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Add grompp check for pull group
2015-08-13
B
erk Hess
A
d
d
ed set_pull_coo
r
d_reference_va
l
ue
commit
|
commitdiff
|
tree
2015-08-12
Berk H
e
ss
A
d
ded const quali
f
iers to core
M
D routines
commit
|
commitdiff
|
tree
2015-07-08
Berk H
e
ss
Sepa
r
ated bonded and Ewald corre
c
t
ion threading
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fix too
sma
l
l GPU pair count estimates
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fix
bug i
n
GPU list balancing
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
Fix DD D
L
B
state issue
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
Fix bug in GPU list balancing
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
O
bey OpenMP thread co
u
nt l
i
m
i
t
with tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
F
ix two
P
ME DLB
t
rigger issues
commit
|
commitdiff
|
tree
2015-07-03
Berk Hess
Correct grompp pu
l
l
warning message
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Fix inconsistent OpenMP automa
t
i
o
n
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
enab
l
ed 1 PP + 1
P
ME node
commit
|
commitdiff
|
tree
2015-06-30
B
erk Hess
Add
c
hecks
f
or ine
f
f
icient resource usag
e
commit
|
commitdiff
|
tree
2015-06-29
Berk He
s
s
Improve DLB+
P
ME tuning wit
h
GPU
s
commit
|
commitdiff
|
tree
2015-06-27
Berk
H
ess
Impr
o
ve pai
r
search thread
lo
a
d ba
l
a
nce
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Improved the intra
-
GPU load balancing
commit
|
commitdiff
|
tree
2015-06-27
B
erk Hess
Reduce the use
of nbnxn_consts
.
h
commit
|
commitdiff
|
tree
2015-06-27
B
erk Hess
Corrected nstcalclr
/
n
stfe
p
/nst_repl_ex checks
commit
|
commitdiff
|
tree
2015-06-26
Berk
Hess
Fixed Verlet
buf
f
er issue with 2-w
i
de SIMD
commit
|
commitdiff
|
tree
2015-06-25
Berk
H
ess
Intermolecul
a
r b
o
nded
interact
i
o
n support a
d
ded
commit
|
commitdiff
|
tree
2015-06-25
Be
r
k Hess
Reenabled
S
IMD kerne
l
s without cut-offs
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
GPU Ew
a
ld t
a
ble kernel now uses
C
P
U
spacing
commit
|
commitdiff
|
tree
2015-06-24
Berk
H
ess
Avoi
d
GPU
s
el
e
ction with GPU
e
mulat
i
on
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Minor reformattin
g
of SIMD mismatch messa
g
e
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
A
d
d
sugar t
o
p
r
int
e
m
pty
l
i
ne in printBinaryInformati
o
n
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Fix g_energy average/RMSD b
u
g
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
U
p
date
l
aunch
c
onfiguratio
n
for physical nodes
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Avoid fp exc
e
ptions in pair
s
ear
c
h de
b
ug
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Replaced
ha
r
d
w
are t
h
reads by lo
g
ical cor
e
s
in output
commit
|
commitdiff
|
tree
2015-06-18
Ber
k
Hess
Reduced the cost of the pull
c
ommunication
commit
|
commitdiff
|
tree
2015-06-17
Berk Hess
R
efac
t
or
e
d p
u
l
l data structures
commit
|
commitdiff
|
tree
2015-06-16
B
erk
H
e
ss
Added mis
s
in
g
DD cycle counting
commit
|
commitdiff
|
tree
2015-06-16
Berk H
e
ss
A
utomated t
h
e -
g
p
u
_id opti
o
n
commit
|
commitdiff
|
tree
2015-06-14
Berk He
s
s
R
ef
a
ctored mdrun reso
u
rce division
commit
|
commitdiff
|
tree
2015-06-13
Be
r
k
Hes
s
Hard
w
ar
e
report
i
ng n
o
w
covers all
n
odes
commit
|
commitdiff
|
tree
2015-06-05
B
erk He
s
s
Do
n
't use PME ranks with GPUs and -npm
e
=
-1
commit
|
commitdiff
|
tree
2015-05-27
B
e
r
k Hess
R
e
factoring of PME load
b
alanci
n
g
commit
|
commitdiff
|
tree
2015-05-23
Berk Hess
R
e
mov
e
d static from var
i
abl
e
s in gmx_
l
apack
commit
|
commitdiff
|
tree
2015-05-16
Berk
Hess
LINCS thread tasks c
a
n now be independent
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fixed CUDA
err
o
r with empty domains
commit
|
commitdiff
|
tree
2015-05-13
Berk
Hess
Fix segv in g_covar
commit
|
commitdiff
|
tree
2015-05-11
Berk Hess
Changed FFTW
w
arning from AVX
t
o no S
S
E
commit
|
commitdiff
|
tree
2015-05-07
B
e
r
k H
e
ss
Rem
o
v
ed no
n
-ff atomtypes from oplsaa and ch
a
rmm
2
7
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fixed
GP
U
n
o
n-loc
a
l F
copy local cond
i
tional
commit
|
commitdiff
|
tree
2015-04-28
Be
r
k Hess
Re-en
a
bled FMA for AVX-128-FMA
commit
|
commitdiff
|
tree
2015-04-22
Berk Hes
s
Merge branch 're
l
ease-5-0'
commit
|
commitdiff
|
tree
2015-04-17
Berk Hess
Ad
d
value_ref and valu
e
to pull_coord_t
commit
|
commitdiff
|
tree
2015-04-17
Berk
H
ess
C
o
rr
e
ct -ntmpi auto for int
e
l nehalem and o
l
d
e
r
commit
|
commitdiff
|
tree
2015-04-08
Be
r
k Hess
Adde
d
pull
g
eometry
direct
i
o
n-rela
t
ive
commit
|
commitdiff
|
tree
2015-04-01
Ber
k
Hess
Co
r
re
c
ted force-swi
t
ch manual
s
ec
t
ion
commit
|
commitdiff
|
tree
2015-03-19
B
e
r
k Hess
R
e
moved reduction of dH/dl without FE
commit
|
commitdiff
|
tree
2015-03-12
Berk Hes
s
Fixed m
d
r
u
n fp exc
e
ption wit
h
-d
e
bug
commit
|
commitdiff
|
tree
2015-03-11
Berk
H
e
s
s
Added update x
c
opy-back
to
update timer
commit
|
commitdiff
|
tree
2015-03-11
B
e
r
k
Hes
s
Re
d
u
c
ed
cost of Berendsen pressure c
o
up
l
ing
commit
|
commitdiff
|
tree
2015-03-06
B
e
rk
Hess
I
m
p
rove
t
hreadin
g
of
b
ondeds
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
Made D
D
exc
l
usion process
i
ng more efficient
commit
|
commitdiff
|
tree
2015-03-05
Ber
k
Hess
SI
M
D acceleration for LI
N
CS
commit
|
commitdiff
|
tree
2015-03-04
Berk He
s
s
Allow pull groups
o
f 1 atom with m
a
ss 0
commit
|
commitdiff
|
tree
2015-03-04
Berk Hess
COM pul
l
ing opti
o
ns
per coor
d
,
i
m
p
rove
d
cylin
d
er
commit
|
commitdiff
|
tree
2015-03-03
Berk
Hess
Fix div by
z
e
ro in PP/PME r
a
tio
commit
|
commitdiff
|
tree
2015-03-02
Berk H
e
s
s
Ad
d
ed paren
t
h
e
ses for c
a
sts in
S
IMD mac
r
os
commit
|
commitdiff
|
tree
2015-02-24
Ber
k
Hess
Fixed parallel dis
t
ribution and thread co
u
nt re
p
orting
commit
|
commitdiff
|
tree
2015-02-12
Berk H
e
ss
R
e-fixed PME bug with
h
i
gh OpenMP th
r
ead count
commit
|
commitdiff
|
tree
2015-02-06
Berk Hess
Re-enable
d
SIMD fo
r
an
g
l
es and d
i
hedrals
commit
|
commitdiff
|
tree
2015-02-04
Berk Hess
Correct CUDA kernel
e
nergy fla
g
commit
|
commitdiff
|
tree
2015-01-21
Berk Hess
Corrected
R
DT
S
CP warning
t
ext
commit
|
commitdiff
|
tree
2015-01-15
Berk Hess
Fix allocation issue with VV integra
t
or
commit
|
commitdiff
|
tree
2014-12-22
B
erk Hes
s
F
ixed pbc=xy + 2 walls + Verlet scheme
commit
|
commitdiff
|
tree
2014-12-22
Ber
k
Hess
Fix bug FE
+ G
P
U + 2/3D d
o
m
a
in d
e
compo
s
ition
commit
|
commitdiff
|
tree
2014-12-11
B
e
r
k
H
e
ss
Added
g
r
ompp erro
r
for pullin
g
to
negat
i
ve di
s
tance
commit
|
commitdiff
|
tree
2014-12-09
Berk Hess
Fix re
c
ent bug
w
ith trilinic 1D
D
D
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Fixed pull coord init with r
a
te!=0, t_start!=0
commit
|
commitdiff
|
tree
2014-12-08
Be
r
k H
e
ss
Added
PBC note
t
o comm
-
mode=angul
a
r warning
commit
|
commitdiff
|
tree
2014-12-05
B
e
rk Hess
Make domdec a proper mod
u
le
commit
|
commitdiff
|
tree
2014-12-05
Berk Hes
s
Clar
i
fi
e
d grompp p
u
ll error messag
e
s
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
A
v
oid race on dvdl w
i
t
h
Verlet+OpenMP+LINCS+F
E
+
V
V
commit
|
commitdiff
|
tree
2014-12-01
Berk Hess
Added warni
n
g
f
o
r
unnecessa
r
y soft-core
commit
|
commitdiff
|
tree
2014-11-26
Ber
k
Hess
Fixed triclinic 1xNx1 dom
a
in de
c
ompositi
o
n
commit
|
commitdiff
|
tree
2014-11-25
Berk Hess
Fixed twin-ran
g
e +
f
reeze
+
co
n
strain
t
s
commit
|
commitdiff
|
tree
2014-11-24
Ber
k
Hess
Avoid NaN in rlist
buffer c
a
lcu
l
a
tio
n
commit
|
commitdiff
|
tree
2014-11-12
B
erk He
s
s
Corr
e
cted parameter for
s
orting on
search grid
commit
|
commitdiff
|
tree
2014-11-12
Berk
H
ess
Fix DD
b
onded in
t
eraction range
p
rint
commit
|
commitdiff
|
tree
2014-10-20
Ber
k
He
s
s
R
e
moved
f_novi
r
sum re
d
uction in V
e
rlet scheme
commit
|
commitdiff
|
tree
2014-10-07
Berk Hes
s
Fixes issue with vsiten
a
n
d V
e
rl
e
t buffe
r
s
commit
|
commitdiff
|
tree
2014-09-30
Berk Hess
Avoid DLB w
i
th o
v
erload
e
d P
M
E ran
k
s
commit
|
commitdiff
|
tree
2014-09-30
Berk Hess
Added GPU local w
a
it to load bala
n
cing
commit
|
commitdiff
|
tree
2014-09-29
Be
r
k He
s
s
Domain
decom
p
osi
t
ion now chec
k
s the
r
list buffer
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
SIMD
a
cc
e
leration for RB dihedrals
commit
|
commitdiff
|
tree
2014-09-29
Be
r
k
Hess
Avoid
PME tunin
g
decreas
i
ng rcoulom
b
commit
|
commitdiff
|
tree
2014-09-29
Ber
k
Hes
s
Fix
c
alc_grid avoiding PME grid
f
a
ctor 84
commit
|
commitdiff
|
tree
2014-09-09
Ber
k
Hess
Fi
x
e
d
DD sta
t
e collec
t
ion issue
commit
|
commitdiff
|
tree
2014-09-08
Berk Hess
Check for implic
i
t solv
e
nt + Verlet
s
cheme
commit
|
commitdiff
|
tree
2014-08-28
Be
r
k
Hess
Fixed two PME i
s
sues with
M
PI+OpenMP
commit
|
commitdiff
|
tree
2014-08-25
Berk Hess
Fixed bugs in vs
i
teN with OpenMP
commit
|
commitdiff
|
tree
2014-08-24
Berk Hess
Initialize unused velocity con
s
traint compo
n
ents
commit
|
commitdiff
|
tree
2014-08-17
Berk H
e
ss
Halved the cost of the
pul
l
communicati
o
n
commit
|
commitdiff
|
tree
2014-08-14
B
erk Hess
Corrected SIMD
m
ath ove
r
flow documenta
t
ion
commit
|
commitdiff
|
tree
2014-08-10
Berk H
e
ss
Added checks
f
o
r
TP
I
+
Verl
e
t
s
cheme
commit
|
commitdiff
|
tree
2014-08-05
Berk H
e
ss
Fix
h
ang with LJ-
P
ME and
empty domains
commit
|
commitdiff
|
tree
2014-08-02
Berk Hess
F
i
xed
PME bug wit
h
hig
h
OpenMP threa
d
count
commit
|
commitdiff
|
tree
next