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Merge branch release-5-1
2015-07-26
Erik
Lindahl
Merge br
a
nch release-5-1
commit
|
commitdiff
|
tree
2015-07-17
Er
i
k Lindahl
Moved sta
t
i
stics source t
o
C++
commit
|
commitdiff
|
tree
2015-07-17
Erik
L
indahl
Fixed stati
c
analyzer w
a
r
nings
commit
|
commitdiff
|
tree
2015-07-17
E
r
ik Linda
h
l
Fix incorr
e
ct
warni
n
g
abou
t
onl
y
using si
n
g
le core
commit
|
commitdiff
|
tree
2015-07-14
E
r
i
k Lindahl
Move fileio sources t
o
C++
commit
|
commitdiff
|
tree
2015-07-14
Eri
k
Lindahl
M
o
ve remaining C file
s
in utility
to
C++
commit
|
commitdiff
|
tree
2015-07-10
E
r
ik Li
n
d
ahl
Use cmakedef
i
n
e01 for
m
o
r
e trivial defin
e
s
commit
|
commitdiff
|
tree
2015-07-10
Er
i
k
Lindahl
Moved tools
f
iles t
o
C++
commit
|
commitdiff
|
tree
2015-07-09
Erik Lindahl
M
e
rg
e
"Mer
g
e relea
s
e
-5-1 into mas
t
er"
commit
|
commitdiff
|
tree
2015-07-08
Erik
L
indahl
Move generalize
d
b
or
n
t
o
C++
commit
|
commitdiff
|
tree
2015-07-08
E
rik Lindah
l
Mov
e
F
FT defines to u
s
e cmakede
f
i
n
e
0
1
commit
|
commitdiff
|
tree
2015-07-08
E
r
ik Lindahl
Move en
d
ia
n
,
float
f
o
rmat an
d
XDR settings to
cma
k
edefine01
commit
|
commitdiff
|
tree
2015-07-08
Erik Lin
d
ahl
Cleanup
and
r
e
m
ove unused S
S
E2 gene
r
a
lized
born code
commit
|
commitdiff
|
tree
2015-07-08
Erik
L
i
ndahl
Move old n
e
i
g
hborsear
c
h
code to C++
commit
|
commitdiff
|
tree
2015-07-07
Er
i
k
Lindah
l
M
o
ve
Q
MMM sou
r
ce to C++
commit
|
commitdiff
|
tree
2015-06-29
Erik Lindahl
F
ix O
S
X openCL b
u
ild
s
commit
|
commitdiff
|
tree
2015-06-29
Eri
k
Lindahl
Fi
x
b
u
g
s
in gmx dos
commit
|
commitdiff
|
tree
2015-06-29
Erik
L
indahl
Repl
a
c
e functions
d
eprecated i
n
O
p
e
n
CL
1
.
2
commit
|
commitdiff
|
tree
2015-06-29
Erik L
i
ndahl
F
i
x bug removing
m
u
ltiple
d
ihedrals
i
n
main
rtp en
t
ri
e
s
commit
|
commitdiff
|
tree
2015-06-29
Erik Li
n
dahl
Remove
d
gmx prot
o
nate to
o
l
commit
|
commitdiff
|
tree
2015-06-28
Erik Lindahl
Fix double precis
i
o
n
referenc
e
SI
M
D and g
c
c b
u
g
commit
|
commitdiff
|
tree
2015-06-28
Erik L
i
ndahl
Fix one
e
r
r
or and compiler war
n
i
ngs with Cuda & cl
a
ng-3
.
6
commit
|
commitdiff
|
tree
2015-06-27
Erik Li
n
dahl
Fi
x
IBM VSX SI
M
D
c
ompiles with
x
lc
commit
|
commitdiff
|
tree
2015-06-27
Erik Lindahl
Fix single-
p
rec
.
soft
c
ore issue i
n
4
.
6 branch
commit
|
commitdiff
|
tree
2015-06-27
Erik Lindahl
Merge "Merg
e
release-5-0 into
master"
commit
|
commitdiff
|
tree
2015-06-26
Erik Lindahl
Fix c
o
mpil
e
issue
s
on K computer
commit
|
commitdiff
|
tree
2015-06-26
Erik L
i
ndahl
Fix buffer size issu
e
s in st
r
ing
d
a
t
a
base
commit
|
commitdiff
|
tree
2015-06-25
Erik Lindahl
Fix edr appending
and ex
a
ct
c
ontinuatio
n
commit
|
commitdiff
|
tree
2015-06-25
Erik
L
i
ndahl
Fix binary exact
co
n
tinuat
i
on for trajector
i
es
commit
|
commitdiff
|
tree
2015-06-24
Erik L
i
ndahl
Avoid accessing h
a
c
k
b
locks for x2top
commit
|
commitdiff
|
tree
2015-06-23
Er
i
k Lin
d
ahl
Upd
a
t
ed physica
l
constants
f
rom NIST 2010 COD
A
T
A
commit
|
commitdiff
|
tree
2015-06-23
Er
i
k Lindahl
Rem
o
ved b
u
ggy -
s
mooth hack in hbond module
commit
|
commitdiff
|
tree
2015-06-22
Erik Lindahl
F
ix compiler warnings in cmake
tests
commit
|
commitdiff
|
tree
2015-06-22
E
rik L
i
ndahl
Use MPI_THREAD_FUNNELED
w
hen ava
i
l
a
ble
commit
|
commitdiff
|
tree
2015-06-22
E
rik Lindahl
Fix
s
egfault in random access XTC s
e
arching
commit
|
commitdiff
|
tree
2015-06-22
E
r
ik Lindahl
F
ix argum
e
nt ord
e
r
error
for g_
r
msdist
commit
|
commitdiff
|
tree
2015-06-22
E
rik Lindahl
Fix
gro error
s
with PDB insertion codes
commit
|
commitdiff
|
tree
2015-06-20
Erik
L
indahl
U
pdated
d
o
c
s
for g_gyrate
commit
|
commitdiff
|
tree
2015-06-20
E
rik Li
n
dah
l
F
i
x potential buffe
r
o
verflow in pdb2gmx
commit
|
commitdiff
|
tree
2015-06-20
E
rik
L
indahl
Disall
o
w i
n
finite e
p
silon wi
t
h P
M
E or GB
.
commit
|
commitdiff
|
tree
2015-06-20
Eri
k
Lindahl
Remov
e
G
M
X_M
A
X_MPI_THREADS
commit
|
commitdiff
|
tree
2015-06-20
Erik
L
indahl
Fi
x
reproduci
b
ility bug in
ff
t
5d
commit
|
commitdiff
|
tree
2015-06-20
E
r
ik Lindahl
Handle multidir/m
u
ltis
i
m
with sing
l
e argument correctl
y
commit
|
commitdiff
|
tree
2015-06-19
Erik Lin
d
ahl
F
i
x incorrect shif
t
wit
h
g_dens
i
ty -center
commit
|
commitdiff
|
tree
2015-06-16
Erik Linda
h
l
Fix CUDA versi
o
n in
f
o in NVML a
p
plicat
i
on c
l
ock w
a
rn
i
ng
commit
|
commitdiff
|
tree
2015-06-16
Er
i
k Lindah
l
Add m
e
mb
r
ane embedding
d
ocs
commit
|
commitdiff
|
tree
2015-06-16
Er
i
k L
i
ndahl
Upd
a
t
e
d FFTW recommendations in in
s
tall-
g
uide
.
commit
|
commitdiff
|
tree
2015-06-16
Erik Lindahl
Fix seg
f
ault with timer reset a
n
d -nb cpu
commit
|
commitdiff
|
tree
2015-06-16
Erik Lindahl
Avoid warning about affini
t
y on Blue
G
ene, re
d
uce warnings
commit
|
commitdiff
|
tree
2015-06-15
Erik
Lindahl
F
i
x
O
S X FFTW build failures intr
o
du
c
e
d
86a772
commit
|
commitdiff
|
tree
2015-06-15
Erik
Lindahl
Fi
x
ed
SIMD detection and fla
g
s common
for IB
M
archs
commit
|
commitdiff
|
tree
2015-06-07
E
r
ik Linda
h
l
Fix out-of
-
range
i
n
t
eger literals for
t
hr
e
efry
commit
|
commitdiff
|
tree
2015-06-04
E
r
ik
L
indahl
More n
e
w
q
uotes
commit
|
commitdiff
|
tree
2015-05-17
Er
i
k
Lindahl
Added
h
acks for SIM
D
rvec
/
load store in
l
incs & b
o
ndeds
commit
|
commitdiff
|
tree
2015-03-30
E
r
ik Linda
h
l
Quote f
r
om
Szilard
'
s talk at GTC2015
commit
|
commitdiff
|
tree
2015-03-25
E
rik
L
indahl
Quote
f
r
om Jen-
H
sun
at the NVIDIA GTC
conference
2015
commit
|
commitdiff
|
tree
2015-03-03
Erik Li
n
d
a
h
l
Ad
d
ed
sin
g
le-ac
c
uracy SIMD double ma
t
h
fu
n
ctions
commit
|
commitdiff
|
tree
2015-02-24
Erik Lindahl
Added
AVX-512ER SIM
D
suppor
t
commit
|
commitdiff
|
tree
2015-02-24
E
r
ik
Li
n
dahl
Add AVX-512F SIMD supp
o
rt
commit
|
commitdiff
|
tree
2015-02-20
Erik L
i
ndahl
Fa
m
ous quote from Colleen McCullou
g
h
commit
|
commitdiff
|
tree
2015-02-20
Erik Linda
h
l
A
dded two pop-c
u
lture qu
o
te
s
from Andy Warhol
.
commit
|
commitdiff
|
tree
2015-01-19
Erik
L
indahl
Added t
w
o quot
e
s from Jul
i
e Bernauer
h
ab
i
li
t
a
t
ion
commit
|
commitdiff
|
tree
2014-09-30
Erik Lindahl
Ad
d
Power8 VSX SIMD s
u
pport
commit
|
commitdiff
|
tree
2014-09-30
Erik Lin
d
ahl
Avoid using function calls in Open
M
P directives
commit
|
commitdiff
|
tree
2014-09-22
Erik Lindahl
More
q
uo
t
es
commit
|
commitdiff
|
tree
2014-09-20
E
r
ik
L
indahl
F
i
x RelWith
D
ebInfo name
b
ugs, and use full
opt
i
mization
.
commit
|
commitdiff
|
tree
2014-09-20
Erik Lindahl
Added a b
u
nch of new and old
q
uot
e
s
.
commit
|
commitdiff
|
tree
2014-09-18
Erik Lindahl
Add Power/PowerPC VMX SIMD suppo
r
t
commit
|
commitdiff
|
tree
2014-09-11
Eri
k
Lin
d
ahl
Enab
l
e stati
c
anon
n
a
me
s
pace workaround on pathscale
commit
|
commitdiff
|
tree
2014-09-10
Erik Lind
a
hl
Improve performance of MIC expo
n
e
n
t
ial
commit
|
commitdiff
|
tree
2014-09-08
Eri
k
Lindahl
A
dd
6
4-bi
t
AArch64 asimd SIMD supp
o
rt
commit
|
commitdiff
|
tree
2014-09-08
Erik Li
n
dahl
Add 32-bit A
R
M Neon SIMD sup
p
ort
commit
|
commitdiff
|
tree
2014-09-04
Eri
k
Lindahl
K
-
c
o
mp
u
ter spec
i
fic modif
i
cations
commit
|
commitdiff
|
tree
2014-09-03
E
r
ik Lindahl
Fix
e
d sc_power=
=
48 crash in single preci
s
ion
commit
|
commitdiff
|
tree
2014-09-03
Erik Lindahl
F
i
xed preproce
s
sor error
for AVX_128_FMA
s
imd
commit
|
commitdiff
|
tree
2014-09-02
Erik Lin
d
ahl
Fix formatting of
fatal erro
r
s in
g
_ba
r
commit
|
commitdiff
|
tree
2014-09-02
E
rik Lin
d
ahl
Fixed string var exp
a
ns
i
o
n in CMake due to CMP0053
commit
|
commitdiff
|
tree
2014-08-31
E
rik Lindahl
A
dded negative zero prepro
c
e
s
s
o
r constants
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
A
d
d _GNU_SOURCE=1 to find clone
(
) with PGI
commit
|
commitdiff
|
tree
2014-08-20
Eri
k
Li
n
dahl
Fix ma
t
r
i
x poin
t
er d
e
referen
c
e bug i
n
update
.
c
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Enable SIMD register calling conven
t
ion with gmx
_
simdca
l
l
commit
|
commitdiff
|
tree
2014-08-20
E
r
ik L
i
ndahl
Ad
d
cycle counte
r
s
for 64-bit ARM
commit
|
commitdiff
|
tree
2014-08-20
Erik Lind
a
h
l
Shorten plugin conf
i
gura
t
ion mess
a
ge
commit
|
commitdiff
|
tree
2014-08-17
Erik
L
i
n
dahl
Fix Portland
compiler warn
i
ngs
commit
|
commitdiff
|
tree
2014-08-10
E
r
i
k
Lindah
l
Make
i
nternal
B
LAS/L
A
PAC
K
mess
a
ges
less noisy
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindahl
Improve
Gromacs portabili
t
y
commit
|
commitdiff
|
tree
2014-08-10
Eri
k
Lindahl
Replace
_
_LP64__
with
c
he
c
k for
pointer size
commit
|
commitdiff
|
tree
2014-08-07
Erik Lindahl
F
i
x
p
o
rta
b
il
i
ty issu
e
with Arra
y
R
ef in
i
t
ializ
e
r over
l
oad
i
ng
commit
|
commitdiff
|
tree
2014-08-07
Erik Lindahl
Changed names of t
e
st files
to avoid Fujitsu
compiler b
u
g
commit
|
commitdiff
|
tree
2014-08-01
Erik Lind
a
hl
Added te
s
ts for denormal and u
n
derflow for s
i
m
d
e
x
p()
commit
|
commitdiff
|
tree
2014-07-27
Erik
Lindahl
Fix selection
o
f
x
t
c groups n
o
t
starting a
t
index 0
commit
|
commitdiff
|
tree
2014-07-13
Erik Linda
h
l
Avoid clan
g
/
32
optimizati
o
n
a
ffect
i
ng IEEE
e
n
dian detecti
o
n
commit
|
commitdiff
|
tree
2014-07-11
Erik
Lind
a
hl
Make AVX2 check
mor
e
r
o
bust
commit
|
commitdiff
|
tree
2014-07-08
Eri
k
Lindahl
Mak
e
IEEE754 check more robust
commit
|
commitdiff
|
tree
2014-06-29
Er
i
k
L
inda
h
l
Fixed free e
n
ergy
w
ith LJ-PME
commit
|
commitdiff
|
tree
2014-06-29
Erik
L
i
ndahl
Enable rtp angle/dihedral
entries not connec
t
ed by
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Erik Lindahl
F
i
xed CMAP generation for alanine dipep
t
ide speci
a
l
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
E
r
i
k Lindahl
Always
set b-s
t
ate pos
r
es, even
i
f identical to a-state
commit
|
commitdiff
|
tree
2014-06-27
E
r
ik Lindah
l
Update g_density to handle
b
ilayers bet
t
er
commit
|
commitdiff
|
tree
2014-06-27
Erik
L
indahl
Fix L
J
PME Lorentz-Berthelot combinati
o
n rules
commit
|
commitdiff
|
tree
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