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Change use of t_inpfile to std::vector
2018-06-07
Paul Bauer
Change use
o
f t_inpfile
to
s
t
d::ve
c
to
r
commit
|
commitdiff
|
tree
2018-06-07
Paul
B
auer
Remo
v
e ma
c
ros in
i
nput file rea
d
ing
commit
|
commitdiff
|
tree
2018-06-06
K
evin Boyd
Added t
o
PME on
GPU i
n
form
a
tion in mdrun perfo
r
manc
e
commit
|
commitdiff
|
tree
2018-03-12
Mark
Abraham
Test gcc-6 and c
u
da-9
.
0
commit
|
commitdiff
|
tree
2018-01-05
Erik
Lindahl
Te
s
t t
h
at nvcc/host compiler c
o
m
b
o wor
k
s
commit
|
commitdiff
|
tree
2018-01-05
Er
i
k Lindahl
M
a
ke TN
G
w
riting work with multiple id
e
ntical
s
t
eps
commit
|
commitdiff
|
tree
2018-01-05
Erik Lindahl
Add AVX
_
5
12 and KNC symbo
l
s to FFTW SIMD test
commit
|
commitdiff
|
tree
2018-01-05
Mark Abraham
Remo
v
e Fi
n
d
C
UDA from source tar
b
all
commit
|
commitdiff
|
tree
2018-01-03
Mark
A
braham
Ad
d
c
ool quot
e
commit
|
commitdiff
|
tree
2018-01-03
Eri
k
L
indahl
Fix complexity for
l
arge exclusi
o
n order
s
commit
|
commitdiff
|
tree
2018-01-03
Mark
Abraham
Fix d
u
plicate wa
r
n
i
n
g
commit
|
commitdiff
|
tree
2018-01-03
E
rik Li
n
dahl
Don't allow multi
p
le energy groups for GP
U
r
uns
commit
|
commitdiff
|
tree
2018-01-02
Erik Lindahl
Document required positi
o
n
restraint files
commit
|
commitdiff
|
tree
2018-01-02
Erik
L
indahl
Allo
w
e
m
pty lines in hdb file
s
commit
|
commitdiff
|
tree
2018-01-02
Mark Abraham
Fix membed by
c
al
l
i
n
g the prop
e
r mtop finalization
.
.
.
commit
|
commitdiff
|
tree
2018-01-01
Erik Lindahl
C
l
ar
i
fy XTC
e
rror message
commit
|
commitdiff
|
tree
2017-12-29
Mark Abr
a
ham
Separate
canDetectGpus and f
i
ndGpus futher, and
f
i
x
.
.
.
commit
|
commitdiff
|
tree
2017-12-28
R
o
la
n
d S
c
hulz
Replace GMX_A
L
I
GNED wit
h
ali
g
nas an
d
SIMD alignment
.
.
.
commit
|
commitdiff
|
tree
2017-12-20
Car
s
ten Kut
z
ner
De
s
t
r
uct
M
DModules/force
p
ro
v
i
de
r
s
p
rior to calling
.
.
.
commit
|
commitdiff
|
tree
2017-12-20
Ale
k
sei
I
upin
o
v
Remove pote
n
tially wrong
"per user
r
equ
e
st" note
f
rom
.
.
.
commit
|
commitdiff
|
tree
2017-12-15
R
oland
Schulz
Remove incorrect
/
mislea
d
ing Ope
n
MP message
commit
|
commitdiff
|
tree
2017-12-15
R
o
land Schu
l
z
Revert "Use
t
a
ble Ewald for
S
k
ylake"
commit
|
commitdiff
|
tree
2017-12-15
Mark Abraham
Make Op
e
nC
L
implementation
o
f gpu_utils test
s
conform
commit
|
commitdiff
|
tree
2017-12-14
Mark
Abraham
Avoid confusing message
a
t
en
d
of non-dynamical run
s
commit
|
commitdiff
|
tree
2017-12-14
Mark Abraham
Fix
r
e
t
urn
v
alues
of frame-reading funct
i
ons
commit
|
commitdiff
|
tree
2017-12-14
M
a
r
k
A
b
raham
Ma
k
e AVX-
5
12 CMake detction work
commit
|
commitdiff
|
tree
2017-12-14
Paul Bauer
R
e
move PBC before ge
n
erating TPR wi
t
h gr
o
up scheme
commit
|
commitdiff
|
tree
2017-12-14
R
oland Schulz
Simplify CMAP
l
oop
commit
|
commitdiff
|
tree
2017-12-14
Erik Linda
h
l
Work around AVX-5
1
2 is
s
ues in gc
c
-5
.
4 and 7
.
1
commit
|
commitdiff
|
tree
2017-12-12
E
rik Lindahl
D
o
c
umented pow
e
r
spectrum to gmx
velacc
commit
|
commitdiff
|
tree
2017-12-12
B
erk He
s
s
Ch
e
ck fo
r
large ener
g
y at first st
e
p
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Avoid yell
i
ng about thread pinning
twice
commit
|
commitdiff
|
tree
2017-12-11
Mark
A
b
r
ah
a
m
Leave
N
VM
L
u
s
e
off by default
commit
|
commitdiff
|
tree
2017-12-11
Mar
k
Abraha
m
Check for G
P
U
d
etecti
o
n
s
upport b
e
fore detecting
commit
|
commitdiff
|
tree
2017-12-11
M
a
rk Abra
h
am
Avoid s
i
gned-ove
r
f
l
ow warning with gcc
7
commit
|
commitdiff
|
tree
2017-12-11
Mark Abraham
Remove
S
IMD shift
o
perators
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remove SIMD
w
ar
n
ing for
A
MD
Z
en
commit
|
commitdiff
|
tree
2017-12-10
Be
r
k Hess
Tone down n
o
te about not p
i
nning thr
e
ads
commit
|
commitdiff
|
tree
2017-12-10
Szilárd Pál
l
Disable default-on
NVML su
p
po
r
t in
C
Make
commit
|
commitdiff
|
tree
2017-12-07
Roland Schu
l
z
Fix C++1
1
li
b
rary check'
s
thread
d
e
pendency
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Clear
vsite velocities for simpl
e
i
nte
g
rators
commit
|
commitdiff
|
tree
2017-12-03
Mark
A
br
a
ham
F
i
x fft5d
pinning
commit
|
commitdiff
|
tree
2017-12-02
B
er
k
Hess
Avoid assertion
f
ailure in
A
WH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
Change the
G
PU
SMT cut-off to quadrat
i
c
commit
|
commitdiff
|
tree
2017-11-28
Erik Lindahl
Fix
A
VX-512 SIMD test for C
commit
|
commitdiff
|
tree
2017-11-27
A
leksei Iupin
o
v
Do not force separate PME rank to recompute reciproc
a
l
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Erik Lindahl
T
est mor
e
AVX-5
1
2F inst
r
u
c
tions before enabling suppo
r
t
commit
|
commitdiff
|
tree
2017-11-24
Erik Lin
d
ahl
Det
e
ct AV
X
-
5
12 FM
A
units to choose best
SIMD
commit
|
commitdiff
|
tree
2017-11-24
B
e
r
k Hes
s
Limit S
M
T with PME on GPU
commit
|
commitdiff
|
tree
2017-11-20
V
i
veca Linda
h
l
A
dd readin
g
and
w
riting to AW
H
m
o
d
u
le
commit
|
commitdiff
|
tree
2017-11-20
Mark
Abraha
m
Fi
x
nightly matrix config
commit
|
commitdiff
|
tree
2017-11-19
Berk Hess
Add SI
M
D fo
r
AWH
commit
|
commitdiff
|
tree
2017-11-18
Mag
n
us
Lundborg
A
dded
M
agnus Lundborg as cont
r
i
b
u
t
or
i
n the
manual
.
commit
|
commitdiff
|
tree
2017-11-18
Alek
s
ei Iupi
n
ov
Asynchronous
C
U
D
A
transfers are
a
sserted to a
l
ways
.
.
.
commit
|
commitdiff
|
tree
2017-11-10
Roland Schulz
Revert "Use -
m
avx2 -mf
m
a instead of -march with AVX2
"
commit
|
commitdiff
|
tree
2017-11-08
Roland Schulz
F
i
x scalar b
l
end
commit
|
commitdiff
|
tree
2017-11-08
Magnus Lundbor
g
Update to TNG
v
1
.
8
.
1
commit
|
commitdiff
|
tree
2017-09-09
Berk Hess
Avoid inf in SIMD do
u
b
le
sqrt()
commit
|
commitdiff
|
tree
2017-07-19
Ma
r
k A
b
raham
Improve CMak
e
implementat
i
on for GM
X
_SIM
D
commit
|
commitdiff
|
tree
2017-06-29
Teem
u
Mu
r
tol
a
Generalize IForceP
r
ov
i
d
er
commit
|
commitdiff
|
tree
2017-06-15
Szilárd Pál
l
Allo
w
d
i
sabling the e
x
plicit us
e
o
f
CUDA t
e
xtures
commit
|
commitdiff
|
tree
2017-06-14
Mark Abraham
Simpli
f
y
r
e
p
orting
from ini
t
_gpu
commit
|
commitdiff
|
tree
2017-06-13
Erik Li
n
dah
l
M
o
re quotes
commit
|
commitdiff
|
tree
2017-06-07
Vedra
n
Mil
e
ti
ć
Document floating-p
o
int arithmetic
commit
|
commitdiff
|
tree
2017-05-29
Sz
i
lárd Páll
Quo
t
es are cool, typo-fre
e
ones are eve
n
"coo
l
er"
commit
|
commitdiff
|
tree
2017-05-27
Mark Abraham
Quote
s
fro
m
Gottingen wo
r
kshop
commit
|
commitdiff
|
tree
2017-05-14
Be
r
k H
e
ss
Fix bugs in
d
ou
b
le Simd4
i
m
plementat
i
ons
commit
|
commitdiff
|
tree
2017-03-19
Erik Lin
d
ahl
Use
O
penMP up to 16 threads with AMD Ryzen
commit
|
commitdiff
|
tree
2017-03-19
E
rik Linda
h
l
1
2
8-bit AVX2
SIMD fo
r
A
MD Ry
z
en
commit
|
commitdiff
|
tree
2017-03-19
Mark Abra
h
a
m
Fix strin
g
han
d
ling f
o
r gcc
7
commit
|
commitdiff
|
tree
2017-03-14
Erik Linda
h
l
Fix gcc comp
i
le
s
of A
V
X-512 SIMD
commit
|
commitdiff
|
tree
2017-02-14
Mark Abraham
Fix handling of previo
u
s virials
commit
|
commitdiff
|
tree
2017-02-10
Roland Schulz
Remove duplicate AVX
5
1
2
gat
h
er
d
efinitions
commit
|
commitdiff
|
tree
2017-02-09
Erik Lindahl
Work around false xl
c
-13
.
1
.
5 b
u
g
in SIMD test
commit
|
commitdiff
|
tree
2017-02-09
Mar
k
Abraham
Remove
EST_DIST
R
from state
.
h
commit
|
commitdiff
|
tree
2017-02-09
Mark Abraham
E
n
hance warninp
commit
|
commitdiff
|
tree
2017-02-08
Roland Schulz
AVX512: Use double-sized gat
h
er for pa
i
r
s of floats
commit
|
commitdiff
|
tree
2017-02-07
M
ark Abraham
Intr
o
duce
d
syst
e
m pre
p
aration s
e
ction
t
o
u
se
r
g
u
i
de
commit
|
commitdiff
|
tree
2017-02-03
David van de
r
Spoel
Fixes SE
G
V in g
m
x
order
.
commit
|
commitdiff
|
tree
2017-01-11
Roland
Schulz
Ti
d
y
:
moderni
z
e-use-nullptr
commit
|
commitdiff
|
tree
2016-11-03
Roland Schulz
Supres
s
I
CC
1
6
on Wind
o
ws f
a
lse p
o
s
tives
commit
|
commitdiff
|
tree
2016-10-30
T
eemu
M
urt
o
l
a
Support
n
orm
a
lizi
n
g values in
K
eyVal
u
e
Tree
commit
|
commitdiff
|
tree
2016-10-30
R
o
l
a
nd Sc
h
ul
z
Replace qsort
/
bsea
r
ch w
i
t
h
std::sort/
l
ow
e
r_bound
commit
|
commitdiff
|
tree
2016-10-11
Mark Abra
h
am
Update for F
F
T
W
3
.
3
.
5
commit
|
commitdiff
|
tree
2016-09-26
D
a
vid van der S
p
oel
Fi
x
es issue wi
t
h
Release
buil
d
i
n correlatio
n
function
s
.
commit
|
commitdiff
|
tree
2016-09-18
Rol
a
nd Schulz
F
ix
math-t
e
st false po
s
i
t
ive
commit
|
commitdiff
|
tree
2016-09-18
Rolan
d
Schulz
B
etter optim
i
ze
d
ICC release flags
commit
|
commitdiff
|
tree
2016-09-12
Mark Abr
a
h
a
m
Preliminary
c
l
ean up of NVML code
commit
|
commitdiff
|
tree
2016-09-12
B
erk H
e
ss
Add
const to thread
-
M
PI functions
commit
|
commitdiff
|
tree
2016-09-12
V
e
dran Miletić
Docu
m
ent wallcycle counters
a
n
d
su
b
counter
s
commit
|
commitdiff
|
tree
2016-09-12
Teemu
M
u
r
t
o
l
a
Fi
x
va
r
io
u
s memory leaks
commit
|
commitdiff
|
tree
2016-07-31
Ja
m
es Gra
h
am
A
v
oid blank l
i
ne in
writi
n
g
index
fil
e
commit
|
commitdiff
|
tree
2016-07-30
Roland
S
c
hulz
Update
GCC
version for refer
e
nce bu
i
ld
commit
|
commitdiff
|
tree
2016-07-30
Vedran
M
ilet
i
ć
Document
gmx_cgsort_t
and gmx_domdec_sort_t structs
commit
|
commitdiff
|
tree
2016-07-09
Erik Lindahl
Prevent fragile use
c
a
ses of chec
k
p
o
int ap
p
en
d
ing
commit
|
commitdiff
|
tree
2016-07-08
Erik Lindahl
Update
affin
i
ty checking for Intel co
m
piler
commit
|
commitdiff
|
tree
2016-07-08
Erik Lindahl
Work aro
u
nd compiler
i
s
sue with random test
commit
|
commitdiff
|
tree
2016-07-08
Szi
l
árd Páll
A
d
d
P
DF
m
e
tadata t
o
the manual
commit
|
commitdiff
|
tree
2016-07-07
Eri
k
Lindah
l
Reduc
e
h
wloc
&
c
puid test requirements
commit
|
commitdiff
|
tree
2016-07-07
Teemu Murtola
Change
h
a
n
d
ling for m
i
s
sin
g
r
eleng
d
ocs
commit
|
commitdiff
|
tree
next