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Clarify use of tau-p and pcoupltype
2016-09-06
Ber
k
H
ess
Fi
x
bug
w
ith conjugate-
g
radien
t
and OpenMP
commit
|
commitdiff
|
tree
2016-09-02
Berk
H
ess
Fix Parrine
l
l
o
-Rahman with ns
t
pcouple
>
1
commit
|
commitdiff
|
tree
2016-08-24
Berk Hess
Fi
x
Ewald surfa
c
e+3DC
c
o
rrections
commit
|
commitdiff
|
tree
2016-08-09
B
e
rk Hes
s
Fix t
w
in-cu
t
off for GPU
LJ pot-switch
commit
|
commitdiff
|
tree
2016-06-28
Berk
H
e
ss
Proper
l
y
re
s
et CU
D
A app
l
ication clocks
commit
|
commitdiff
|
tree
2016-06-27
Berk He
s
s
Use sysconf(_
S
C
_NPROCESSORS_ON
L
N
)
commit
|
commitdiff
|
tree
2016-06-21
Be
r
k
H
ess
Fix b
u
g wit
h
fbposr
e
s+MPI
+
Op
e
n
M
P
commit
|
commitdiff
|
tree
2016-06-14
Be
r
k Hess
Fix OpenCL error
with em
p
ty
d
o
m
ains
commit
|
commitdiff
|
tree
2016-06-03
Berk
H
e
s
s
Handl
e
partially
f
rozen and constrained a
t
o
m
s
commit
|
commitdiff
|
tree
2016-04-14
Berk
H
e
ss
Add QMMM checks
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
Corre
c
t
n
rdf for 1D/2D systems
commit
|
commitdiff
|
tree
2016-03-30
Be
r
k
H
es
s
C
o
rrect md
r
un tMPI (non-)parallel error m
e
ssage
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Avoid a
s
sertion fa
i
lure in pme_
l
oadba
l
_do
commit
|
commitdiff
|
tree
2016-03-18
Be
r
k Hess
Fix non
-
norm
a
li
z
ati
o
n of F
F
T a
u
tocorr
commit
|
commitdiff
|
tree
2016-03-14
Berk
Hess
Remo
v
e
rest
r
i
c
tion
on dihdraltypes order
commit
|
commitdiff
|
tree
2016-03-09
Berk Hess
Fix Ewald 3DC dipole wi
t
h Ver
l
et scheme
commit
|
commitdiff
|
tree
2016-02-19
B
e
rk Hess
Fix excess
i
ve
l
ist split
t
ing
commit
|
commitdiff
|
tree
2016-02-07
Ber
k
He
s
s
Fix
i
ncorrect c
m
ap pars
i
ng
commit
|
commitdiff
|
tree
2016-02-05
Be
r
k Hess
Fix incorrect cmap pa
r
sin
g
commit
|
commitdiff
|
tree
2016-02-03
Be
r
k Hes
s
Fix
mdrun
r
emovi
n
g Verlet
buff
e
r
wit
h
E
M
commit
|
commitdiff
|
tree
2016-02-03
Berk
Hess
Fix SETTL
E
err
o
r handling
commit
|
commitdiff
|
tree
2016-01-29
Berk H
e
ss
Fix TP
I
igno
r
ing PME mesh contrib
u
ti
o
n
s
.
commit
|
commitdiff
|
tree
2016-01-29
B
erk Hess
Add check for d
o
ubl
e
perturbation
commit
|
commitdiff
|
tree
2016-01-29
Berk H
e
ss
Fix
L
INCS tr
i
angle c
o
nstraint th
r
e
a
d issue
commit
|
commitdiff
|
tree
2016-01-28
Berk Hess
Upd
a
t
e
p
air-list buff
e
r manua
l
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix exac
t
continuati
o
n from non-
e
nergy
s
teps
commit
|
commitdiff
|
tree
2016-01-24
B
erk Hes
s
Fi
x
ener
g
y fil
e
con
t
inuat
i
on with md-vv
commit
|
commitdiff
|
tree
2016-01-24
Ber
k
Hess
F
ix energy average with con
t
inuat
i
on
commit
|
commitdiff
|
tree
2016-01-08
Be
r
k Hess
Fi
x
PM
E
load bala
n
ci
n
g sk
i
ppi
n
g a
s
e
tup
commit
|
commitdiff
|
tree
2015-12-29
Berk Hess
Corre
c
t v
e
ctor c
h
eck of
gmx che
c
k
commit
|
commitdiff
|
tree
2015-12-19
Berk
H
ess
Brin
g
p
e
r
formance
e
stimation u
p
to date
commit
|
commitdiff
|
tree
2015-12-11
Berk
Hes
s
Fi
x
bu
g
with pull gr
o
up w
e
ights
commit
|
commitdiff
|
tree
2015-11-19
Berk Hess
Removed mdrun
fatal_err
o
r with P3M-AD
commit
|
commitdiff
|
tree
2015-11-09
Berk Hess
Correct LINCS dHd
l
contr
i
bu
t
ion
commit
|
commitdiff
|
tree
2015-11-02
B
erk Hess
Fix interm
o
l
ecu
l
ar in
t
eracti
o
ns with small mols
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
F
ixed nbnxn_4xN performance regression
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
Fix bugs with intermol in
t
erac
t
ions a
n
d
DD
commit
|
commitdiff
|
tree
2015-09-15
Berk He
s
s
Detect incorre
c
t cycle counting
commit
|
commitdiff
|
tree
2015-08-14
Berk
Hess
Make mdrun -
n
t
w
ork agai
n
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fix
t
o
o smal
l
GPU
pair count es
t
imates
commit
|
commitdiff
|
tree
2015-07-06
Berk H
e
ss
Fix bug in GPU list balanci
n
g
commit
|
commitdiff
|
tree
2015-07-05
Berk
H
ess
Fix DD
DLB
s
tate issue
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
Fix b
u
g in GPU list balancing
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
Obe
y
OpenMP thre
a
d co
u
nt limit with tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
Fix
t
wo PME DLB
trigger issues
commit
|
commitdiff
|
tree
2015-07-03
Berk Hess
C
orrect
g
rompp
pull
w
arning mess
a
ge
commit
|
commitdiff
|
tree
2015-06-30
Ber
k
H
ess
Fix
inconsistent OpenMP
autom
a
tion
commit
|
commitdiff
|
tree
2015-06-30
B
e
r
k
Hess
enabled 1 P
P
+
1 PME no
d
e
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Add checks f
o
r ineffici
e
nt
r
eso
u
rce usage
commit
|
commitdiff
|
tree
2015-06-29
Berk Hess
Impr
o
ve
D
LB
+
PME
t
uning with GPUs
commit
|
commitdiff
|
tree
2015-06-27
B
erk Hess
Improve pa
i
r sear
c
h thread load balance
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Improved the i
n
tra-GPU load
b
al
a
nc
i
ng
commit
|
commitdiff
|
tree
2015-06-27
B
erk Hes
s
Reduce the use of
n
bnxn_consts
.
h
commit
|
commitdiff
|
tree
2015-06-27
Berk H
e
ss
Corrected nstcalclr/n
s
tfep/nst_re
p
l
_ex c
h
e
cks
commit
|
commitdiff
|
tree
2015-06-26
Berk He
s
s
Fixe
d
Verlet bu
f
fe
r
issue with 2-wide
SIMD
commit
|
commitdiff
|
tree
2015-06-25
Berk Hes
s
Interm
o
lec
u
l
a
r bonded i
n
teracti
o
n
s
u
pport
add
e
d
commit
|
commitdiff
|
tree
2015-06-25
B
erk Hess
Reena
b
l
ed SIMD ker
n
els
w
i
t
hout cut-offs
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
GP
U
Ewald table k
e
rnel now u
s
es CPU sp
a
cing
commit
|
commitdiff
|
tree
2015-06-24
Berk H
e
ss
A
void GP
U
select
i
on with
G
P
U emulati
o
n
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Mino
r
refor
m
atting
o
f SIMD m
i
smatch m
e
s
sage
commit
|
commitdiff
|
tree
2015-06-24
Berk He
s
s
Add sugar to print emp
t
y
line
i
n
p
rintBinar
y
Inform
a
tion
commit
|
commitdiff
|
tree
2015-06-22
B
erk Hess
Fix g_ene
r
g
y a
v
erage/RM
S
D bug
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
U
pdate launch configura
t
ion
for physical nodes
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Avoid fp exce
p
tions in pair search de
b
ug
commit
|
commitdiff
|
tree
2015-06-22
Ber
k
Hess
Replaced h
a
rdware threads
b
y
logical cores
in
out
p
ut
commit
|
commitdiff
|
tree
2015-06-18
Berk Hess
Reduced the c
o
st of t
h
e pull communication
commit
|
commitdiff
|
tree
2015-06-17
Berk Hess
Ref
a
c
tored
p
ull
d
ata structures
commit
|
commitdiff
|
tree
2015-06-16
Berk
H
e
s
s
Added mi
s
si
n
g DD c
y
cle counting
commit
|
commitdiff
|
tree
2015-06-16
Ber
k
Hess
Automated the -gpu_id option
commit
|
commitdiff
|
tree
2015-06-14
Be
r
k Hess
Ref
a
ctored mdrun resource divis
i
on
commit
|
commitdiff
|
tree
2015-06-13
Berk H
e
s
s
Hardware reporting now covers al
l
n
o
des
commit
|
commitdiff
|
tree
2015-06-05
Berk Hess
D
o
n't use PME
ranks with GP
U
s a
n
d -npme=-1
commit
|
commitdiff
|
tree
2015-05-27
Berk
H
ess
Refactoring of PM
E
load balancing
commit
|
commitdiff
|
tree
2015-05-23
Berk Hess
Removed
stat
i
c from variables in gmx
_
l
a
pack
commit
|
commitdiff
|
tree
2015-05-16
Berk Hess
LINC
S
threa
d
tas
k
s
c
a
n
now be
inde
p
en
d
e
nt
commit
|
commitdiff
|
tree
2015-05-13
Berk He
s
s
F
i
x
ed CUDA error with empty d
o
mains
commit
|
commitdiff
|
tree
2015-05-13
Berk
H
e
s
s
Fix
se
g
v in g_
c
ovar
commit
|
commitdiff
|
tree
2015-05-11
Berk Hess
Changed FFTW
warning
f
ro
m
A
VX to no
S
S
E
commit
|
commitdiff
|
tree
2015-05-07
B
e
rk Hess
Removed
non-ff atomtype
s
f
rom oplsaa and ch
a
rmm
2
7
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fixed GPU
n
on-
l
ocal F co
p
y loc
a
l conditional
commit
|
commitdiff
|
tree
2015-04-28
Berk He
s
s
R
e
-enabl
e
d FMA for AVX-12
8
-FMA
commit
|
commitdiff
|
tree
2015-04-22
Ber
k
Hess
Merge bra
n
ch 'release-5-0'
commit
|
commitdiff
|
tree
2015-04-17
Be
r
k Hess
Add value_ref
an
d
value to pull_coord_
t
commit
|
commitdiff
|
tree
2015-04-17
Be
r
k
Hess
Correct -ntmpi auto for int
e
l nehalem and older
commit
|
commitdiff
|
tree
2015-04-08
B
er
k
Hess
Added pu
l
l geometry direc
t
ion-relative
commit
|
commitdiff
|
tree
2015-04-01
Berk Hess
Correct
e
d force-swi
t
ch manual
section
commit
|
commitdiff
|
tree
2015-03-19
Berk Hess
Remove
d
reduction
o
f dH/dl without FE
commit
|
commitdiff
|
tree
2015-03-12
Be
r
k Hess
Fi
x
ed mdrun fp exc
e
p
t
i
on with
-
debug
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Added update x copy-back to update timer
commit
|
commitdiff
|
tree
2015-03-11
Berk
H
ess
Reduced cos
t
o
f
Be
r
en
d
s
en pressure coupling
commit
|
commitdiff
|
tree
2015-03-06
Berk Hess
Im
p
rove threading of bondeds
commit
|
commitdiff
|
tree
2015-03-05
B
erk Hess
Made DD exclu
s
ion processin
g
more
eff
i
c
i
e
n
t
commit
|
commitdiff
|
tree
2015-03-05
Be
r
k Hess
SIMD acceleration for L
I
NCS
commit
|
commitdiff
|
tree
2015-03-04
B
erk Hes
s
Allow pull groups
of 1
atom with mas
s
0
commit
|
commitdiff
|
tree
2015-03-04
Berk Hess
COM
p
ul
l
ing op
t
io
n
s per coord, improved cylinder
commit
|
commitdiff
|
tree
2015-03-03
Ber
k
Hess
Fix
d
iv by zero in PP/PME
r
atio
commit
|
commitdiff
|
tree
2015-03-02
Berk Hess
Ad
d
e
d
p
a
renthes
e
s fo
r
c
a
s
ts in SIMD
mac
r
os
commit
|
commitdiff
|
tree
2015-02-24
Berk Hes
s
Fixed parallel distri
b
ution and thread count re
p
orting
commit
|
commitdiff
|
tree
2015-02-12
Berk Hess
Re-fixed PME bug with high O
p
enMP thr
e
a
d
c
o
unt
commit
|
commitdiff
|
tree
2015-02-06
Berk Hess
R
e-
e
nabled SIMD for an
g
les
a
n
d
dihedrals
commit
|
commitdiff
|
tree
next