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Updated OpenCLTODOList.txt
2016-06-22
Berk Hess
Updated OpenCLTODO
L
ist
.
tx
t
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraham
Fix conf
i
g
u
ration-t
i
me
cpuin
f
o code
commit
|
commitdiff
|
tree
2016-06-22
David
v
an d
e
r
Spoel
Removed sp
u
rious r_i
j
in
f
or
c
e for M
o
rse potential
.
.
.
commit
|
commitdiff
|
tree
2016-06-22
Ma
r
k Ab
r
aham
Merge bra
n
ch r
e
lease-5-1 into relea
s
e-2016
commit
|
commitdiff
|
tree
2016-06-22
B
e
r
k
H
ess
Add
n
b
nxn pair-l
i
st
r
ebalancing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Remove OpenM
P
overhea
d
at hi
g
h para
l
l
eliza
t
ion
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Correct G
P
U pa
i
r
e
stimat
e
f
o
r
l
ist splitti
n
g
commit
|
commitdiff
|
tree
2016-06-22
M
ark Abraham
Ad
j
ust a
n
d document
C++
1
1 com
p
iler tests
commit
|
commitdiff
|
tree
2016-06-20
Mark Abraham
Update pre-su
b
mi
t
matrix co
n
ten
t
s
commit
|
commitdiff
|
tree
2016-06-19
Berk Hess
R
e
move warn
i
ng
s
on checkpoint mismatch
commit
|
commitdiff
|
tree
2016-06-19
Mark Abraham
Improve doc
s
for
l
inking stdl
i
bc++ ne
e
ded by icc
commit
|
commitdiff
|
tree
2016-06-17
B
erk Hess
Remove
s
t
d
::thread::h
a
rdware_
c
oncu
r
r
ency()
commit
|
commitdiff
|
tree
2016-06-17
Vedran Mileti
ć
Report the
f
i
lenam
e
a
nd the line number on failure
commit
|
commitdiff
|
tree
2016-06-17
Ma
r
k A
b
raham
M
er
g
e bran
c
h release-5-1 int
o
r
e
lease-2016
commit
|
commitdiff
|
tree
2016-06-17
M
a
r
k Abraham
Fix multi-sim
+
DD + s
i
mple d
i
stance restrai
n
ts
commit
|
commitdiff
|
tree
2016-06-13
B
e
rk Hess
Han
d
le constrain
t
error
s
with EM
commit
|
commitdiff
|
tree
2016-06-10
Mark Abraham
Find python for docs build quietly
commit
|
commitdiff
|
tree
2016-06-08
Er
i
k Linda
h
l
D
isabl
e
static libcudart on OS X
commit
|
commitdiff
|
tree
2016-06-07
Mark Abraham
Re-add
s
u
ppo
r
t for li
n
king against external
T
inyX
M
L
-
2
commit
|
commitdiff
|
tree
2016-06-07
M
a
rk Abraha
m
Updates to do
c
umentation
commit
|
commitdiff
|
tree
2016-06-07
Ber
k
Hess
F
ix
d
a
t
a race in hwinfo with
thread-MPI
commit
|
commitdiff
|
tree
2016-06-02
M
a
r
k Abraha
m
F
ix com
p
a
t
i
b
il
i
t
y with older C
M
ake
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Make more CM
a
ke variables advance
d
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
Ignore stderr w
h
en det
e
c
t
ing SIMD and
bu
i
ld info
commit
|
commitdiff
|
tree
2016-05-31
Mar
k
Abraham
Fix
reference to
v
mdio
.
c to b
e
vmdio
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
Second
2016 beta re
l
ease
commit
|
commitdiff
|
tree
2016-05-31
Berk
Hes
s
Reposit
i
o
n
n
b
nxn fi
l
le
r
particles
commit
|
commitdiff
|
tree
2016-05-31
Berk
H
e
s
s
Avoid numerical o
v
e
rflow with
o
verlapping atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk
Hess
Ad
d
check for finit
e
energies
commit
|
commitdiff
|
tree
2016-05-28
Rol
a
nd Schulz
Fix build
w
i
t
h
cl
a
ng 3
.
1+3
.
2
commit
|
commitdiff
|
tree
2016-05-27
Mark Abra
h
am
Fix readin
g
o
f bonded tables
commit
|
commitdiff
|
tree
2016-05-26
Mar
k
Abraham
New quote
commit
|
commitdiff
|
tree
2016-05-21
Eri
k
Lindahl
Disabl
e
automated F
F
TW
3
builds on Wind
o
ws
commit
|
commitdiff
|
tree
2016-05-17
Roland Schulz
Add reference to TopoTools
1
.
6
commit
|
commitdiff
|
tree
2016-05-17
T
e
e
mu
Murto
l
a
Fix
some thread
a
ffin
i
ty
cases
commit
|
commitdiff
|
tree
2016-05-13
Ro
l
and Schulz
Don
'
t use
a
bort
f
or fatal errors
commit
|
commitdiff
|
tree
2016-05-12
Mark Abrah
a
m
M
erge bra
n
ch rele
a
se-5-1 into relea
s
e
-2016
commit
|
commitdiff
|
tree
2016-05-12
Mark Abraham
GROMACS 2016 beta1 release
commit
|
commitdiff
|
tree
2016-05-12
Ve
d
ran Milet
i
ć
Remove s
t
atic function quali
f
ie
r
in OpenCL kernel
u
t
i
ls
commit
|
commitdiff
|
tree
2016-05-10
T
e
emu Mu
r
tola
Addi
t
iona
l
J
enki
n
s d
o
c
u
menta
t
ion
commit
|
commitdiff
|
tree
2016-05-10
Mar
k
Abraham
Bump
c
lang
s
tatic analyzer to version 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mark Abrah
a
m
Minor
update t
o
sphinx
dependenc
y
commit
|
commitdiff
|
tree
2016-05-10
Teemu
Murtola
Include releng
d
o
c
umen
t
at
i
on to
d
e
veloper
g
u
i
d
e
commit
|
commitdiff
|
tree
2016-05-10
E
rik
L
i
n
dahl
F
ix precision l
o
s
s
in tabul
a
ted
normal distribution
commit
|
commitdiff
|
tree
2016-05-10
Mark A
b
r
a
ham
Fac
i
l
itate link
i
ng with
l
ibcxx
commit
|
commitdiff
|
tree
2016-05-10
Erik Linda
h
l
Flush strea
m
s when not wri
t
i
ng n
e
wline character
commit
|
commitdiff
|
tree
2016-05-10
Berk
H
ess
Optimized the v
s
ite thread
i
ng
commit
|
commitdiff
|
tree
2016-05-10
R
o
l
and Schulz
Add OpenMP for fun
c
tio
n
s limiting scal
i
n
g
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
Fixes for
clang 3
.
7 on Power
P
C
commit
|
commitdiff
|
tree
2016-05-08
Jam
e
s W
.
Barnett
C
orrect and
c
larify o
u
t
p
ut units f
o
r fluct_props
commit
|
commitdiff
|
tree
2016-05-08
E
r
ik Lin
d
ahl
F
i
x
Luzar/Chander literature referenc
e
in g_hb
o
nd
commit
|
commitdiff
|
tree
2016-05-08
David
v
an der
Spoel
Modify lmfit library to avoi
d
c
l
ashes w
i
th
other versions
.
commit
|
commitdiff
|
tree
2016-04-28
Tee
m
u Murtola
Use HardwareTopology to
s
et nthre
a
ds_
h
w_avail
commit
|
commitdiff
|
tree
2016-04-28
Teem
u
M
urtola
Remove gmx_hw_info_t::ncore
commit
|
commitdiff
|
tree
2016-04-28
S
z
ilárd Páll
Workaround for gcc false p
o
sitive warning
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Improve
releas
e
w
orkfl
o
w testing
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
D
i
sable m
u
l
t
iple ranks for non-
M
P
I
unit tests
commit
|
commitdiff
|
tree
2016-04-27
Mark Abraham
Merge bran
c
h rel
e
ase-5-1
commit
|
commitdiff
|
tree
2016-04-27
Szilárd Páll
Fix multiple
MPI rank
s
per node with OpenCL
commit
|
commitdiff
|
tree
2016-04-27
T
ee
m
u Mur
t
ola
Fix issues with failing thread affinity setting
commit
|
commitdiff
|
tree
2016-04-19
Roland Schulz
Fix numeric
a
lly u
n
stable selection test
commit
|
commitdiff
|
tree
2016-04-19
Sz
i
l
ár
d
Páll
Move out CUDA
p
r
ofil
e
r t
r
iggers from NBNXN
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Allow rcoulomb>rvd
w
with PME
commit
|
commitdiff
|
tree
2016-04-19
Mark Ab
r
aham
R
e
p
l
a
ce libxml2 wi
t
h tinyxml2 for
u
se in test code
commit
|
commitdiff
|
tree
2016-04-19
R
o
land Schulz
Tune nstl
i
s
t increase for KNL
commit
|
commitdiff
|
tree
2016-04-19
M
a
r
k
Abraham
Fix parse_digits_from_string
commit
|
commitdiff
|
tree
2016-04-19
Be
r
k
Hess
Br
o
adca
s
t pull ext
e
rnal
p
o
tential provider string
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
F
ix mdp label gene
r
ation
commit
|
commitdiff
|
tree
2016-04-19
B
e
rk
H
ess
F
ix gmx hbond group overlap check
commit
|
commitdiff
|
tree
2016-04-14
Mar
k
Abraham
Merge branch
relea
s
e-5-1
commit
|
commitdiff
|
tree
2016-04-14
Carsten K
u
tzner
Corrected
v
al
u
e
of electric conve
r
sion factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
R
o
la
n
d S
c
hulz
AV
X
512 t
r
ansposeScatterIncr/DecrU with l
o
a
d
/
store
commit
|
commitdiff
|
tree
2016-04-04
Erik Lind
a
hl
Fi
x
compile
e
rror fo
r
IBM VMX on ppc64
commit
|
commitdiff
|
tree
2016-04-04
Eri
k
Lindahl
F
i
x
SIMD det
e
cti
o
n
o
n new AMD
A
VX CPUs w/o fma
commit
|
commitdiff
|
tree
2016-04-03
Erik Lin
d
ahl
Fix unit test s
e
gfaults with gcc-6
.
0
commit
|
commitdiff
|
tree
2016-04-03
Erik L
i
ndahl
Fix incorre
c
t return type
f
o
r scalar ver
s
ion
of
sim
d
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Semen Yesylevs
k
yy
Added refe
r
ences to ProtSq
u
eeze an
d
g_m
e
mbed to the
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
Ro
l
and
S
chul
z
Fix coolqu
o
tes
commit
|
commitdiff
|
tree
2016-04-01
Mark Abraham
R
evert to treati
n
g -1 as "ge
n
e
r
ate a se
e
d" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Add option for extern
a
l pull potential
commit
|
commitdiff
|
tree
2016-03-31
James W
.
Barnett
Revert
be
h
a
vior
for
h
andl
i
ng SETTLE error
s
commit
|
commitdiff
|
tree
2016-03-31
Szilárd Páll
r
efact
o
r CUDA texture-based table ini
t
i
a
lizati
o
n
commit
|
commitdiff
|
tree
2016-03-31
S
z
i
lard Pall
a
void
C
P
U oversubscription with
GPUs
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
LJ c
o
mbination ru
l
e
kernel
s
for OpenCL
commit
|
commitdiff
|
tree
2016-03-30
Szi
l
árd
Páll
Re-enable i-atom type l
o
cal
m
em
p
ref
e
t
c
h
in OpenCL
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
Correct mdrun tMPI (non-)
p
arallel
error
message
commit
|
commitdiff
|
tree
2016-03-30
Teemu
M
urt
o
la
Make includesorter
.
py work wit
h
Doxygen 1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
Descr
i
be AMD APPSDK 3
.
0 issue
s
i
n the guide
commit
|
commitdiff
|
tree
2016-03-30
Teemu M
u
rtola
Fix
error
reporting for documen
t
a
t
i
o
n build
commit
|
commitdiff
|
tree
2016-03-30
Ma
r
k Abraham
Cl
e
a
n
up vsite code
commit
|
commitdiff
|
tree
2016-03-22
C
arste
n
Ku
t
z
ner
Clean-up code for swapcoords
.
commit
|
commitdiff
|
tree
2016-03-22
B
e
r
k
Hess
LJ combination
ru
l
e
kernels for CUDA
commit
|
commitdiff
|
tree
2016-03-19
Mark Abra
h
am
Add more con
s
t correct
n
e
ss
commit
|
commitdiff
|
tree
2016-03-19
Mark Abra
h
a
m
I
m
proved some mdru
n
integration tests
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
Warn about Open
M
PI 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fix n
o
n-n
o
rmal
i
zati
o
n of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
Fix typo
i
n
Fourier di
h
edral equation
commit
|
commitdiff
|
tree
2016-03-18
Viveca
Li
n
da
h
l
Added pu
l
l coordinate
ge
o
metry angle
.
commit
|
commitdiff
|
tree
2016-03-18
Davi
d
va
n
der Spoel
Fixe
d
d
ivision by
z
ero in p
o
larize
.
commit
|
commitdiff
|
tree
2016-03-18
Nicholas Bree
n
Various
m
inor spelling fixes
-
message
s
a
n
d code comments
.
.
.
commit
|
commitdiff
|
tree
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