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Fixed PME bug with #OpenMP-threads a large prime
2014-06-14
Ber
k
H
ess
Fixed PME bug
w
i
t
h #OpenMP-threads a large pr
i
m
e
commit
|
commitdiff
|
tree
2014-06-13
Berk H
e
ss
Ch
a
nged app
e
nding
f
ile name error message
commit
|
commitdiff
|
tree
2014-06-13
Berk
H
ess
Made shells work wit
h
t
h
e
V
e
rlet scheme
commit
|
commitdiff
|
tree
2014-06-12
Berk Hess
Fixe
d
perturbed
wa
l
l in
t
erac
t
ions
commit
|
commitdiff
|
tree
2014-06-12
Berk H
e
ss
Made gmxcheck -rmsd work
a
g
a
in
with
f
orc
e
s
commit
|
commitdiff
|
tree
2014-06-11
Ber
k
Hess
M
a
de repl_ex
time
s
t
ep m
o
re readable
commit
|
commitdiff
|
tree
2014-06-05
Berk Hess
Fixed shift and switch modifie
r
s, p
a
rticular
l
y fo
r
.
.
.
commit
|
commitdiff
|
tree
2014-06-05
Berk Hess
F
ix co
n
s
t
raint virial wit
h
m
u
lt
i
ple ti
m
e stepping
commit
|
commitdiff
|
tree
2014-06-02
Berk Hess
Fixed g_energy Einstein
viscosity
commit
|
commitdiff
|
tree
2014-04-29
Be
r
k He
s
s
Rem
o
ved trunc
a
ti
o
n
of nrdf in
v
-rescale thermo
s
tat
commit
|
commitdiff
|
tree
2014-03-24
Berk Hess
Adds cut-off checks for tri
c
linic domain de
c
omp
o
sition
commit
|
commitdiff
|
tree
2014-03-23
Berk Hess
Fi
x
ed bug in parallel v/f
cons
t
raining
commit
|
commitdiff
|
tree
2013-11-26
B
e
rk
H
ess
Fix
e
d retu
r
n v
a
lue
o
f gmx_
m
top_bondeds_f
r
ee_energy
commit
|
commitdiff
|
tree
2013-11-15
Berk Hess
corrected
p
o
t
e
n
t
ial nbnxn SIMD memory i
s
s
ue
commit
|
commitdiff
|
tree
2013-11-08
Berk Hess
fix n
b
nxn at
o
m
s
ort
i
ng w
i
t
h
dis
t
ant
bo
n
deds
commit
|
commitdiff
|
tree
2013-11-07
Berk Hess
correc
t
ed
d
ynam
i
c
load bal
a
ncing when sha
r
i
n
g G
P
Us
commit
|
commitdiff
|
tree
2013-11-05
Berk
Hess
GPU detection is
done once per phy
s
ic
a
l node
commit
|
commitdiff
|
tree
2013-11-05
Be
r
k Hess
removed (harmless) left
-
over in nbnxn S
I
MD kern
e
ls
commit
|
commitdiff
|
tree
2013-10-31
Berk
Hess
r
e
o
r
g
anized GPU detection and selection
commit
|
commitdiff
|
tree
2013-10-29
Berk Hess
corrected
v
olume wit
h
serial NPT repl
i
ca exchange
commit
|
commitdiff
|
tree
2013-10-28
B
e
r
k Hess
improved
t
he nb
n
xn buffer size estimate with GPUs
commit
|
commitdiff
|
tree
2013-10-22
Berk Hess
fixed
r
e
c
ent bug
with
C
UDA
t
exture
objects
commit
|
commitdiff
|
tree
2013-10-22
Berk Hess
fixed OpenMP threads b
e
i
n
g pi
n
ned to
the s
a
me cores
commit
|
commitdiff
|
tree
2013-10-16
B
erk
H
ess
a
voi
d
divis
i
on by zero in SIMD angles and dihe
d
rals
commit
|
commitdiff
|
tree
2013-10-16
Berk Hess
fi
x
ed a half bin misal
i
g
nment in gmx_vanhove
-
or
commit
|
commitdiff
|
tree
2013-10-11
Ber
k
H
e
ss
introduced general 4-wide
SIMD support
commit
|
commitdiff
|
tree
2013-10-10
Berk Hess
fix
e
d n
b
nxn 4x8 pair search without AVX
commit
|
commitdiff
|
tree
2013-10-02
Berk Hess
Fixes rea
c
tion f
i
eld free energy bug
commit
|
commitdiff
|
tree
2013-09-24
Be
r
k Hess
o
p
t
imized
g
eneric SIMD
invsqrt
commit
|
commitdiff
|
tree
2013-09-21
Berk H
e
ss
fixed multiple dis
t
a
nce restraints with OpenMP
commit
|
commitdiff
|
tree
2013-09-18
Berk Hess
made
f
ree en
e
rgy PME kernel 40% fast
e
r
commit
|
commitdiff
|
tree
2013-09-16
Berk
Hess
mdrun with
o
ut O
p
enMP
with t
h
r
ead-MPI now uses all
cores
commit
|
commitdiff
|
tree
2013-09-13
Berk Hess
corrected grompp constraint/DOF warning with vsites
commit
|
commitdiff
|
tree
2013-08-25
Berk He
s
s
introd
u
c
ed n
b
n
xn
da
t
a
structure
for
b
o
u
n
d
ing boxes
commit
|
commitdiff
|
tree
2013-08-20
Berk Hess
fixed
p
a
rallel normal
m
ode
s
with PME
commit
|
commitdiff
|
tree
2013-07-24
Berk Hess
impleme
n
ted plain-C SIMD
m
acros fo
r
refere
n
ce
commit
|
commitdiff
|
tree
2013-06-20
B
erk Hess
fixed SD and BD
i
ntegrator
O
penMP performance
commit
|
commitdiff
|
tree
2013-06-20
B
e
rk Hes
s
flops table now reports
C
UDA a
n
alytical Ewald
commit
|
commitdiff
|
tree
2013-06-14
Berk Hess
fixed mi
n
o
r
g
_
b
ar outp
u
t is
s
ues
commit
|
commitdiff
|
tree
2013-06-05
B
e
rk
H
e
ss
fixe
d
DD internal state
c
or
r
uption with
e
ner
g
y mi
n
im
i
z
a
tion
commit
|
commitdiff
|
tree
2013-06-03
Berk Hess
fixed deadlock
w
ith
r
eplica excha
n
ge
and -maxh
commit
|
commitdiff
|
tree
2013-05-08
Berk H
e
ss
fixed incorrect scaling of cos-acceleration viscosity
commit
|
commitdiff
|
tree
2013-04-29
Berk
Hess
g
e
n
e
r
al SIMD acc
e
l
e
rat
i
o
n for an
g
les+d
i
h
e
d
r
als
commit
|
commitdiff
|
tree
2013-04-26
Berk Hess
PME load b
a
lancing
now checks for
P
M
E
grid restri
c
tions
commit
|
commitdiff
|
tree
2013-04-18
Be
r
k Hess
chan
g
ed mdr
u
n
-nste
p
s to
gmx_lar
g
e_in
t
_
t
commit
|
commitdiff
|
tree
2013-04-12
Berk He
s
s
improved lo
a
d
b
a
l
ancin
g
wi
t
h Verlet cut-off
scheme
commit
|
commitdiff
|
tree
2013-03-27
Berk Hess
rem
o
ved x86 specifics fr
o
m nbnxn SIMD
kernels
commit
|
commitdiff
|
tree
2013-03-27
Berk
Hess
cor
r
ected log f
i
le wall time breakdown
commit
|
commitdiff
|
tree
2013-03-21
Berk
Hes
s
made PME
wo
r
k wi
t
h a mix of 1 and more
threads
commit
|
commitdiff
|
tree
2013-03-14
B
e
rk
Hess
corre
c
t
e
d grompp rv
d
w
charg
e
-group radi
i
check
commit
|
commitdiff
|
tree
2013-03-05
Berk
Hess
fixe
d
bug with DD cut-off check an
d
PM
E
DLB
commit
|
commitdiff
|
tree
2013-03-05
B
erk
H
ess
fixed
r
ec
e
n
t
b
ug with sorting atoms
f
or
G
PUs
commit
|
commitdiff
|
tree
2013-02-26
Berk Hes
s
fixed PME time pr
i
n
t w
i
th
-
n
t
omp_pm
e
!=
-ntomp
commit
|
commitdiff
|
tree
2013-02-20
Berk He
s
s
add
e
d md
r
un check for Verlet+pert
u
rbed at
o
ms
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
f
i
xed i
s
su
e
s
wit
h
FEP so
f
t-core
and cut-off's
commit
|
commitdiff
|
tree
2013-02-18
B
erk Hess
fix
e
d GPU pa
r
ticle gr
i
dding
performance
i
ssue
commit
|
commitdiff
|
tree
2013-02-15
Berk
H
ess
improved PME load b
a
lancin
g
reporting
commit
|
commitdiff
|
tree
2013-02-06
Berk Hess
fixed
b
ug with sd i
n
tegrator a
n
d OpenMP threading
commit
|
commitdiff
|
tree
2013-02-05
B
e
r
k
H
e
s
s
improved load balancing
o
n th
e
GPU
commit
|
commitdiff
|
tree
2013-02-04
B
e
rk Hess
fixed s
e
gv in
i
nit_f
o
r
c
e
rec
with f
r
->hwinfo=NULL
commit
|
commitdiff
|
tree
2013-02-01
Berk Hess
PME-on
l
y counters are now
r
eset
w
ith -max
h
-resethway
commit
|
commitdiff
|
tree
2013-01-18
Berk Hess
thre
a
d affinity now uses some topol
o
gy informa
t
ion
commit
|
commitdiff
|
tree
2013-01-17
B
er
k
Hess
f
ixed SD+BD in
t
egration slowing down with Op
e
nMP
thr
e
a
ds
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
impro
v
e
d
CUDA
kerne
l
p
e
rf
o
rmance by p
r
e-loading cj
commit
|
commitdiff
|
tree
2013-01-17
Berk He
s
s
fixed nb
n
xn hybrid m
o
de with OpenMP
commit
|
commitdiff
|
tree
2013-01-17
Be
r
k
H
e
ss
m
ade PME load balancing + DD DLB more eff
i
cient
commit
|
commitdiff
|
tree
2013-01-16
Berk Hess
s
p
l
it o
f
f
pick_nbnxn_resource from nbnxn_pick_n
b
nxn
commit
|
commitdiff
|
tree
2013-01-13
Berk Hess
fixed
reset
t
ing sta
t
es with para
l
lel Verlet scheme
commit
|
commitdiff
|
tree
2013-01-12
Berk
Hess
prepared t
h
e
n
bnxn code for n
o
n-x8
6
SIMD
commit
|
commitdiff
|
tree
2013-01-11
Berk Hes
s
made SHAKE work again
wi
t
h par
t
icle decom
p
ostion
commit
|
commitdiff
|
tree
2013-01-10
Be
r
k Hess
fixed nb
n
xn no LJ comb
.
r
ule AVX256 PME kernel
commit
|
commitdiff
|
tree
2013-01-10
B
e
rk Hess
fixed bug with V
e
rle
t
+
D
D
+ bonded a
t
om co
m
munication
commit
|
commitdiff
|
tree
2013-01-07
Berk
H
ess
fixed
n
bnxn AVX-2
5
6 Ewald
table pointe
r
alig
n
m
e
nt
commit
|
commitdiff
|
tree
2013-01-02
Be
r
k Hess
m
i
no
r
speed
-
up and code clean-up in nb
n
xn kernels
commit
|
commitdiff
|
tree
2012-12-20
Be
r
k
He
s
s
f
i
xed r
e
cent bugs
in LINCS
for derivatives
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
renamed gmx_x
8
6_sim
d
_macros
.
h to gmx_s
i
md_mac
r
os
.
h
commit
|
commitdiff
|
tree
2012-12-18
Be
r
k
H
ess
im
p
lemente
d
nbnx
n
AVX-256
2x(N+N) kernels
commit
|
commitdiff
|
tree
2012-12-11
Berk Hess
reduc
e
d
PLINCS communi
c
ation wit
h
H-bond
const
r
aints
commit
|
commitdiff
|
tree
2012-12-07
B
erk He
s
s
fixed GPU pair-sea
r
ch with G
M
X_
C
PU_ACCELERATI
O
N
=
None
commit
|
commitdiff
|
tree
2012-12-06
Berk H
e
ss
rem
o
ved last OpenMP O(nt
h
reads) bottleneck
commit
|
commitdiff
|
tree
2012-12-05
Berk
H
e
s
s
fi
x
ed incorrect virial with virt
u
al sites and O
p
enMP
commit
|
commitdiff
|
tree
2012-12-05
Ber
k
Hess
fixed
s
egv
i
n V
e
rlet pair-s
e
arc
h
with tr
i
li
n
i
c
DD
commit
|
commitdiff
|
tree
2012-11-30
Berk Hess
fixed issue
with -mu
l
ti and GPU
s
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
f
i
xed th
r
e
a
d pinning with m
d
run -multi
commit
|
commitdiff
|
tree
2012-11-28
Berk
Hess
extended nbnx
n
x
86 SIMD
k
ernel
b
lendv support
commit
|
commitdiff
|
tree
2012-11-27
Berk H
e
ss
fixed bu
g
in nbnxn OpenMP non-bon
d
ed
for
c
e reduction
commit
|
commitdiff
|
tree
2012-11-26
Ber
k
Hess
made nbn
x
n
analy
t
ical Ewald consistent
commit
|
commitdiff
|
tree
2012-11-26
B
erk Hess
a
dded
nbnxn analytical Ewald corr
e
ction k
e
r
nels
commit
|
commitdiff
|
tree
2012-11-16
B
e
rk Hess
red
u
c
e
d th
e
cost of the nb
n
xn O
p
enMP nb-force redu
c
t
ion
commit
|
commitdiff
|
tree
2012-11-15
Berk Hess
fixed i
n
corre
c
t 1-4 energies with
OpenMP + energy gro
u
ps
commit
|
commitdiff
|
tree
2012-11-14
Berk Hess
fixed nbnx
n
x
8
6 SIMD non-bonded performance regr
e
ssion
commit
|
commitdiff
|
tree
2012-11-12
B
e
r
k Hess
nbnxn CPU fo
r
ce buffer reduction no
w
u
s
es SIMD
commit
|
commitdiff
|
tree
2012-11-06
Berk Hess
Merge "Add o
p
tion to install
l
ibcuda
r
t" in
t
o rele
a
se-4-6
commit
|
commitdiff
|
tree
2012-11-06
Berk Hess
M
erge "don't execut
e
any mp
i
_
i
nfo/mpiname in the path
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
B
e
rk Hess
Merge "up
d
ated several things related with Ope
n
MP t
h
read
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
Berk He
s
s
updated sever
a
l things rela
t
ed with
OpenM
P
t
hread cou
n
t
commit
|
commitdiff
|
tree
2012-10-26
Berk
Hess
fix
e
d in
c
or
r
ec
t
PME load
ba
l
ancing limitatio
n
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
s
e
t the
default for nstdhdl to 100
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
fixed incorrect group en
e
r
g
ies
w
ith
nbnxn CP
U
kernel
s
commit
|
commitdiff
|
tree
2012-10-23
Berk
Hess
fixed bondf
r
e
e
.
c thre
a
d
safet
y
wi
t
h free ene
r
g
y
commit
|
commitdiff
|
tree
next