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Minor reformatting of SIMD mismatch message
2015-06-24
Berk
H
ess
Mi
n
or reformatting of S
I
MD mism
a
tch message
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Add sugar to prin
t
e
m
pty line in printBi
n
aryInf
o
rmation
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Up
d
ate launch co
n
figuration for phy
s
ical
nodes
commit
|
commitdiff
|
tree
2015-06-22
B
er
k
Hess
Avoid
f
p
e
x
ceptions
i
n
p
a
ir search
debug
commit
|
commitdiff
|
tree
2015-06-22
Berk He
s
s
Re
p
laced hard
w
are threa
d
s by logica
l
c
ores in output
commit
|
commitdiff
|
tree
2015-06-18
Berk Hess
Reduced
th
e
c
o
st of
t
h
e
pu
l
l
c
o
mmuni
c
ation
commit
|
commitdiff
|
tree
2015-06-17
Berk Hes
s
R
efactore
d
pull da
t
a structures
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Added m
i
ssing DD cycle count
i
ng
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Automate
d
th
e
-gpu_id
o
pt
i
on
commit
|
commitdiff
|
tree
2015-06-14
Berk
Hess
Refactore
d
mdrun resource div
i
s
i
on
commit
|
commitdiff
|
tree
2015-06-13
B
e
rk
H
ess
Hardware reporting now cove
r
s
a
ll nodes
commit
|
commitdiff
|
tree
2015-06-05
Berk Hess
Don't
use PME ran
k
s with G
P
Us
a
nd -n
p
me
=
-
1
commit
|
commitdiff
|
tree
2015-05-27
Berk Hess
Re
f
actoring of PME load
b
al
a
ncing
commit
|
commitdiff
|
tree
2015-05-23
B
e
rk Hess
Removed static from variables in
gm
x
_lapack
commit
|
commitdiff
|
tree
2015-05-16
Berk Hess
LINCS thread
t
a
sk
s
can
n
ow
b
e
in
d
ependent
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
F
i
x
e
d CUD
A
err
o
r with empty do
m
ains
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fix segv in
g
_co
v
ar
commit
|
commitdiff
|
tree
2015-05-11
Berk Hess
Changed
FFTW
w
arnin
g
fro
m
A
V
X
to no SSE
commit
|
commitdiff
|
tree
2015-05-07
Berk He
s
s
Removed n
o
n-ff atomtyp
e
s f
r
om op
l
s
aa an
d
charm
m
2
7
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fi
x
ed GPU n
o
n-local F cop
y
local
conditional
commit
|
commitdiff
|
tree
2015-04-28
Berk He
s
s
Re-enabled FMA for AVX-128-FMA
commit
|
commitdiff
|
tree
2015-04-22
B
erk He
s
s
Merge branch 'releas
e
-5
-
0'
commit
|
commitdiff
|
tree
2015-04-17
Berk Hes
s
Add value_ref and va
l
ue to pull_coord_t
commit
|
commitdiff
|
tree
2015-04-17
B
erk Hes
s
Correct
-
nt
m
pi auto for int
e
l
n
e
halem and
o
lder
commit
|
commitdiff
|
tree
2015-04-08
B
e
rk Hes
s
Adde
d
pull ge
o
metr
y
direction
-
rel
a
t
i
ve
commit
|
commitdiff
|
tree
2015-04-01
Berk
H
e
s
s
Co
r
rected for
c
e-swi
t
c
h
manual
sec
t
ion
commit
|
commitdiff
|
tree
2015-03-19
Berk Hess
Remo
v
ed r
e
d
uction of dH/dl
w
ithout FE
commit
|
commitdiff
|
tree
2015-03-12
Berk Hess
Fi
x
ed mdru
n
fp exception wit
h
-debug
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Added update x co
p
y-back to update timer
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Reduced c
o
st
of Berendsen pressure co
u
pling
commit
|
commitdiff
|
tree
2015-03-06
Berk
He
s
s
Im
p
rove th
r
eading of b
o
ndeds
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
Made
DD exclusion processin
g
more
e
fficient
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
SI
M
D acceleration for LINCS
commit
|
commitdiff
|
tree
2015-03-04
Berk Hess
Allow pull g
r
oup
s
of 1 atom wi
t
h mass 0
commit
|
commitdiff
|
tree
2015-03-04
Be
r
k He
s
s
COM
p
ull
i
ng
o
ptions
pe
r
coord,
i
mpr
o
v
ed
c
ylinder
commit
|
commitdiff
|
tree
2015-03-03
Berk Hess
Fix div by zero in
P
P/PME
ratio
commit
|
commitdiff
|
tree
2015-03-02
B
e
rk
Hess
Added parenthese
s
for casts in SIMD
m
a
c
ros
commit
|
commitdiff
|
tree
2015-02-24
Berk Hess
Fi
x
ed
parallel
d
i
stribution and thr
e
ad c
o
unt
r
eport
i
ng
commit
|
commitdiff
|
tree
2015-02-12
Berk Hes
s
Re-fixed PME bu
g
w
ith high OpenMP
t
hre
a
d c
o
unt
commit
|
commitdiff
|
tree
2015-02-06
Berk Hess
Re-enab
l
e
d
S
I
M
D for angles and
d
ihedrals
commit
|
commitdiff
|
tree
2015-02-04
Berk Hess
Correct CUDA kernel energy flag
commit
|
commitdiff
|
tree
2015-01-21
Berk Hess
C
orrected RDTSCP
w
a
rning text
commit
|
commitdiff
|
tree
2015-01-15
Berk Hess
Fix allo
c
ation i
s
sue with VV integ
r
ator
commit
|
commitdiff
|
tree
2014-12-22
Berk Hess
Fixed pbc=xy + 2 walls + Verlet
s
che
m
e
commit
|
commitdiff
|
tree
2014-12-22
Berk Hes
s
Fix
b
ug FE + GPU + 2/3D domain decomposition
commit
|
commitdiff
|
tree
2014-12-11
Berk
H
ess
Added
grompp
error fo
r
pulling to negative distance
commit
|
commitdiff
|
tree
2014-12-09
Berk Hess
Fix recent
bug wit
h
trilinic 1D DD
commit
|
commitdiff
|
tree
2014-12-08
Ber
k
H
ess
Fi
x
ed pu
l
l
c
oord init with ra
t
e!=0, t_start!=0
commit
|
commitdiff
|
tree
2014-12-08
Ber
k
Hess
Added
PBC note to c
o
mm-mode=angular warning
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Make domdec a proper
m
o
dule
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Clarifi
e
d
grompp pull
error
m
essages
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Avoid race on dvdl
w
i
t
h Ver
l
et
+
OpenMP+LINC
S
+FE
+
VV
commit
|
commitdiff
|
tree
2014-12-01
B
erk Hess
A
d
ded warning fo
r
unnec
e
s
sary so
f
t-
c
or
e
commit
|
commitdiff
|
tree
2014-11-26
Berk Hess
Fix
e
d tri
c
linic 1xNx1 d
o
main decomposition
commit
|
commitdiff
|
tree
2014-11-25
Berk
Hess
Fixed twin-range +
fre
e
ze +
c
onstrain
t
s
commit
|
commitdiff
|
tree
2014-11-24
Be
r
k Hess
Avoid
N
a
N
in rlist buffer c
a
lculation
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
Corrected p
a
ram
e
t
e
r
for sorting
o
n
search gr
i
d
commit
|
commitdiff
|
tree
2014-11-12
Ber
k
H
ess
F
i
x DD bonded
interaction
range print
commit
|
commitdiff
|
tree
2014-10-20
Berk Hess
Remo
v
ed
f
_novirsum re
d
ucti
o
n in Verle
t
schem
e
commit
|
commitdiff
|
tree
2014-10-07
Berk
Hess
Fi
x
es is
s
ue with vsiten and Verl
e
t b
u
f
f
ers
commit
|
commitdiff
|
tree
2014-09-30
Berk He
s
s
Avoid DLB with
o
verl
o
ad
e
d PME ranks
commit
|
commitdiff
|
tree
2014-09-30
Be
r
k Hess
Added G
P
U l
o
cal w
a
i
t to l
o
ad b
a
lancing
commit
|
commitdiff
|
tree
2014-09-29
Berk Hes
s
Domain decompos
i
tio
n
n
o
w
c
h
ecks t
h
e rl
i
st buffer
commit
|
commitdiff
|
tree
2014-09-29
B
er
k
H
e
ss
SIMD acc
e
lera
t
ion f
o
r RB dihedra
l
s
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
A
voi
d
P
M
E
tuning decreasing rco
u
lomb
commit
|
commitdiff
|
tree
2014-09-29
Berk
H
ess
Fix calc_grid avoid
i
n
g
PME
g
ri
d
f
a
c
t
or
8
4
commit
|
commitdiff
|
tree
2014-09-09
Berk Hes
s
Fixed DD sta
t
e collec
t
io
n
issue
commit
|
commitdiff
|
tree
2014-09-08
B
e
rk H
e
ss
Check for im
p
lici
t
s
o
l
v
ent + Verl
e
t
scheme
commit
|
commitdiff
|
tree
2014-08-28
Berk Hess
Fix
e
d
t
wo PM
E
issues
with MPI+O
p
e
nMP
commit
|
commitdiff
|
tree
2014-08-25
Berk
H
es
s
F
i
xed bug
s
in vsit
e
N
w
ith OpenMP
commit
|
commitdiff
|
tree
2014-08-24
Berk Hess
Initialize unused velo
c
ity constrai
n
t components
commit
|
commitdiff
|
tree
2014-08-17
Berk Hess
Halved
the
c
ost of the pull communicatio
n
commit
|
commitdiff
|
tree
2014-08-14
Berk Hess
Corrected SIMD math
o
ver
f
low documentation
commit
|
commitdiff
|
tree
2014-08-10
Berk
Hess
Added check
s
f
or T
P
I + Verlet scheme
commit
|
commitdiff
|
tree
2014-08-05
Berk Hess
Fix hang with
L
J-PME and empty domains
commit
|
commitdiff
|
tree
2014-08-02
Berk Hess
Fi
x
ed PME bu
g
w
ith high Ope
n
MP
t
hre
a
d co
u
nt
commit
|
commitdiff
|
tree
2014-07-31
Berk Hess
A
v
oid
d
ivision
b
y 0
in nbnxn_s
e
arch
commit
|
commitdiff
|
tree
2014-06-29
Berk He
s
s
T
a
ke
LJ-PME into account for table spacing
commit
|
commitdiff
|
tree
2014-06-29
Berk
H
e
ss
Updated LJ-PME
d
o
cumentat
i
on
commit
|
commitdiff
|
tree
2014-06-24
Berk Hess
Fixe
d
the
s
ign of mass pe
r
t
u
rbed cont
r
ibution
commit
|
commitdiff
|
tree
2014-06-20
B
e
rk Hess
Fix g_m
i
nd
i
st
w
ith pbc=
X
Y
commit
|
commitdiff
|
tree
2014-06-20
B
erk Hess
F
i
x
ed shells
w
i
t
h particle de
c
ompo
s
ition
commit
|
commitdiff
|
tree
2014-06-18
Be
r
k He
s
s
Fixed sign
e
rror
i
n posres d
v
dl
commit
|
commitdiff
|
tree
2014-06-17
B
e
rk Hess
U
p
da
t
ed md
r
un -npme documentation
commit
|
commitdiff
|
tree
2014-06-17
Berk Hess
Remo
v
ed
rounding issu
e
in nbnxn Ewa
l
d t
a
ble
commit
|
commitdiff
|
tree
2014-06-14
Berk Hess
F
ixed PME bug with #OpenMP-threads
a large prime
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
Changed a
p
pending
f
i
l
e name error message
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
Made s
h
ells
w
ork wit
h
the Verlet scheme
commit
|
commitdiff
|
tree
2014-06-12
Be
r
k Hess
Fixed perturbed
wal
l
inte
r
actions
commit
|
commitdiff
|
tree
2014-06-12
B
e
rk
Hess
Made gmxcheck -r
m
sd
w
ork ag
a
i
n
wit
h
forces
commit
|
commitdiff
|
tree
2014-06-11
Berk He
s
s
Decoupled repl
_
e
x_nst from nstcalcenergy
commit
|
commitdiff
|
tree
2014-06-11
Berk Hess
Made repl
_
ex time step more read
a
ble
commit
|
commitdiff
|
tree
2014-06-10
B
e
r
k Hess
Re
p
laced gmx_hostname_
n
um by gmx_physicaln
o
de_id_h
a
s
h
commit
|
commitdiff
|
tree
2014-06-09
Berk Hess
Set make_ndx max n
a
me
leng
t
h and
coun
t
to
10
2
4
commit
|
commitdiff
|
tree
2014-06-05
Berk He
s
s
Fixed shift and sw
i
tch modifiers, particularly
for
.
.
.
commit
|
commitdiff
|
tree
2014-06-05
Berk Hess
F
ix c
o
nstraint virial
with multiple tim
e
steppi
n
g
commit
|
commitdiff
|
tree
2014-06-02
Berk Hess
Fixed g_ene
r
gy Einst
e
in viscosity
commit
|
commitdiff
|
tree
2014-05-22
B
e
r
k
He
s
s
Avo
i
d
energy drift w
i
th verlet-
b
uffer-t
o
lera
n
ce
commit
|
commitdiff
|
tree
2014-05-09
Berk Hess
Min
o
r tweaks to
t
he DD setup
commit
|
commitdiff
|
tree
2014-04-29
Ber
k
H
e
ss
Removed tru
n
cation of nrdf in v-rescale t
h
ermostat
commit
|
commitdiff
|
tree
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