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Merge branch release-5-1
2015-07-26
Er
i
k
L
indahl
Merge branch rel
e
ase-5-1
commit
|
commitdiff
|
tree
2015-07-17
Eri
k
Lindahl
Mov
e
d stat
i
sti
c
s source to C++
commit
|
commitdiff
|
tree
2015-07-17
E
r
ik L
i
ndahl
Fixed static analyzer warnings
commit
|
commitdiff
|
tree
2015-07-17
E
rik
L
indahl
Fix in
c
orrect w
a
r
ning about o
n
ly
u
sing single core
commit
|
commitdiff
|
tree
2015-07-14
Erik Lindahl
M
o
ve fileio sou
r
ces to C++
commit
|
commitdiff
|
tree
2015-07-14
Erik Lindahl
Move remaining C f
i
les
i
n ut
i
lity to
C
++
commit
|
commitdiff
|
tree
2015-07-10
E
rik Lindahl
Use c
m
akedefine01 for
m
or
e
trivial defines
commit
|
commitdiff
|
tree
2015-07-10
Erik Lin
d
ah
l
Moved tools fi
l
es
t
o C++
commit
|
commitdiff
|
tree
2015-07-08
Erik
L
indahl
M
ove generali
z
ed bo
r
n to C++
commit
|
commitdiff
|
tree
2015-07-08
Erik Lindah
l
Move FFT defines to us
e
cmakedefine01
commit
|
commitdiff
|
tree
2015-07-08
Erik
Lindah
l
Mo
v
e
endian, float format an
d
XDR s
e
tti
n
gs to cmakedefine0
1
commit
|
commitdiff
|
tree
2015-07-08
Erik Lindahl
Cleanup and remove
u
n
us
e
d SSE
2
g
e
neralized born cod
e
commit
|
commitdiff
|
tree
2015-07-08
Erik Lindahl
Move old
n
ei
g
hbors
e
arch code
t
o C++
commit
|
commitdiff
|
tree
2015-07-07
Erik Linda
h
l
Move
Q
MMM source to C++
commit
|
commitdiff
|
tree
2015-06-29
Erik Linda
h
l
Fix OS X openCL builds
commit
|
commitdiff
|
tree
2015-06-29
Erik Lin
d
ahl
F
i
x bugs in
g
mx dos
commit
|
commitdiff
|
tree
2015-06-29
Erik Lindahl
R
e
place functions depreca
t
ed in OpenCL 1
.
2
commit
|
commitdiff
|
tree
2015-06-29
E
r
ik Li
n
dahl
F
ix
b
u
g removin
g
m
u
l
tiple dihedrals in
m
ain rtp entri
e
s
commit
|
commitdiff
|
tree
2015-06-29
Er
i
k
Lindahl
Removed gmx protonate tool
commit
|
commitdiff
|
tree
2015-06-28
Eri
k
Lindahl
F
ix double precis
i
on re
f
eren
c
e SIMD and gc
c
bug
commit
|
commitdiff
|
tree
2015-06-28
E
rik Lin
d
ah
l
Fi
x
one err
o
r and co
m
pi
l
er warnings with Cuda &
c
lang-3
.
6
commit
|
commitdiff
|
tree
2015-06-27
Erik Lindahl
Fix IBM
VSX SI
M
D co
m
piles with xlc
commit
|
commitdiff
|
tree
2015-06-27
Erik Lind
a
h
l
F
ix single-prec
.
so
f
tcor
e
issue
i
n 4
.
6 branch
commit
|
commitdiff
|
tree
2015-06-26
Er
i
k Li
n
dahl
Fix compil
e
issues on K computer
commit
|
commitdiff
|
tree
2015-06-26
Erik
L
i
n
d
ahl
Fix bu
f
fer s
i
ze issues in
string data
b
ase
commit
|
commitdiff
|
tree
2015-06-25
Erik Lin
d
ahl
Fix edr
a
ppendi
n
g
and exa
c
t cont
i
nuation
commit
|
commitdiff
|
tree
2015-06-25
Erik Lind
a
h
l
Fix
bi
n
ar
y
exact conti
n
u
ation for t
r
aje
c
tories
commit
|
commitdiff
|
tree
2015-06-24
Erik Lindahl
Avoid a
c
cessing
h
a
ckblocks for x2top
commit
|
commitdiff
|
tree
2015-06-23
E
r
i
k L
i
ndahl
Updated
p
h
y
s
i
c
al c
o
nstants fr
o
m NIST
2010 CODATA
commit
|
commitdiff
|
tree
2015-06-23
Erik
L
inda
h
l
R
emove
d
buggy -s
m
ooth h
a
ck
i
n h
b
ond module
commit
|
commitdiff
|
tree
2015-06-22
Erik
Lindahl
Fix compiler wa
r
nin
g
s in c
m
ake tests
commit
|
commitdiff
|
tree
2015-06-22
E
r
ik Lindahl
U
s
e MPI_T
H
READ_FUNNELED
whe
n
a
vaila
b
le
commit
|
commitdiff
|
tree
2015-06-22
E
rik
Lindahl
Fi
x
segfa
u
lt
in rand
o
m access XT
C
searchi
n
g
commit
|
commitdiff
|
tree
2015-06-22
Eri
k
Lindahl
Fix argu
m
ent order e
r
ror for g_rm
s
dist
commit
|
commitdiff
|
tree
2015-06-22
Erik Lindahl
Fi
x
gro errors
with
P
D
B insert
i
o
n code
s
commit
|
commitdiff
|
tree
2015-06-20
Erik Lindahl
Updated doc
s
for g_gyrate
commit
|
commitdiff
|
tree
2015-06-20
Erik Li
n
d
a
hl
F
i
x potential buffer overflow in pdb2gmx
commit
|
commitdiff
|
tree
2015-06-20
Erik Linda
h
l
Disal
l
o
w infin
i
te e
p
silon w
i
th PME or GB
.
commit
|
commitdiff
|
tree
2015-06-20
Er
i
k Lindahl
Rem
o
ve GMX
_
MAX_MPI_THREADS
commit
|
commitdiff
|
tree
2015-06-20
Er
i
k Li
n
d
ah
l
Fix reproducibili
t
y
bu
g
in
f
ft5d
commit
|
commitdiff
|
tree
2015-06-20
Erik Lindah
l
H
andle
multi
d
ir/multis
i
m wit
h
singl
e
argument correctly
commit
|
commitdiff
|
tree
2015-06-19
Eri
k
Lin
d
ahl
F
i
x in
c
or
r
ect
s
hift with g_density -center
commit
|
commitdiff
|
tree
2015-06-16
Erik
L
indahl
Fix
C
UDA version in
f
o in
NVML
applicat
i
on clock w
a
rn
i
n
g
commit
|
commitdiff
|
tree
2015-06-16
Erik Lindahl
Add membr
a
ne
embedding docs
commit
|
commitdiff
|
tree
2015-06-16
Erik Lindahl
Updated F
F
TW recommendations in in
s
t
a
ll-guide
.
commit
|
commitdiff
|
tree
2015-06-16
E
r
i
k Lindahl
Fix segfault with timer r
e
s
e
t and -nb cpu
commit
|
commitdiff
|
tree
2015-06-16
Erik
Lind
a
hl
Avoid wa
r
n
ing about affi
n
it
y
on Blue G
e
ne
,
re
d
uce
w
arnings
commit
|
commitdiff
|
tree
2015-06-15
Erik Lindahl
Fix OS X FFTW build failures
i
ntroduced
8
6a
7
72
commit
|
commitdiff
|
tree
2015-06-15
Erik L
i
ndahl
F
ix
e
d SIMD det
e
cti
o
n and f
l
ags c
o
m
mon for IBM a
r
chs
commit
|
commitdiff
|
tree
2015-06-07
Eri
k
Lindahl
Fix out-of
-
range int
e
ger
literals fo
r
threefry
commit
|
commitdiff
|
tree
2015-06-04
Erik
L
indahl
More
new quotes
commit
|
commitdiff
|
tree
2015-05-17
Erik Lindahl
Added hack
s
f
o
r SIM
D
rve
c
/load store
i
n
lincs & bondeds
commit
|
commitdiff
|
tree
2015-03-30
Erik Linda
h
l
Quot
e
from Sz
i
lard's
t
a
lk at GTC2015
commit
|
commitdiff
|
tree
2015-03-25
Erik Lindahl
Q
uote from
Jen-Hsun at t
h
e
N
VIDIA GTC conference 2015
commit
|
commitdiff
|
tree
2015-03-03
Er
i
k Li
n
d
a
hl
Ad
d
ed singl
e
-accuracy
SI
M
D
d
ouble math functions
commit
|
commitdiff
|
tree
2015-02-24
Erik Lindahl
Adde
d
AVX-512E
R
SIMD
s
upport
commit
|
commitdiff
|
tree
2015-02-24
Erik Lin
d
a
h
l
Add AV
X
-512F SIMD suppo
r
t
commit
|
commitdiff
|
tree
2015-02-20
Er
i
k L
i
ndahl
Famo
u
s quo
t
e from Col
l
ee
n
McCul
l
ough
commit
|
commitdiff
|
tree
2015-02-20
Erik
L
indahl
Added two
p
op-culture
quo
t
es fro
m
Andy Warhol
.
commit
|
commitdiff
|
tree
2015-01-19
Er
i
k
Lin
d
a
h
l
Added t
w
o q
u
ot
e
s from Juli
e
Bernaue
r
habilitati
o
n
commit
|
commitdiff
|
tree
2014-09-30
Erik L
i
ndahl
Add
P
ower8 VSX
S
IMD su
p
por
t
commit
|
commitdiff
|
tree
2014-09-30
Erik L
i
ndahl
Av
o
id using fun
c
tio
n
calls in
OpenMP d
i
re
c
tiv
e
s
commit
|
commitdiff
|
tree
2014-09-22
Erik Lindahl
More quotes
commit
|
commitdiff
|
tree
2014-09-20
E
r
ik
L
indahl
F
ix RelWith
D
ebInfo
name bugs,
a
nd
u
se full optimi
z
ation
.
commit
|
commitdiff
|
tree
2014-09-20
Erik Lindahl
A
dded a bunch of new and
o
ld quo
t
e
s
.
commit
|
commitdiff
|
tree
2014-09-18
Erik Li
n
d
a
h
l
Add Power/PowerPC
VMX SIMD
s
upport
commit
|
commitdiff
|
tree
2014-09-11
Erik Lindahl
Enable
s
tatic a
n
on namespace work
a
r
o
und on p
a
thscale
commit
|
commitdiff
|
tree
2014-09-10
Erik Lindahl
Improve pe
r
forman
c
e of MIC
e
x
ponent
i
al
commit
|
commitdiff
|
tree
2014-09-08
Erik Lindahl
Add 64-b
i
t
A
Arch64 asi
m
d
S
IMD support
commit
|
commitdiff
|
tree
2014-09-08
E
r
ik Li
n
dahl
Add 32-bit ARM Neon SIMD su
p
port
commit
|
commitdiff
|
tree
2014-09-04
Erik Lindahl
K-c
o
mput
e
r spec
i
fic mod
i
ficatio
n
s
commit
|
commitdiff
|
tree
2014-09-03
Erik L
i
ndah
l
Fixed sc_
p
ower==48 crash in
single precision
commit
|
commitdiff
|
tree
2014-09-03
Erik Lindahl
Fixed prepr
o
ces
s
or error fo
r
AVX_128_F
M
A simd
commit
|
commitdiff
|
tree
2014-09-02
Erik Lindahl
Fix
formatting of fatal error
s
in g_bar
commit
|
commitdiff
|
tree
2014-09-02
Erik Lind
a
hl
Fi
x
ed stri
n
g var expansio
n
in
C
Make due to CMP0053
commit
|
commitdiff
|
tree
2014-08-31
E
r
ik Lindahl
Added negative zero preprocessor c
o
nstants
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Add _G
N
U_SOURCE=1
to find clo
n
e
(
) with PGI
commit
|
commitdiff
|
tree
2014-08-20
E
r
ik
Lindah
l
Fix matrix
p
ointer dereference bug i
n
update
.
c
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
E
n
able SI
M
D regi
s
ter call
i
ng conventio
n
with gmx_si
m
dcall
commit
|
commitdiff
|
tree
2014-08-20
E
r
i
k Lindahl
Add cy
c
le c
o
un
t
ers for 64-bit ARM
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Shorten plugin
configu
r
ation
message
commit
|
commitdiff
|
tree
2014-08-17
Erik Lindahl
F
i
x Por
t
l
and comp
i
ler
w
arni
n
gs
commit
|
commitdiff
|
tree
2014-08-10
E
ri
k
Lin
d
ahl
M
a
ke internal
B
LAS/LAPACK
m
essages less
noisy
commit
|
commitdiff
|
tree
2014-08-10
Er
i
k Lindah
l
Improve Gromacs
p
o
rtab
i
lity
commit
|
commitdiff
|
tree
2014-08-10
E
r
i
k Lindah
l
Replace __L
P
64__ wi
t
h
check for p
o
i
n
ter siz
e
commit
|
commitdiff
|
tree
2014-08-07
Erik
Lindahl
Fix porta
b
ility issue
w
it
h
Ar
r
ayRef initialize
r
o
ve
r
loa
d
ing
commit
|
commitdiff
|
tree
2014-08-07
Erik
L
inda
h
l
Changed
names of test file
s
to av
o
id Fujitsu compil
e
r
b
u
g
commit
|
commitdiff
|
tree
2014-08-01
Erik Lindahl
Added tests for denormal and und
e
rfl
o
w
f
or simd exp
(
)
commit
|
commitdiff
|
tree
2014-07-27
Erik Lindahl
Fix sele
c
tion of xtc groups not starting at index
0
commit
|
commitdiff
|
tree
2014-07-13
Erik Lindahl
Avoid clang/32 optimization af
f
ecting IEEE e
n
dian detectio
n
commit
|
commitdiff
|
tree
2014-07-11
Er
i
k Lindahl
Make AVX2 check more robust
commit
|
commitdiff
|
tree
2014-07-08
E
r
ik Li
n
dahl
Make IEEE754 check more robust
commit
|
commitdiff
|
tree
2014-06-29
Erik
L
indahl
Fixe
d
free energy with LJ-
P
ME
commit
|
commitdiff
|
tree
2014-06-29
E
rik Li
n
dahl
E
nable rtp angle
/
di
h
edra
l
entries not
c
onnec
t
ed
b
y
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Erik Lindahl
Fixed CMAP generation for ala
n
ine dip
e
ptide specia
l
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Erik
L
i
n
dahl
Always se
t
b-
s
tate posres, even if identi
c
al
to a-state
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Update g_den
s
ity
to
h
a
n
d
le b
i
layer
s
b
ette
r
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Fix
L
JPME Lorentz-Berthelot com
b
i
nation ru
l
es
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
I
m
prove PDB
I
/O (keep occupancy,
b-fa
c
t
or, element)
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Avoid warn
i
n
g
s about
c
oupling
w
hen free_e
n
er
g
y=n
o
commit
|
commitdiff
|
tree
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