e
d and updated Open
C
L compilat
i
on
commit
|
commitdiff
|
tree
2016-05-27
Mark Abraha
m
Fix rea
d
ing
o
f
b
ond
e
d
ta
b
les
commit
|
commitdiff
|
tree
2016-05-26
Mark Abr
a
ham
New q
u
o
te
commit
|
commitdiff
|
tree
2016-05-12
Mark Abra
h
am
M
erge branch release-5-1 int
o
release-2016
commit
|
commitdiff
|
tree
2016-05-12
Mark Abraham
G
R
O
M
ACS 2016
b
eta1 release
commit
|
commitdiff
|
tree
2016-05-10
Mark
A
brah
a
m
Bu
m
p clang s
t
atic analyzer to
v
ersion 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mar
k
Abraham
Min
o
r update to sphinx
d
epe
n
dency
commit
|
commitdiff
|
tree
2016-05-10
Mark
A
braham
F
ac
i
l
itate linking with libcxx
commit
|
commitdiff
|
tree
2016-05-08
Mark Abr
a
ham
Fixes fo
r
c
l
an
g
3
.
7
o
n
P
owerPC
commit
|
commitdiff
|
tree
2016-05-08
M
a
rk
Abr
a
ha
m
Fix constants, units
a
n
d conversion factors
commit
|
commitdiff
|
tree
2016-04-27
Mark
A
braham
Merge branch release-5-1
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraha
m
Repl
a
ce libxml2 with tinyxml
2
for u
s
e in test
co
d
e
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Fix parse_digits_from_
s
tr
i
n
g
commit
|
commitdiff
|
tree
2016-04-19
M
a
rk Abraham
Fix m
d
p
l
abel gen
e
rati
o
n
commit
|
commitdiff
|
tree
2016-04-18
Mar
k
Abra
h
am
Red
u
ce compilation coup
l
ing of SIM
D
mo
d
ule
commit
|
commitdiff
|
tree
2016-04-14
Mark Abr
a
ham
Merge branch release-5-1
commit
|
commitdiff
|
tree
2016-04-01
M
ark
A
b
r
a
ham
Revert
t
o treatin
g
-1 as "g
e
nerate a seed" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Mark Abraham
Add test and improved docs for c
u
stom check
S
eq
u
ence
commit
|
commitdiff
|
tree
2016-03-30
M
a
rk Abraha
m
Clean u
p
v
s
ite code
commit
|
commitdiff
|
tree
2016-03-19
M
ark Abraham
Add more
c
o
nst correctne
s
s
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Fix warning f
r
om GC
C
6
commit
|
commitdiff
|
tree
2016-03-19
Mar
k
Abraham
Improved
s
ome mdrun int
e
gration
tests
commit
|
commitdiff
|
tree
2016-03-18
Mark
A
braham
W
a
r
n
about OpenMPI 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Mark
A
braham
Fix typ
o
in Four
i
er
dihedral equation
commit
|
commitdiff
|
tree
2016-03-15
Mark
Abra
h
am
Merge branch release-5-0 into release-5
-
1
commit
|
commitdiff
|
tree
2016-03-12
Mark Abraham
U
pdate use of
isnan in
linearalgebra
commit
|
commitdiff
|
tree
2016-03-12
Mark
Abraham
Find
hwloc q
u
i
etly i
f
it's already been found
commit
|
commitdiff
|
tree
2016-03-11
Mark Abraham
Add infras
t
ructure for
t
ests
t
o
compare mdr
u
ns
commit
|
commitdiff
|
tree
2016-03-11
Ma
r
k Abraham
Me
r
ge bran
c
h
r
elease-5-0
i
nto release
-
5
-
1
commit
|
commitdiff
|
tree
2016-03-10
Mark Abraham
R
equir
e
2015 versi
o
n
for MSVC
commit
|
commitdiff
|
tree
2016-03-05
Mar
k
Abrah
a
m
Add SETTL
E
u
n
it tests
commit
|
commitdiff
|
tree
2016-02-26
Mark
Abra
h
a
m
Separated test
of CDATA end tag h
a
ndling from oth
e
rs
commit
|
commitdiff
|
tree
2016-02-23
Mark Abr
a
ham
Replace cp
p
ch
e
ck suppressi
o
n i
n
checkpoint code
commit
|
commitdiff
|
tree
2016-02-22
Mark Abra
h
am
Move init
of specialized dynamical a
l
gorithms to do_md
commit
|
commitdiff
|
tree
2016-02-21
Mark Abraham
Separa
t
e t
a
bl
e
construction
commit
|
commitdiff
|
tree
2016-02-19
M
a
rk
Ab
r
aham
Merge b
r
an
c
h release-5-1
commit
|
commitdiff
|
tree
2016-02-19
Mark
A
braham
M
a
ke both
f
t
p
and
h
ttp links f
o
r sour
c
e download
commit
|
commitdiff
|
tree
2016-02-18
Mark Abraham
Updated refe
r
e
nce manu
a
l text about
P
ME tuning
commit
|
commitdiff
|
tree
2016-02-16
Mark Abraham
M
e
r
g
e bran
c
h re
l
ease-5-
0
i
nto re
l
ea
s
e-5-
1
commit
|
commitdiff
|
tree
2016-02-14
M
ark
A
bra
h
am
Re-generated eps for fig
u
re 4
.
8
commit
|
commitdiff
|
tree
2016-02-10
M
a
r
k
Abraham
Re-re
m
ove *_st
o
c
h
d_state f
u
n
ctio
n
d
e
c
l
arations
commit
|
commitdiff
|
tree
2016-02-10
Mark Abraham
Improved u
p
date_
c
oords handl
i
n
g of xprim
e
commit
|
commitdiff
|
tree
2016-02-10
M
ark Abraham
Fix issues t
o
update cppc
h
e
c
k sup
p
ort to 1
.
7
2
commit
|
commitdiff
|
tree
2016-02-08
Mark Abraham
M
erge b
r
anch release-5-0 i
n
to
release-5-
1
commit
|
commitdiff
|
tree
2016-02-06
Mark Abra
h
am
Merge branch r
e
lease-5-1
commit
|
commitdiff
|
tree
2016-02-03
Mark
A
braham
Bumped pa
t
ch nu
m
ber
to pr
e
p
a
r
e
for future 5
.
1
.
3 release
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Ve
r
sion 5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mark Abra
h
am
Fix
g
rompp no
t
warning when
.
mdp
v
alues
have wrong
.
.
.
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
M
erge release-5-0 into
release-5-1
commit
|
commitdiff
|
tree
2016-02-03
M
a
rk Abraha
m
F
i
x dE
k
in/
d
l handlin
g
with mu
l
tiple
r
anks
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Merge br
a
n
ch release-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Fix u
s
e
of
__APPLE__ in O
p
enCL code
commit
|
commitdiff
|
tree
2016-01-28
Mark Abra
h
a
m
Add
O
penCL
s
ource file types
t
o
c
opyright checker
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Avoi
d
F
P
ex
c
eption
commit
|
commitdiff
|
tree
2016-01-27
Mark Abraham
Merge
b
ranch relea
s
e-
5
-1
commit
|
commitdiff
|
tree
2016-01-27
Mark Abraham
Remove
bNotLastFrame
commit
|
commitdiff
|
tree
2016-01-27
M
a
r
k Abraham
Add sug
g
estions for updating bi
n
utils
commit
|
commitdiff
|
tree
2016-01-26
Mark Abr
a
h
a
m
F
i
x default f
o
r GMX_USE
_
N
V
M
L
commit
|
commitdiff
|
tree
2016-01-25
Mark Abraham
Merge bran
c
h release-5-1
commit
|
commitdiff
|
tree
2016-01-24
Mark Ab
r
ah
a
m
F
ix duplicate
L
aTeX
equation
l
abel
commit
|
commitdiff
|
tree
2016-01-24
Mark
Abraham
Update references to HTML and on
l
ine
d
ocumentation
commit
|
commitdiff
|
tree
2016-01-14
Mark Abraham
Permit customize
d
testing of grom
p
p and mdrun
commit
|
commitdiff
|
tree
2016-01-13
Mark Abraham
Allowed NVML suppo
r
t to be toggled
commit
|
commitdiff
|
tree
2016-01-12
Ma
r
k Abraham
Merge branc
h
release-5-0 into release-5-1
commit
|
commitdiff
|
tree
2016-01-11
Mark Abraham
Improved update
_
coords
commit
|
commitdiff
|
tree
2016-01-08
Mark Abraham
Im
p
rove
tpr heade
r
version handl
i
ng
commit
|
commitdiff
|
tree
2016-01-08
Mark
Ab
r
aham
Merge branch release-5-1
commit
|
commitdiff
|
tree
2016-01-07
M
a
r
k
A
b
r
a
ham
Fix some mdrun header depen
d
e
n
c
i
es
commit
|
commitdiff
|
tree
2016-01-07
Mark Abr
a
ham
A
void more C++ b
i
n
d
i
ng
s
for MPI
commit
|
commitdiff
|
tree
next