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Simplify SIMD compiler flag construction
2016-07-08
Ma
r
k Abraham
Simplify SI
M
D comp
i
l
er flag constr
u
c
ti
o
n
commit
|
commitdiff
|
tree
2016-07-08
Erik
Lindahl
Add detect
i
on for ARMv7 cycle counter suppor
t
commit
|
commitdiff
|
tree
2016-07-07
Mark Abraha
m
Move
c
o
n
si
s
tency check for
n
um
b
er of
t
hreads
commit
|
commitdiff
|
tree
2016-07-04
Mark Abra
h
am
Fixes for Power7 big-endian
commit
|
commitdiff
|
tree
2016-07-04
Szilárd Páll
Disable NVIDIA JI
T
c
a
che with
O
p
e
nCL
commit
|
commitdiff
|
tree
2016-06-30
M
a
rk A
b
raham
Merge
b
r
an
c
h release-5-1 into release
-
2016
commit
|
commitdiff
|
tree
2016-06-29
Mark Ab
r
a
ham
Refactor
sysconf checking
commit
|
commitdiff
|
tree
2016-06-29
Mark Abraham
W
ork aro
u
nd glibc 2
.
23 with CUDA
commit
|
commitdiff
|
tree
2016-06-28
Ber
k
Hess
P
rop
e
rly r
e
set CU
D
A ap
p
lication clocks
commit
|
commitdiff
|
tree
2016-06-28
Mar
k
Abraha
m
Up
d
a
t
e to incl
u
de a
g
cc 6
.
1 conf
i
g
uration
commit
|
commitdiff
|
tree
2016-06-28
Mark Abraham
Fix SIMD configuration management
commit
|
commitdiff
|
tree
2016-06-27
M
ark Abraham
Removed unn
e
c
e
ssary
int
e
r-simulati
o
n
signalling
commit
|
commitdiff
|
tree
2016-06-27
Berk Hess
Use
sy
s
conf(_SC_NPRO
C
ESSORS_ONLN)
commit
|
commitdiff
|
tree
2016-06-27
M
a
r
k
Abraham
Merge branch release-5-1 into release-2016
commit
|
commitdiff
|
tree
2016-06-24
Berk Hess
Fix
Verlet buffer calculation with nstlist=1
commit
|
commitdiff
|
tree
2016-06-23
B
erk
H
ess
More accu
r
ate GPU
l
ist split
t
ing
commit
|
commitdiff
|
tree
2016-06-23
M
a
rk Abraham
Allow
use of external lmfit packa
g
e
commit
|
commitdiff
|
tree
2016-06-23
Mark Ab
r
aham
Pre
v
e
nt
use o
f
mdrun -
m
axh -multi
commit
|
commitdiff
|
tree
2016-06-22
B
e
r
k Hess
Updated O
p
e
n
CLTODOLi
s
t
.
txt
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
Fix configuration-time cp
u
info code
commit
|
commitdiff
|
tree
2016-06-22
David van der Spoel
R
e
m
oved spu
r
ious r_ij in
f
o
rce
for
Morse potential
.
.
.
commit
|
commitdiff
|
tree
2016-06-22
Mark
Abraham
Merge
branch releas
e
-5-1 in
t
o relea
s
e-2016
commit
|
commitdiff
|
tree
2016-06-22
Berk
H
ess
Add nbnxn pair-list rebalancing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Remove OpenMP over
h
ead at high para
l
l
e
lization
commit
|
commitdiff
|
tree
2016-06-22
Berk He
s
s
C
orrect GPU pai
r
estimate fo
r
l
ist splitti
n
g
commit
|
commitdiff
|
tree
2016-06-22
M
a
rk Abra
h
a
m
A
djust
and
d
ocument C++11 compiler tests
commit
|
commitdiff
|
tree
2016-06-20
Mark
A
braham
Update pre-sub
m
it matrix contents
commit
|
commitdiff
|
tree
2016-06-19
B
e
rk Hess
Remove warni
n
gs on checkpoin
t
mismatch
commit
|
commitdiff
|
tree
2016-06-19
Mark Abrah
a
m
Improve do
c
s for l
i
nki
n
g
std
l
ibc+
+
nee
d
ed by
icc
commit
|
commitdiff
|
tree
2016-06-17
Berk Hess
Remove
s
td::t
h
read::har
d
ware_concu
r
r
e
ncy()
commit
|
commitdiff
|
tree
2016-06-17
Vedr
a
n Miletić
Re
p
ort the f
i
len
a
me a
n
d
the l
i
ne
num
b
er
o
n
f
a
ilure
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraha
m
Merge
b
ranch release-5-1 into release-
2
016
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Fix multi-sim + DD + simple
d
istance restraints
commit
|
commitdiff
|
tree
2016-06-13
B
e
r
k
H
e
ss
Ha
n
dle constra
i
n
t
e
rrors with EM
commit
|
commitdiff
|
tree
2016-06-10
Mark Abraham
Fi
n
d p
y
thon for docs bui
l
d qu
i
etl
y
commit
|
commitdiff
|
tree
2016-06-08
Erik
L
inda
h
l
Disable static libcu
d
art on
O
S X
commit
|
commitdiff
|
tree
2016-06-07
Mark Abraham
Re-add supp
o
rt for linkin
g
against ex
t
e
rna
l
T
inyXML-
2
commit
|
commitdiff
|
tree
2016-06-07
Mark A
b
raham
Updates to doc
u
m
e
n
tation
commit
|
commitdiff
|
tree
2016-06-07
Be
r
k
Hess
Fix dat
a
ra
c
e
i
n hwi
n
fo wit
h
thre
a
d
-
MPI
commit
|
commitdiff
|
tree
2016-06-02
Mark Abrah
a
m
Fix compatibility with ol
d
er CMake
commit
|
commitdiff
|
tree
2016-06-02
M
a
rk Abraham
Make
m
ore CMake variable
s
adv
a
nced
commit
|
commitdiff
|
tree
2016-06-02
Mark A
b
ra
h
am
Ignore stderr when detect
i
ng SIMD and build info
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
Fix refer
e
nce to vmd
i
o
.
c to be
v
mdio
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mark
A
bra
h
a
m
Second 2
0
16 be
t
a re
l
ease
commit
|
commitdiff
|
tree
2016-05-31
Ber
k
Hess
R
eposi
t
ion nbnxn
filler partic
l
es
commit
|
commitdiff
|
tree
2016-05-31
Be
r
k Hess
Av
o
id numerical overflow with overlapping atoms
commit
|
commitdiff
|
tree
2016-05-31
B
erk
Hess
Add check fo
r
f
in
i
t
e
energ
i
es
commit
|
commitdiff
|
tree
2016-05-28
Rolan
d
S
chulz
Fix build wit
h
clang 3
.
1+3
.
2
commit
|
commitdiff
|
tree
2016-05-27
Mark Abraham
Fix reading of bonded
tables
commit
|
commitdiff
|
tree
2016-05-26
Mark Abraham
Ne
w
quote
commit
|
commitdiff
|
tree
2016-05-21
E
r
i
k
Linda
h
l
Disa
b
l
e automated F
F
TW3 buil
d
s on Wi
n
dows
commit
|
commitdiff
|
tree
2016-05-17
Rola
n
d Sc
h
ulz
Add refer
e
n
c
e to TopoTools
1
.
6
commit
|
commitdiff
|
tree
2016-05-17
Te
e
mu Murtola
Fix so
m
e threa
d
affinity
c
ases
commit
|
commitdiff
|
tree
2016-05-13
Ro
l
and S
c
hulz
Do
n
't use abo
r
t for
f
a
tal
error
s
commit
|
commitdiff
|
tree
2016-05-12
Mark A
b
raham
Merge branch release
-
5-1 into rele
a
se
-
2016
commit
|
commitdiff
|
tree
2016-05-12
Mark Abra
h
am
GROMACS
2016
beta1 release
commit
|
commitdiff
|
tree
2016-05-12
V
edr
a
n Miletić
Rem
o
ve static fu
n
cti
o
n
qu
a
li
f
i
e
r
i
n OpenCL kernel
u
tils
commit
|
commitdiff
|
tree
2016-05-10
Teemu
Murtola
Addi
t
iona
l
Jenkin
s
doc
u
mentation
commit
|
commitdiff
|
tree
2016-05-10
M
ark Abra
h
a
m
Bum
p
clang static an
a
l
yzer to vers
i
on 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
M
ino
r
update to
s
phinx depend
e
ncy
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
I
nc
l
ud
e
releng doc
u
m
e
ntation to d
e
veloper guide
commit
|
commitdiff
|
tree
2016-05-10
Erik Lindahl
Fi
x
precision
l
o
ss
i
n tabulat
e
d
n
ormal
dis
t
ribution
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraha
m
Facili
t
ate linking
with libcx
x
commit
|
commitdiff
|
tree
2016-05-10
Erik Lindahl
Flus
h
streams when
no
t
writin
g
new
l
ine
character
commit
|
commitdiff
|
tree
2016-05-10
B
e
r
k Hess
O
p
timiz
e
d the vsite th
r
ea
d
ing
commit
|
commitdiff
|
tree
2016-05-10
Rola
n
d S
c
hulz
Add OpenMP for functions
limi
t
ing scaling
commit
|
commitdiff
|
tree
2016-05-08
Mark
A
b
rah
a
m
Fixes for clang 3
.
7 on Pow
e
r
P
C
commit
|
commitdiff
|
tree
2016-05-08
J
a
mes W
.
Ba
r
nett
Correc
t
and clarif
y
output
un
i
ts for fluct_prop
s
commit
|
commitdiff
|
tree
2016-05-08
Erik Lindahl
Fix L
u
za
r
/Chan
d
er li
t
e
rature reference in g_hbond
commit
|
commitdiff
|
tree
2016-05-08
David van der Spoel
Modify
l
mfit
l
ib
r
a
ry to avoi
d
cla
s
hes with other version
s
.
commit
|
commitdiff
|
tree
2016-04-28
Teemu
M
urtola
Use H
a
rdwareTop
o
logy
t
o set nthrea
d
s_hw_
a
vail
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtola
R
emo
v
e gmx_hw_info_t::ncore
commit
|
commitdiff
|
tree
2016-04-28
Szilá
r
d Páll
Workaround for gcc
f
alse
p
o
s
itive warni
n
g
commit
|
commitdiff
|
tree
2016-04-27
T
eemu Murto
l
a
Improve r
e
le
a
se workflo
w
testing
commit
|
commitdiff
|
tree
2016-04-27
Te
e
mu Murtola
Disable multiple r
a
nks for non
-
MPI unit tests
commit
|
commitdiff
|
tree
2016-04-27
Mark Abraham
Merge branc
h
release-5-1
commit
|
commitdiff
|
tree
2016-04-27
S
zilárd P
á
ll
F
i
x
m
u
lt
i
ple MPI r
a
nks pe
r
node with OpenCL
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Fix
i
ssues with failin
g
thread affini
t
y
setting
commit
|
commitdiff
|
tree
2016-04-19
R
ol
a
nd Schulz
Fi
x
numerica
l
ly unstable selection t
e
st
commit
|
commitdiff
|
tree
2016-04-19
Szilárd Páll
M
ove out CUDA profiler triggers fr
o
m NB
N
XN
commit
|
commitdiff
|
tree
2016-04-19
B
e
r
k Hess
Allo
w
rcoulomb>rvdw wit
h
PME
commit
|
commitdiff
|
tree
2016-04-19
Mar
k
Abraham
Replac
e
libxm
l
2 with
tinyxml2
f
or use in
t
est cod
e
commit
|
commitdiff
|
tree
2016-04-19
Roland Schulz
Tune nstlis
t
inc
r
ease for KNL
commit
|
commitdiff
|
tree
2016-04-19
Mark Abrah
a
m
Fix
p
a
r
se_digit
s
_from_string
commit
|
commitdiff
|
tree
2016-04-19
B
e
r
k
Hess
Broadcast p
u
ll ext
e
rnal pot
e
ntial
p
r
o
v
i
der string
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Fix mdp label generation
commit
|
commitdiff
|
tree
2016-04-19
Ber
k
Hes
s
Fix gmx
h
bond group
overlap che
c
k
commit
|
commitdiff
|
tree
2016-04-14
Mark
A
b
r
aham
Merge branch rele
a
se
-
5-1
commit
|
commitdiff
|
tree
2016-04-14
Carsten Kutzner
C
o
rrected value of electric conv
e
rs
i
on
f
acto
r
f in
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
Roland Schulz
AVX5
1
2 transposeScatterInc
r
/De
c
r
U wit
h
load/sto
r
e
commit
|
commitdiff
|
tree
2016-04-04
Erik
L
in
d
ahl
F
i
x compil
e
err
o
r
f
or I
B
M VMX on
p
pc64
commit
|
commitdiff
|
tree
2016-04-04
Erik Lind
a
hl
Fix SIMD
detecti
o
n on ne
w
AMD AVX CPUs w/o
fma
commit
|
commitdiff
|
tree
2016-04-03
Erik Linda
h
l
Fix unit
t
est segfau
l
ts wit
h
gc
c
-6
.
0
commit
|
commitdiff
|
tree
2016-04-03
Erik Lindahl
Fix incorrect return
type for
s
calar vers
i
o
n
of simd
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Semen Yesylevskyy
A
d
ded
ref
e
rences to
ProtSqueeze
a
nd g_membed to the
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
Rola
n
d Schulz
Fix coolquotes
commit
|
commitdiff
|
tree
2016-04-01
Mark Abraham
R
eve
r
t to treatin
g
-1
a
s "generate
a
seed" in
.
m
dp
commit
|
commitdiff
|
tree
2016-03-31
Berk
Hess
A
d
d option for exte
r
nal pull
potent
i
al
commit
|
commitdiff
|
tree
2016-03-31
James
W
.
Barnett
R
evert
b
eha
v
ior
f
or handling SETTLE e
r
rors
commit
|
commitdiff
|
tree
2016-03-31
Szilárd
Páll
refactor CUDA texture-based ta
b
l
e
initialization
commit
|
commitdiff
|
tree
next