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Bumped version to prepare for next patch release
2017-02-07
M
a
rk Abraham
Bumpe
d
vers
i
on t
o
prepare f
o
r next
p
atch release
commit
|
commitdiff
|
tree
2017-02-07
Mark Abraham
I
ntr
o
d
uc
e
d system preparation secti
o
n to u
s
er
g
uide
commit
|
commitdiff
|
tree
2017-02-07
M
a
r
k Abra
h
am
Version 2016
.
2
commit
|
commitdiff
|
tree
2017-02-05
Mark Abr
a
ham
Merge branch release-5-1 i
n
to r
e
leas
e
-20
1
6
commit
|
commitdiff
|
tree
2017-02-02
Mar
k
Abraham
Clarify use of tau-p and p
c
oup
l
type
commit
|
commitdiff
|
tree
2017-01-31
Mark A
b
ra
h
a
m
Merge bra
n
ch
r
elease-5-1 into r
e
lease-2016
commit
|
commitdiff
|
tree
2017-01-30
Mark A
b
raham
Fix m
u
l
ti-domain reruns
commit
|
commitdiff
|
tree
2017-01-30
Mark
A
b
raham
Don
'
t
p
rint invalid perfor
m
ance
data
commit
|
commitdiff
|
tree
2017-01-22
Mar
k
Ab
r
a
h
am
F
i
x
e
d gmx rmsf
-q -
o
q
.
commit
|
commitdiff
|
tree
2017-01-04
Mark
A
braham
Sto
p
tryin
g
to use objdum
p
--reloc
on Mac
commit
|
commitdiff
|
tree
2017-01-03
Mark Ab
r
aham
Merge bran
c
h release-5-1 into release-20
1
6
commit
|
commitdiff
|
tree
2016-12-20
Mark Abra
h
am
Corr
e
cted
d
ocumentat
i
on about eigen
v
alue han
d
ling
commit
|
commitdiff
|
tree
2016-12-20
M
ark Abraham
Improve buil
d
s
y
stem
f
or plugin suppor
t
commit
|
commitdiff
|
tree
2016-12-15
Mark Abraham
Ha
n
d
l
e
warninp c
o
rrectly in xpm2ps and m
e
mb
e
d
commit
|
commitdiff
|
tree
2016-12-14
Mar
k
Abraham
Fix
misleading
parallelization docs for gmx wham
commit
|
commitdiff
|
tree
2016-12-09
Mark Abra
h
am
F
ix logic of TRR read
i
ng
commit
|
commitdiff
|
tree
2016-12-07
Mark A
b
raham
Fix memory handl
i
n
g in gmx dump of TNG files
commit
|
commitdiff
|
tree
2016-12-05
Ma
r
k Abr
a
ham
Remove
un
d
ue
narr
o
wing of integ
e
r in TNG reading
commit
|
commitdiff
|
tree
2016-12-01
Mark Ab
r
aham
Fi
x
minor trjconv bu
g
commit
|
commitdiff
|
tree
2016-10-28
Mark Abrah
a
m
Bumped versio
n
to pr
e
p
are for next patch rel
e
ase
commit
|
commitdiff
|
tree
2016-10-28
Mark Abrah
a
m
V
ersion 201
6
.
1
commit
|
commitdiff
|
tree
2016-10-21
M
a
rk Abraham
Updat
e
i
ns
t
all guide
commit
|
commitdiff
|
tree
2016-10-18
Mark Abrah
a
m
F
ix
S
I
MD suggest
i
o
n
for VMX
commit
|
commitdiff
|
tree
2016-10-11
Mark Abraham
Update fo
r
FFTW 3
.
3
.
5
commit
|
commitdiff
|
tree
2016-10-07
Mark Abraham
Add script
f
or Jenkins regressiontest
update
j
ob
commit
|
commitdiff
|
tree
2016-10-03
M
ark
Abraham
Merge branch release-5-1 int
o
release-2016
commit
|
commitdiff
|
tree
2016-10-03
Mark Abra
h
am
Re
p
lace use of deprec
a
ted readdir_r
commit
|
commitdiff
|
tree
2016-09-08
Mark Abraham
M
erge b
r
anch r
e
lease-
5
-1 int
o
release-2
0
16
commit
|
commitdiff
|
tree
2016-09-08
M
ar
k
Abr
a
ham
Bumped patch n
u
mber
to pre
p
are for future 5
.
1
.
5
rele
a
se
commit
|
commitdiff
|
tree
2016-09-07
Ma
r
k
Abraha
m
Versio
n
5
.
1
.
4
commit
|
commitdiff
|
tree
2016-09-07
M
a
rk Abraham
Removed HIS1 from oplsaa and charmm definition
s
commit
|
commitdiff
|
tree
2016-09-07
Mark Abraham
Fix LYN c
h
arges in amber03
commit
|
commitdiff
|
tree
2016-09-07
M
a
rk Abrah
a
m
F
i
x
a
mb
e
r
0
3 HI
P
charges
commit
|
commitdiff
|
tree
2016-09-06
Mark Abraham
Work around
g
libc 2
.
23 with CU
D
A
commit
|
commitdiff
|
tree
2016-08-27
Mark Abraham
Stop us
i
n
g
gmx_
f
atal in grompp
commit
|
commitdiff
|
tree
2016-08-15
Mark Abrah
a
m
Fixes for
B
G/Q platform f
i
l
es
a
nd i
n
stall guide
commit
|
commitdiff
|
tree
2016-08-12
Mar
k
Abraham
B
ump number to prepare for fi
r
st patch
release
commit
|
commitdiff
|
tree
2016-08-04
Mark
A
braham
Ve
r
s
ion 20
1
6
commit
|
commitdiff
|
tree
2016-07-29
Mark Abraham
Im
p
rove hand
l
i
n
g of
g
m
o
c
k
an
d
gcc6
commit
|
commitdiff
|
tree
2016-07-29
M
a
rk
Abraham
Merge branch release-5-1 int
o
r
e
l
e
a
s
e
-20
1
6
commit
|
commitdiff
|
tree
2016-07-28
Mark Abraham
Add t
o
olchain flags for SSE2 co
m
p
ilation
commit
|
commitdiff
|
tree
2016-07-21
Mark A
b
raham
Bumped p
a
t
ch nu
m
ber to prepare for fu
t
ure 5
.
1
.
4 release
commit
|
commitdiff
|
tree
2016-07-14
Mark Abraham
F
ix iss
u
es
wi
t
h u
s
ing int for number of steps
commit
|
commitdiff
|
tree
2016-07-13
Mark
A
br
a
ham
V
ersion 5
.
1
.
3
commit
|
commitdiff
|
tree
2016-07-12
Mark Abraham
Fix trr magic n
u
mb
e
r reading
commit
|
commitdiff
|
tree
2016-07-11
Mark Abraham
Fix gmx mdru
n
-
m
embed -ntmpi
-
1
commit
|
commitdiff
|
tree
2016-07-11
Mark Abraham
Fix re
g
ressiontest dow
n
load md5s
u
m
commit
|
commitdiff
|
tree
2016-07-09
Mar
k
A
braham
First 2016 release ca
n
didat
e
commit
|
commitdiff
|
tree
2016-07-08
M
a
r
k Abr
a
ham
Merg
e
bran
c
h r
e
lease-5-1
i
nto releas
e
-20
1
6
commit
|
commitdiff
|
tree
2016-07-08
Mark Abraha
m
S
impl
i
fy SIMD compiler
flag
c
on
s
t
r
uction
commit
|
commitdiff
|
tree
2016-07-07
Ma
r
k Abraham
Move consis
t
ency check for number of threads
commit
|
commitdiff
|
tree
2016-07-07
M
a
rk Abraham
Fi
x
bu
i
ld if libcuda i
s
found but
n
vcc is
no
t
commit
|
commitdiff
|
tree
2016-07-04
Mark Abraham
Fix
e
s for P
o
w
e
r7 big-endian
commit
|
commitdiff
|
tree
2016-07-01
Mark Abraham
Fi
x
u
s
e
o
f _POSIX_
T
HREAD*
commit
|
commitdiff
|
tree
2016-06-30
Mark Ab
r
aha
m
Me
r
ge
b
r
a
nch release-5
-
1 into release-2016
commit
|
commitdiff
|
tree
2016-06-29
M
a
rk Abraham
Refactor sysc
o
nf checking
commit
|
commitdiff
|
tree
2016-06-29
Mark Abra
h
am
W
o
rk a
r
oun
d
g
libc
2
.
23 wit
h
CUDA
commit
|
commitdiff
|
tree
2016-06-28
Ma
r
k Abraham
Update
t
o
i
nclude
a
gcc 6
.
1
confi
g
uratio
n
commit
|
commitdiff
|
tree
2016-06-28
M
ark Abraham
Fix SIMD config
u
rat
i
o
n manage
m
ent
commit
|
commitdiff
|
tree
2016-06-27
M
ar
k
Abraham
Remove
d
unnec
e
ssary inter-simu
l
ation signalling
commit
|
commitdiff
|
tree
2016-06-27
Ma
r
k Abrah
a
m
Merge branch
r
el
e
ase-5-1 in
t
o releas
e
-2016
commit
|
commitdiff
|
tree
2016-06-23
Mark Abrah
a
m
Allow use of exte
r
n
al
lmfit
packag
e
commit
|
commitdiff
|
tree
2016-06-23
Mark A
b
raham
Prevent use of mdr
u
n -maxh -multi
commit
|
commitdiff
|
tree
2016-06-22
Mark A
b
r
a
ham
Fix c
o
nfiguration-ti
m
e cpuin
f
o
c
ode
commit
|
commitdiff
|
tree
2016-06-22
Mar
k
Abraham
M
e
rge bran
c
h rele
a
se-5-1 into rele
a
se-2016
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
A
djust and document C++11 compiler tests
commit
|
commitdiff
|
tree
2016-06-20
Mark Abraham
U
pda
t
e pre-submit mat
r
ix contents
commit
|
commitdiff
|
tree
2016-06-19
Ma
r
k Abraham
I
mprove d
o
cs for linking stdlibc++ needed b
y
icc
commit
|
commitdiff
|
tree
2016-06-17
Mark
A
braham
M
e
rge b
r
a
n
ch rel
e
ase-5-1 into rele
a
s
e-2016
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Fix multi
-
sim + DD + simple distance restra
i
n
ts
commit
|
commitdiff
|
tree
2016-06-10
Mark Abraham
Find python for docs build qu
i
etl
y
commit
|
commitdiff
|
tree
2016-06-08
Ma
r
k
A
b
raham
M
erge bran
c
h rele
a
se-5-1 in
t
o
release
-
2016
commit
|
commitdiff
|
tree
2016-06-07
Mark A
b
raham
Re-a
d
d support for linkin
g
a
g
ainst exter
n
al TinyX
M
L-2
commit
|
commitdiff
|
tree
2016-06-07
Mark Abraham
Updates to documentation
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Fix compatibili
t
y with
o
lder
CMake
commit
|
commitdiff
|
tree
2016-06-02
Mark Abrah
a
m
Mak
e
m
o
r
e
C
M
a
ke v
a
riables ad
v
a
n
ced
commit
|
commitdiff
|
tree
2016-06-02
Mark Abr
a
ham
Ignore std
e
rr when detecting
S
IMD and
build inf
o
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
Fi
x
r
e
ference to
vmdio
.
c to be
vmdio
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
S
e
cond 2016 beta release
commit
|
commitdiff
|
tree
2016-05-29
Mark Abr
a
ham
Si
m
p
l
i
fied and updat
e
d Ope
n
CL compi
l
atio
n
commit
|
commitdiff
|
tree
2016-05-27
M
ark Abraham
Fix reading of
bonded tab
l
e
s
commit
|
commitdiff
|
tree
2016-05-26
Mark
A
br
a
ham
New quot
e
commit
|
commitdiff
|
tree
2016-05-12
Ma
r
k Abraham
Merge branc
h
release-5-1 i
n
t
o re
l
e
ase-2016
commit
|
commitdiff
|
tree
2016-05-12
Ma
r
k Abraham
GROMAC
S
2
016
beta1 rel
e
ase
commit
|
commitdiff
|
tree
2016-05-10
Mar
k
Abr
a
ham
Bump
c
lang static analyzer to version
3
.
8
commit
|
commitdiff
|
tree
2016-05-10
M
ar
k
Abraham
Mi
n
or update to sp
h
inx depe
n
d
e
n
cy
commit
|
commitdiff
|
tree
2016-05-10
Mark
Abraham
Facilitate l
i
nk
i
ng wit
h
libc
x
x
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
Fixes fo
r
clang 3
.
7 on
P
owerPC
commit
|
commitdiff
|
tree
2016-05-08
Mar
k
Ab
r
aham
Fi
x
c
o
nstant
s
, u
n
its and
c
onvers
i
o
n
f
a
c
t
ors
commit
|
commitdiff
|
tree
2016-04-27
M
ark Abraham
Merge branch release-5-1
commit
|
commitdiff
|
tree
2016-04-19
Mark Ab
r
aham
Replace libxml2 with tin
y
xml2 for use in
t
est code
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Fix parse_
d
igits_from_string
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraha
m
Fi
x
m
d
p
la
b
el generation
commit
|
commitdiff
|
tree
2016-04-18
Ma
r
k A
b
raham
Reduce compi
l
ati
o
n
co
u
pling of SIMD module
commit
|
commitdiff
|
tree
2016-04-14
Mark Abra
h
am
M
e
rge branc
h
release-5
-
1
commit
|
commitdiff
|
tree
2016-04-01
Mark Abraha
m
Revert
to tre
a
tin
g
-1
a
s "generate a seed" in
.
md
p
commit
|
commitdiff
|
tree
2016-03-31
Mark Abra
h
am
Add te
s
t and improved docs for c
u
stom checkSequence
commit
|
commitdiff
|
tree
2016-03-30
M
ark Abraham
Clean
u
p
vsite code
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Add more const
c
orrectness
commit
|
commitdiff
|
tree
2016-03-19
Mark
Abraham
F
i
x warning f
r
om GCC
6
commit
|
commitdiff
|
tree
next