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Bring performance estimation up to date
2015-12-19
Berk Hess
Brin
g
perfo
r
mance e
s
tima
t
ion up
to date
commit
|
commitdiff
|
tree
2015-12-11
Berk Hes
s
Fix b
u
g with
p
u
ll group weights
commit
|
commitdiff
|
tree
2015-11-19
Berk
Hess
Removed mdrun
f
a
tal_error
w
ith P3M-
A
D
commit
|
commitdiff
|
tree
2015-11-09
Berk He
s
s
Corre
c
t LINCS
d
Hd
l
con
t
r
ibution
commit
|
commitdiff
|
tree
2015-09-15
Berk Hess
Detect incorrec
t
cycle cou
n
t
ing
commit
|
commitdiff
|
tree
2015-06-30
Berk Hes
s
Fix in
c
onsistent OpenMP automation
commit
|
commitdiff
|
tree
2015-06-26
Alexe
y
Shvetsov
Fix recent compilat
i
on issue i
n
pullco
d
e
commit
|
commitdiff
|
tree
2015-06-22
Be
r
k Hess
F
ix g_
e
ner
g
y a
v
erage/RM
S
D
bug
commit
|
commitdiff
|
tree
2015-05-23
Be
r
k
H
ess
Removed stati
c
from
v
a
r
iab
l
e
s in gmx_
l
ap
a
ck
commit
|
commitdiff
|
tree
2015-05-13
B
er
k
Hess
Fixed CUDA error w
i
t
h empt
y
domains
commit
|
commitdiff
|
tree
2015-05-11
Berk He
s
s
Changed
F
FTW war
n
i
n
g f
r
om AVX to n
o
SSE
commit
|
commitdiff
|
tree
2015-05-07
Berk Hess
Removed non
-
ff ato
m
t
ypes from opl
s
aa an
d
ch
a
rmm27
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fixed GPU non-loca
l
F
copy l
o
cal conditional
commit
|
commitdiff
|
tree
2015-04-28
Berk Hess
Re-enabl
e
d FMA
f
or AV
X
-
1
28-FMA
commit
|
commitdiff
|
tree
2015-04-22
Berk Hess
Mer
g
e bran
c
h 'release-
5
-0'
commit
|
commitdiff
|
tree
2015-04-17
Berk
Hess
Correct -ntm
p
i auto for
i
n
t
e
l nehalem and old
e
r
commit
|
commitdiff
|
tree
2015-03-05
B
e
rk Hess
M
ade DD
e
xclusion
p
rocessin
g
more efficient
commit
|
commitdiff
|
tree
2015-02-12
B
e
r
k Hess
R
e-fixed PME bug with high OpenM
P
thre
a
d cou
n
t
commit
|
commitdiff
|
tree
2015-01-21
Be
r
k
Hess
C
orrected
R
DTSCP w
a
rning text
commit
|
commitdiff
|
tree
2014-12-11
Berk Hess
Ad
d
e
d gr
o
m
pp
e
rror for pul
l
ing to n
e
gat
i
ve distance
commit
|
commitdiff
|
tree
2014-12-09
Berk Hess
F
i
x
r
ecent bug with trilinic
1D DD
commit
|
commitdiff
|
tree
2014-11-24
David van
d
er Spoel
Add
e
d warning
s
for ew
a
ld-g
e
ometry an
d
surfa
c
e-epsilon
commit
|
commitdiff
|
tree
2014-10-07
Berk Hess
Fixes
i
ssue w
i
th vsiten and
V
e
rlet bu
f
fers
commit
|
commitdiff
|
tree
2014-09-09
Berk H
e
ss
Fix
e
d
D
D s
t
a
t
e collection i
s
s
ue
commit
|
commitdiff
|
tree
2014-09-08
Berk H
e
ss
Check fo
r
implicit solv
e
nt + Verl
e
t s
c
heme
commit
|
commitdiff
|
tree
2014-08-25
Berk Hess
Fixed bugs in
vsiteN with
OpenMP
commit
|
commitdiff
|
tree
2014-08-02
Berk Hess
F
ixed PME bug with high OpenM
P
thr
e
ad
co
u
nt
commit
|
commitdiff
|
tree
2014-07-31
Berk He
s
s
Avoid divis
i
on by 0 in nb
n
xn_search
commit
|
commitdiff
|
tree
2014-07-28
Christia
n
Wen
n
b
e
rg
Fix
overflow in LJ-PM
E
nbnxn
k
e
rnels
commit
|
commitdiff
|
tree
2014-06-20
Berk
H
ess
F
i
xed shells with part
i
cle de
c
omposition
commit
|
commitdiff
|
tree
2014-06-10
Berk Hess
Replaced gmx_
h
ostname_n
u
m b
y
g
mx_physic
a
lnode_id_h
a
sh
commit
|
commitdiff
|
tree
2014-06-02
Berk Hess
Fixed g_energy Einstein vis
c
osity
commit
|
commitdiff
|
tree
2014-03-24
Berk
He
s
s
A
d
d
s
cut-off checks for
t
ric
l
inic d
o
main deco
m
position
commit
|
commitdiff
|
tree
2013-12-03
Berk Hess
Removed restriction of one reference pull group
commit
|
commitdiff
|
tree
2013-11-15
Berk Hes
s
correct
e
d
potent
i
a
l
nbnxn SIMD memory
issue
commit
|
commitdiff
|
tree
2013-11-08
Berk He
s
s
fix nbnxn atom sorting with distant bondeds
commit
|
commitdiff
|
tree
2013-11-06
Szilard Pa
l
l
enable GP
U
shar
i
ng among tMPI ranks
commit
|
commitdiff
|
tree
2013-10-31
Berk Hess
r
eorg
a
nized GPU detecti
o
n
and select
i
on
commit
|
commitdiff
|
tree
2013-10-22
Berk He
s
s
fi
x
ed r
e
cent b
u
g with CUDA
t
extur
e
obj
e
cts
commit
|
commitdiff
|
tree
2013-10-22
Be
r
k Hess
fixed OpenMP threads being pinned to the same cores
commit
|
commitdiff
|
tree
2013-10-10
Berk He
s
s
fixed
nbnxn 4x8
pair search
w
i
thout AV
X
commit
|
commitdiff
|
tree
2013-06-03
B
e
rk Hess
f
ixed
dead
l
ock wi
t
h r
e
plica exchange and -maxh
commit
|
commitdiff
|
tree
2013-05-08
Berk Hess
fixe
d
incorrect scali
n
g of cos-a
c
celer
a
tion vi
s
cos
i
ty
commit
|
commitdiff
|
tree
2013-04-26
Berk Hess
PME load balanc
i
ng no
w
check
s
for
P
ME
g
rid restrictio
n
s
commit
|
commitdiff
|
tree
2013-04-18
Berk Hess
changed
m
drun
-
nsteps to
g
m
x
_large_int_t
commit
|
commitdiff
|
tree
2013-04-12
Ber
k
Hess
improved load
balancing
with Verlet cut-off s
c
heme
commit
|
commitdiff
|
tree
2013-03-27
Berk
Hess
removed x86 sp
e
ci
f
ics f
r
om nbnx
n
S
I
MD kernels
commit
|
commitdiff
|
tree
2013-03-27
Ber
k
Hess
correc
t
ed log file wall time breakdown
commit
|
commitdiff
|
tree
2013-03-21
Berk Hess
made PME wor
k
with a mix o
f
1
a
nd more
thread
s
commit
|
commitdiff
|
tree
2013-03-14
Berk Hess
c
o
r
rected grompp rvdw charge-gro
u
p ra
d
ii check
commit
|
commitdiff
|
tree
2013-02-26
Berk
Hess
fixed
P
ME time print with -n
t
omp_pme != -ntomp
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
added mdrun check
f
or
Verlet+pert
u
rbe
d
atoms
commit
|
commitdiff
|
tree
2013-02-06
Ber
k
Hess
fixed bug
with sd i
n
tegrator
a
n
d
Ope
n
M
P
threading
commit
|
commitdiff
|
tree
2013-02-05
B
e
r
k
He
s
s
i
m
proved load balancing on the GP
U
commit
|
commitdiff
|
tree
2013-02-04
Berk Hess
fixed segv in init_fo
r
cerec
w
ith
f
r->hwinfo=NULL
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
improved C
U
DA
kernel pe
r
for
m
anc
e
by pre-loa
d
ing cj
commit
|
commitdiff
|
tree
2013-01-16
Carsten K
u
tzner
Made g_tune_pme w
o
r
k
correctly
a
gain with thre
a
d-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Ber
k
H
ess
made SHAKE work
a
gain with part
i
c
l
e
decom
p
osti
o
n
commit
|
commitdiff
|
tree
2013-01-10
Berk He
s
s
fixed bug with Verlet + DD +
bo
n
ded atom c
o
mm
u
nication
commit
|
commitdiff
|
tree
2013-01-10
Er
i
k
L
i
n
d
ah
l
Revert d
e
fault
rlist/rvd
w
/
rcoulomb
to vali
d
value
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-02
B
e
rk Hess
m
inor speed-up
a
n
d
cod
e
c
l
ean-
u
p
in nb
n
xn
ker
n
els
commit
|
commitdiff
|
tree
2012-12-20
Berk Hess
fi
x
ed rece
n
t
bugs in LINCS for derivatives
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
re
n
amed gmx_x86_
s
i
m
d_macros
.
h to g
m
x
_
simd_macros
.
h
commit
|
commitdiff
|
tree
2012-12-18
Berk
H
ess
i
m
plemented
nbnx
n
AVX
-
256 2x(N
+
N) kernels
commit
|
commitdiff
|
tree
2012-12-11
Berk Hess
r
educe
d
PLINCS co
m
mun
i
cation with H-bond c
o
nstraints
commit
|
commitdiff
|
tree
2012-12-07
Berk He
s
s
fixed GPU pair-
s
e
arch with GMX_CPU_
A
CCEL
E
R
ATIO
N
=None
commit
|
commitdiff
|
tree
2012-12-05
Berk Hes
s
fi
x
ed
i
ncorrec
t
vir
i
al with virt
u
al sites and Ope
n
MP
commit
|
commitdiff
|
tree
2012-12-05
Ber
k
H
ess
fixed segv in Verlet pa
i
r
-search with
trilin
i
c DD
commit
|
commitdiff
|
tree
2012-11-30
Berk Hes
s
fi
x
ed is
s
ue
w
ith -multi and GPUs
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
fixed thread
p
inning with mdrun -multi
commit
|
commitdiff
|
tree
2012-11-28
Szil
a
rd Pall
enab
l
e GPU em
u
lat
i
on withou
t
GP
U
support
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
e
x
tended nbn
x
n x86 SI
M
D kernel
b
lendv support
commit
|
commitdiff
|
tree
2012-11-27
Berk Hess
fix
e
d bug in nbnxn OpenM
P
non-bonde
d
force reduc
t
ion
commit
|
commitdiff
|
tree
2012-11-26
Berk
Hess
made nbn
x
n analytica
l
Ewald consi
s
tent
commit
|
commitdiff
|
tree
2012-11-26
Berk Hes
s
add
e
d n
b
nxn
a
nalyt
i
cal Ewald correction kernels
commit
|
commitdiff
|
tree
2012-11-15
Ber
k
Hess
f
ixed
i
ncorrect 1-4 energ
i
e
s with OpenMP + energy group
s
commit
|
commitdiff
|
tree
2012-11-14
Berk
Hess
fixe
d
nbnxn x86 SIMD no
n
-
bonded performance re
g
ression
commit
|
commitdiff
|
tree
2012-11-12
B
erk He
s
s
nbnxn CPU
f
orc
e
bu
f
fe
r
r
e
d
u
c
ti
o
n
n
o
w
us
e
s SIMD
commit
|
commitdiff
|
tree
2012-11-05
Berk Hess
updated
s
e
v
e
ral
t
hings related
with
O
p
e
n
M
P thread count
commit
|
commitdiff
|
tree
2012-10-26
Berk He
s
s
fixed inco
r
rect P
M
E load
b
alanci
n
g limita
t
ion
commit
|
commitdiff
|
tree
2012-10-26
B
e
rk Hes
s
set the default for
n
stdhdl to 100
commit
|
commitdiff
|
tree
2012-10-26
Berk
H
ess
fi
x
ed in
c
orrect g
r
oup energ
i
es
w
ith n
b
nxn CPU
k
e
rne
l
s
commit
|
commitdiff
|
tree
2012-10-22
R
ol
a
nd Schul
z
Fix
c
lang
3
.
2 unintia
l
ized
varia
b
le w
a
rnings
commit
|
commitdiff
|
tree
2012-10-18
Berk Hess
renamed c
o
nst
r
aint variable
s
rmdr to vir_r_m_dr
commit
|
commitdiff
|
tree
2012-10-17
Berk Hes
s
renamed pme_switch
.
.
.
to pm
e
_loa
d
bal
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Berk Hess
mad
e
pa
i
r
-
search with GPU 20% faster
commit
|
commitdiff
|
tree
2012-10-08
Berk Hess
made no
n
-bonded po
t
ential shifts mdp options
commit
|
commitdiff
|
tree
2012-10-03
Berk
Hess
improv
e
d the ene
r
gy conservat
i
on
w
it
h
SETTLE
commit
|
commitdiff
|
tree
2012-09-13
B
e
rk Hess
fixed re
c
e
n
t
b
u
g
wit
h
g
r
ompp
check for P
-
R P
-
couplin
g
commit
|
commitdiff
|
tree
2012-08-29
Berk Hess
bug fix for p
m
e
.
c MPI_COMM_NULL fix dcf
8
b67e
commit
|
commitdiff
|
tree
2012-08-09
Berk Hess
fixed trjconv not writing v
e
l
ocities w
i
th cp
t
input
commit
|
commitdiff
|
tree
2012-08-06
Berk Hess
fixed incorrect TPI
r
esults wi
t
h dynamic
b
o
x
commit
|
commitdiff
|
tree
2012-07-18
Berk H
e
ss
fixed DD charge group di
s
p
l
a
cement erro
r
check
commit
|
commitdiff
|
tree
2012-06-25
Berk
Hess
fixed
segv/hang
w
ith EM and foreign lambda values
commit
|
commitdiff
|
tree
2012-06-25
Berk Hess
added check for log fp!=
N
ULL when disabling acceleration
commit
|
commitdiff
|
tree
2012-05-24
Berk H
e
ss
now
m
drun alw
a
y
s
i
nitializes MPI
commit
|
commitdiff
|
tree
2012-05-21
Ber
k
Hess
g
rompp now retains
t
he order
o
f bonds converte
d
to
.
.
.
commit
|
commitdiff
|
tree
2012-05-21
Berk
H
e
ss
re-introduced fix for real/double issue
i
n gmx_dens
i
ty
commit
|
commitdiff
|
tree
2012-05-08
B
erk
H
ess
fixed
m
drun
-cpi SD and pco
u
pl initializatio
n
commit
|
commitdiff
|
tree
2012-04-27
Berk Hess
f
i
x
ed segv in TPI wit
h
PME,
f
ixes #927
commit
|
commitdiff
|
tree
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