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Correct vector check of gmx check
2015-12-29
Berk Hess
Corr
e
ct ve
c
tor c
h
eck of
g
mx check
commit
|
commitdiff
|
tree
2015-12-19
Berk
He
s
s
Bring performan
c
e estimation up to date
commit
|
commitdiff
|
tree
2015-12-11
B
erk H
e
ss
Fix bug wi
t
h
p
u
ll group weights
commit
|
commitdiff
|
tree
2015-11-19
B
e
rk Hes
s
Removed
m
drun fata
l
_
erro
r
w
i
th
P3
M
-AD
commit
|
commitdiff
|
tree
2015-11-09
Berk Hess
Correct
L
IN
C
S dHd
l
c
o
ntribution
commit
|
commitdiff
|
tree
2015-11-02
Be
r
k Hess
Fix intermolecul
a
r in
t
eractions wit
h
small mols
commit
|
commitdiff
|
tree
2015-10-15
Ber
k
Hes
s
Fixe
d
nbnxn_4xN p
e
rfor
m
an
c
e regression
commit
|
commitdiff
|
tree
2015-10-07
Ber
k
H
ess
Fix bugs w
i
th in
t
ermol i
n
teractions
and DD
commit
|
commitdiff
|
tree
2015-09-15
Berk Hess
D
e
tect
i
n
c
o
rrect cycle cou
n
ti
n
g
commit
|
commitdiff
|
tree
2015-08-14
Berk Hess
Make md
r
un -nt w
o
r
k
again
commit
|
commitdiff
|
tree
2015-07-06
B
erk Hess
F
i
x too small GPU pair cou
n
t estimates
commit
|
commitdiff
|
tree
2015-07-06
Be
r
k He
s
s
F
i
x b
u
g
in GPU li
s
t balan
c
i
n
g
commit
|
commitdiff
|
tree
2015-07-05
Be
r
k Hess
Fix DD
DLB state issue
commit
|
commitdiff
|
tree
2015-07-05
Be
r
k Hess
Fix
b
ug in
G
PU list balan
c
i
n
g
commit
|
commitdiff
|
tree
2015-07-04
B
e
rk Hes
s
Obey O
p
enMP thread co
u
nt
l
imit with tMP
I
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
Fix two
PM
E
DLB t
r
igger issues
commit
|
commitdiff
|
tree
2015-07-03
Berk
H
e
s
s
Correct gr
o
mpp pull warning
m
ess
a
g
e
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Fix i
n
consistent
OpenMP
au
t
omation
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
enable
d
1 PP + 1 PM
E
node
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Add checks for ine
f
ficient
r
esourc
e
u
sage
commit
|
commitdiff
|
tree
2015-06-29
B
erk
H
e
s
s
Imp
r
ove DLB+PME tu
n
i
n
g with GPUs
commit
|
commitdiff
|
tree
2015-06-27
Berk H
e
ss
Improve p
a
ir se
a
rch thread
l
o
a
d balanc
e
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Improve
d
th
e
in
t
ra-GPU l
o
ad balancing
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Re
d
u
c
e the use of nb
n
xn_
c
o
n
s
t
s
.
h
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Corrected nstcalclr/nstfep/nst_
r
epl_
e
x checks
commit
|
commitdiff
|
tree
2015-06-26
Berk Hess
Fixed Verlet buffer is
s
ue with 2-wide SI
M
D
commit
|
commitdiff
|
tree
2015-06-25
B
er
k
Hess
Int
e
r
mo
l
e
cular bonde
d
i
n
teraction
sup
p
ort added
commit
|
commitdiff
|
tree
2015-06-25
B
erk
H
ess
Reenabled SIMD kernels without cut-offs
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
GPU Ewald tabl
e
kernel now uses CPU spacing
commit
|
commitdiff
|
tree
2015-06-24
Berk
H
ess
Avoi
d
GPU
s
e
lection with GPU emula
t
ion
commit
|
commitdiff
|
tree
2015-06-24
B
erk Hess
Minor r
e
formatting
o
f
SIMD mismatch
m
es
s
ag
e
commit
|
commitdiff
|
tree
2015-06-24
Be
r
k He
s
s
Add sugar to pri
n
t empty li
n
e i
n
printBinary
I
nformation
commit
|
commitdiff
|
tree
2015-06-22
Ber
k
Hess
F
ix g_
e
nergy
av
e
rage
/
RMSD bug
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Upda
t
e
l
aunch
configuratio
n
for physical nodes
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Avoid fp ex
c
eptions in pai
r
s
e
arch
debug
commit
|
commitdiff
|
tree
2015-06-22
Ber
k
Hess
Replace
d
hardware
thr
e
ads
by
logical cores in ou
t
put
commit
|
commitdiff
|
tree
2015-06-18
Be
r
k Hess
Redu
c
e
d
t
h
e cost
o
f t
h
e
pull
c
ommunicat
i
on
commit
|
commitdiff
|
tree
2015-06-17
Berk
H
e
ss
Refactored pull data structures
commit
|
commitdiff
|
tree
2015-06-16
B
erk Hess
Added missing DD c
y
cle counting
commit
|
commitdiff
|
tree
2015-06-16
Berk He
s
s
Automated
t
he -gpu_id
op
t
ion
commit
|
commitdiff
|
tree
2015-06-14
Berk Hess
Refactored m
d
run r
e
source
division
commit
|
commitdiff
|
tree
2015-06-13
Berk Hess
H
a
rdware reporti
n
g now
c
ove
r
s a
l
l nodes
commit
|
commitdiff
|
tree
2015-06-05
Berk He
s
s
Don't use PME ra
n
k
s
wi
t
h GPUs and -npme=-1
commit
|
commitdiff
|
tree
2015-05-27
B
erk Hess
Refactor
i
ng
of PME load
balancing
commit
|
commitdiff
|
tree
2015-05-23
Berk Hess
Removed static fro
m
va
r
iabl
e
s in
g
m
x
_
lapack
commit
|
commitdiff
|
tree
2015-05-16
Berk He
s
s
LIN
C
S thread tas
k
s c
a
n now be independent
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fi
x
e
d
CUDA
e
r
r
o
r with
emp
t
y
d
om
a
ins
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
F
i
x
segv
in
g
_covar
commit
|
commitdiff
|
tree
2015-05-11
Berk Hess
C
h
ang
e
d
FFTW warning fr
o
m AVX to no SSE
commit
|
commitdiff
|
tree
2015-05-07
B
e
r
k
H
ess
Remove
d
non-ff atomty
p
es
fro
m
oplsaa and charmm27
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fi
x
e
d
GPU no
n
-loc
a
l F copy l
o
cal
con
d
itional
commit
|
commitdiff
|
tree
2015-04-28
B
erk Hess
Re-
e
nabled FMA f
o
r AVX-128-
F
MA
commit
|
commitdiff
|
tree
2015-04-22
Berk H
e
ss
Merge branc
h
'relea
s
e
-5-0'
commit
|
commitdiff
|
tree
2015-04-17
Berk Hess
Ad
d
value_
r
ef
and v
a
l
ue to pull_coord_t
commit
|
commitdiff
|
tree
2015-04-17
Berk
H
ess
Correct -nt
m
pi auto for intel
n
e
ha
l
em and older
commit
|
commitdiff
|
tree
2015-04-08
Berk Hess
A
dded pull geomet
r
y direction
-
relative
commit
|
commitdiff
|
tree
2015-04-01
Berk Hess
Corrected force-swit
c
h manu
a
l
sec
t
ion
commit
|
commitdiff
|
tree
2015-03-19
Berk Hess
Removed r
e
duction of d
H
/
d
l without FE
commit
|
commitdiff
|
tree
2015-03-12
Berk Hess
F
ixed m
d
run fp exc
e
p
t
ion with -
d
e
b
ug
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
A
dd
e
d upda
t
e x
cop
y
-back
t
o update t
i
mer
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Reduced c
o
st of Beren
d
s
e
n
pressure coupling
commit
|
commitdiff
|
tree
2015-03-06
Berk Hess
Improve threading of b
o
ndeds
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
M
a
d
e DD
exclus
i
on processing more efficient
commit
|
commitdiff
|
tree
2015-03-05
Ber
k
Hess
SIM
D
acceleratio
n
f
o
r LI
N
C
S
commit
|
commitdiff
|
tree
2015-03-04
Berk H
e
ss
Allow pul
l
groups of
1
atom
w
i
th
m
ass 0
commit
|
commitdiff
|
tree
2015-03-04
Ber
k
Hess
COM
pulling options per coord, i
m
proved cylinder
commit
|
commitdiff
|
tree
2015-03-03
B
e
rk
H
ess
Fix div by zer
o
in PP/
P
ME ratio
commit
|
commitdiff
|
tree
2015-03-02
Berk Hess
Added
parentheses for
casts in SIM
D
m
acros
commit
|
commitdiff
|
tree
2015-02-24
B
erk Hess
Fixed parallel dist
r
ibution an
d
thread count re
p
orting
commit
|
commitdiff
|
tree
2015-02-12
Berk Hess
Re-f
i
xed
P
ME
b
u
g wit
h
high OpenM
P
thre
a
d coun
t
commit
|
commitdiff
|
tree
2015-02-06
Berk H
e
ss
Re-enabled S
I
M
D fo
r
a
n
gles
a
nd d
i
hedra
l
s
commit
|
commitdiff
|
tree
2015-02-04
Berk Hess
Correct CU
D
A
kernel e
n
e
r
gy flag
commit
|
commitdiff
|
tree
2015-01-21
Berk Hess
Correc
t
ed RDTSCP warning text
commit
|
commitdiff
|
tree
2015-01-15
Berk H
e
s
s
Fix all
o
ca
t
ion issue with VV
integ
r
ator
commit
|
commitdiff
|
tree
2014-12-22
Berk Hess
Fixed
p
b
c
=xy + 2 walls + Verlet
scheme
commit
|
commitdiff
|
tree
2014-12-22
Berk H
e
ss
Fix b
u
g
F
E + G
P
U + 2
/
3D domain decom
p
ositio
n
commit
|
commitdiff
|
tree
2014-12-11
Berk He
s
s
Added grompp e
r
ror f
o
r pulling to negative distance
commit
|
commitdiff
|
tree
2014-12-09
Ber
k
Hess
F
i
x recent
bug with trilinic 1D DD
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Fixed pull coord init with rate
!
=0, t_start!=0
commit
|
commitdiff
|
tree
2014-12-08
Berk
H
ess
Added
PBC note
t
o comm
-
mode=
a
ngular warning
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Make domdec a
proper modul
e
commit
|
commitdiff
|
tree
2014-12-05
Be
r
k
H
ess
Clarified grompp pull error messa
g
e
s
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Avoid race on dvdl wit
h
Verlet+OpenMP
+
LINCS+
F
E+VV
commit
|
commitdiff
|
tree
2014-12-01
Be
r
k Hess
A
dded warning f
o
r
u
nnecessary
s
of
t
-core
commit
|
commitdiff
|
tree
2014-11-26
Berk Hess
F
ixed triclini
c
1
x
Nx1 d
o
mai
n
deco
m
position
commit
|
commitdiff
|
tree
2014-11-25
Berk Hess
Fixed twin-range + f
r
eeze + constr
a
ints
commit
|
commitdiff
|
tree
2014-11-24
Be
r
k H
e
ss
Avoid NaN in rlist buf
f
er calculation
commit
|
commitdiff
|
tree
2014-11-12
B
e
rk He
s
s
C
o
rrect
e
d
p
arameter for sorting on search grid
commit
|
commitdiff
|
tree
2014-11-12
B
e
rk Hess
Fi
x
DD bonded
i
nteract
i
on r
a
n
ge pr
i
nt
commit
|
commitdiff
|
tree
2014-10-20
B
e
rk
Hes
s
Removed f_novirsum re
d
u
c
tion in Verlet scheme
commit
|
commitdiff
|
tree
2014-10-07
Berk Hess
Fixes
issue with vs
i
ten and Verlet buffers
commit
|
commitdiff
|
tree
2014-09-30
B
erk Hess
Avoid DLB w
i
t
h
overloa
d
e
d
PME ranks
commit
|
commitdiff
|
tree
2014-09-30
B
e
rk Hess
Added GP
U
local wait to loa
d
balanci
n
g
commit
|
commitdiff
|
tree
2014-09-29
B
e
r
k Hess
D
o
main d
e
composition now chec
k
s the rli
s
t buffer
commit
|
commitdiff
|
tree
2014-09-29
Berk H
e
ss
SIMD acceler
a
tio
n
for R
B
d
i
hedrals
commit
|
commitdiff
|
tree
2014-09-29
B
erk Hess
Avoi
d
PME tun
i
ng decreasing rcoulomb
commit
|
commitdiff
|
tree
2014-09-29
B
e
rk Hess
Fix c
a
lc
_
grid avo
i
ding
PME
grid fa
c
tor 84
commit
|
commitdiff
|
tree
2014-09-09
Ber
k
Hess
Fixed
D
D state co
l
lection i
s
sue
commit
|
commitdiff
|
tree
2014-09-08
B
e
rk Hes
s
Check fo
r
implicit solvent + Verlet sche
m
e
commit
|
commitdiff
|
tree
2014-08-28
Berk Hess
Fixed two PME is
s
ues wit
h
MPI+
O
penMP
commit
|
commitdiff
|
tree
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