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Fix data race in hwinfo with thread-MPI
2016-06-07
Berk H
e
ss
Fix da
t
a
r
ace in h
w
in
f
o with
t
h
r
ead-M
P
I
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Reposit
i
on nbnxn filler partic
l
es
commit
|
commitdiff
|
tree
2016-05-31
Berk Hes
s
Avoid n
u
merica
l
over
f
low
w
it
h
o
v
erla
p
pi
n
g a
t
oms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
A
dd check for
f
inite energi
e
s
commit
|
commitdiff
|
tree
2016-05-30
Berk Hess
A
d
d grompp check
f
or unbound
a
to
m
s
commit
|
commitdiff
|
tree
2016-05-23
Berk
Hess
Fix bug in
v-resc
a
le
t
h
e
rmost
a
t
&
r
e
plic
a
exchange
commit
|
commitdiff
|
tree
2016-05-10
Ber
k
Hess
Opt
i
mi
z
ed t
h
e vsite
t
hreading
commit
|
commitdiff
|
tree
2016-05-10
Ber
k
Hess
F
ix CUDA shme
m
bug
commit
|
commitdiff
|
tree
2016-05-10
Be
r
k
Hess
Support cmap
w
ith QMMM
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
U
pd
a
te mdrun termination
i
nfo
commit
|
commitdiff
|
tree
2016-05-06
Ber
k
Hess
OpenMP parallelization f
o
r pull
commit
|
commitdiff
|
tree
2016-04-20
Berk Hess
Fix pull legend
with
external
p
otential
commit
|
commitdiff
|
tree
2016-04-19
Berk H
e
s
s
Allow
rcou
l
omb>rvdw wi
t
h
PME
commit
|
commitdiff
|
tree
2016-04-19
Ber
k
H
e
ss
B
r
oadcast pull external po
t
ential provider string
commit
|
commitdiff
|
tree
2016-04-19
B
e
rk H
e
s
s
F
i
x gm
x
hbond group overla
p
check
commit
|
commitdiff
|
tree
2016-04-14
Berk
H
ess
Add QMM
M
checks
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
Correct
n
rdf for 1D/2D syste
m
s
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Fix incl
u
des in readpu
l
l
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
A
d
d option for
e
xternal pull
p
otenti
a
l
commit
|
commitdiff
|
tree
2016-03-30
Ber
k
H
ess
Correct mdr
u
n
t
MPI (non-)
p
arallel error messa
g
e
commit
|
commitdiff
|
tree
2016-03-26
Be
r
k Hess
Add real/SIMD templ
a
t
e for L
J
-1
4
pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Avoi
d
assertion fai
l
ure in pme_loadbal_do
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Make gmx
vanhove work wit
h
o
u
t
PBC
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ com
b
ination rule k
e
rne
l
s for
C
U
D
A
commit
|
commitdiff
|
tree
2016-03-21
B
e
rk
H
ess
Moved
pul
l
initialization
b
ack to m
d
runner
commit
|
commitdiff
|
tree
2016-03-18
B
e
rk H
e
ss
Fix non-no
r
malization of FFT
autoc
o
rr
commit
|
commitdiff
|
tree
2016-03-14
B
e
rk Hess
Re
m
ov
e
re
s
tricti
o
n on dihd
r
altypes or
d
er
commit
|
commitdiff
|
tree
2016-03-12
Berk
He
s
s
S
plit o
f
f F
e
rmi kernel fro
m
CUDA
kernel
commit
|
commitdiff
|
tree
2016-03-09
B
erk H
e
ss
F
ix E
w
ald
3
D
C
dipole
w
ith Verlet scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk H
e
ss
Converted csettle(
)
to us
e
r
eal/
S
imdReal
t
empl
a
te
commit
|
commitdiff
|
tree
2016-03-03
Be
r
k
Hess
U
se SIMD transpose scatter
i
n bondeds
commit
|
commitdiff
|
tree
2016-03-03
Berk
Hes
s
U
s
e rvec4 for listed force buff
e
r
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Remove
ep
s
f
ac
f
rom GPU k
e
rnel inner-lo
o
ps
commit
|
commitdiff
|
tree
2016-02-27
Berk H
e
s
s
M
i
nor code reor
d
e
r
ing in G
P
U kerne
l
s
commit
|
commitdiff
|
tree
2016-02-26
B
erk Hess
Fix compi
l
ation with Simd4Fl
o
at,
without Simd4D
o
uble
commit
|
commitdiff
|
tree
2016-02-19
Ber
k
He
s
s
Fix exces
s
ive l
i
st s
p
l
i
tting
commit
|
commitdiff
|
tree
2016-02-17
B
erk Hess
Rename
d
nbnxn stati
c
const
i
nts
commit
|
commitdiff
|
tree
2016-02-11
Berk H
e
s
s
Add
S
IMD version of pbc_
d
x_aiuc
commit
|
commitdiff
|
tree
2016-02-09
Berk Hes
s
Replac
e
d nbnxn search+g
r
id s
i
md
macr
o
s
commit
|
commitdiff
|
tree
2016-02-07
B
e
rk Hess
Fix incorr
e
ct cmap parsing
commit
|
commitdiff
|
tree
2016-02-05
Berk
H
e
s
s
Fix incorrect c
m
ap
parsing
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Replaced literals in n
b
nx
n
l
ists by ints
commit
|
commitdiff
|
tree
2016-02-03
Berk Hes
s
Fix mdr
u
n
r
emovin
g
Verle
t
b
uf
f
er with EM
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix
S
ETTL
E
e
r
ror handl
i
ng
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Added documentation
for pme grid ind
e
xing
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix TPI
i
g
noring
P
ME mesh contributi
o
n
s
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Updat
e
-ntomp_pme -npme check
commit
|
commitdiff
|
tree
2016-01-29
Berk H
e
ss
Add check for double pertu
r
b
ation
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix LINCS triangle constraint t
h
read
i
s
sue
commit
|
commitdiff
|
tree
2016-01-28
B
e
rk H
e
ss
Updat
e
pair-list
b
uffer manual
commit
|
commitdiff
|
tree
2016-01-24
Berk
H
ess
Fix exact contin
u
ation fro
m
n
o
n-
e
ner
g
y
steps
commit
|
commitdiff
|
tree
2016-01-24
Be
r
k Hess
F
i
x
energy file
c
ontinuat
i
on
w
ith
md-v
v
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
F
ix energy average with continuatio
n
commit
|
commitdiff
|
tree
2016-01-08
Berk
Hess
Fix
P
ME load balanc
i
ng
ski
p
pin
g
a s
e
tup
commit
|
commitdiff
|
tree
2015-12-29
B
erk
H
ess
Co
r
rect
vector check of gmx
check
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
Reorganized domdec initialization
commit
|
commitdiff
|
tree
2015-12-20
B
e
rk Hess
Merge release-5
-
1 into master
commit
|
commitdiff
|
tree
2015-12-19
Berk H
e
s
s
Br
i
ng perfor
m
ance es
t
imation
u
p to
d
at
e
commit
|
commitdiff
|
tree
2015-12-17
Berk Hess
R
emoved topolo
g
y
p
o
i
nt
e
rs from DD struct
commit
|
commitdiff
|
tree
2015-12-16
Berk Hess
Ad
d
one elem
e
n
t t
o
state rvec array
s
commit
|
commitdiff
|
tree
2015-12-12
Berk Hess
Removed
unused mdrun
option
-
d
n
commit
|
commitdiff
|
tree
2015-12-11
Berk
Hess
Fix b
u
g wit
h
pull group weights
commit
|
commitdiff
|
tree
2015-12-07
Be
r
k
Hess
Moved p
u
ll para
m
s to mdtypes/pull
-
para
m
s
.
h
commit
|
commitdiff
|
tree
2015-12-02
B
erk H
e
ss
Increas
e
pdb
c
hain ids
t
o
62 in output
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Refactored
set_pbc_d
d
commit
|
commitdiff
|
tree
2015-12-02
Berk Hes
s
Made t_i
n
putrec c
o
nst in P
M
E load balan
c
i
ng
commit
|
commitdiff
|
tree
2015-12-01
B
e
rk Hess
Pull gro
u
p
cou
n
t for coords stored
i
n
tpr
commit
|
commitdiff
|
tree
2015-11-19
Berk
H
ess
Removed mdr
u
n fatal_error
wi
t
h P3M-AD
commit
|
commitdiff
|
tree
2015-11-18
B
erk Hess
Removed Reactio
n
-Field-n
e
c
commit
|
commitdiff
|
tree
2015-11-14
B
e
rk He
s
s
Op
t
imized the bo
n
ded t
h
read forc
e
red
u
ction
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
Fixed
(
harmless) fp
exception in
w
allcycle_sum
commit
|
commitdiff
|
tree
2015-11-09
Berk Hess
Co
r
re
c
t
L
INCS
d
Hdl c
o
ntribution
commit
|
commitdiff
|
tree
2015-11-03
Berk H
e
ss
F
i
x no wallcycle sup
p
o
r
t
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Remove
d
nbnxn
kernel
b
lendv
optimization
commit
|
commitdiff
|
tree
2015-11-02
Berk Hess
Fix
intermolecular i
n
teractions with small mols
commit
|
commitdiff
|
tree
2015-10-15
Ber
k
Hess
Fixed nbn
x
n
_4xN
performa
n
ce regression
commit
|
commitdiff
|
tree
2015-10-07
Berk Hes
s
Fix bugs with intermol interac
t
ions and DD
commit
|
commitdiff
|
tree
2015-10-01
Berk Hess
R
emo
v
ed CUDA polling
wait
commit
|
commitdiff
|
tree
2015-09-27
Berk Hess
Move gmx_domdec_comm_t
d
efi
n
ition
commit
|
commitdiff
|
tree
2015-09-22
B
e
rk
Hess
Removed useles
s
multiple
s
h
ifts in pb
c
.
c
pp
commit
|
commitdiff
|
tree
2015-09-16
Berk Hess
Split nbnxn_grid
.
c off fro
m
nbnxn_search
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk Hes
s
Detect
i
ncorrect cycle counting
commit
|
commitdiff
|
tree
2015-08-25
Berk
Hess
Simplify changing the
tpx_ver
s
ion
commit
|
commitdiff
|
tree
2015-08-14
B
e
r
k
H
e
s
s
Make mdrun -n
t
work
a
gain
commit
|
commitdiff
|
tree
2015-08-13
Be
r
k Hess
Added
set
_
pull
_
c
oord_reference_valu
e
commit
|
commitdiff
|
tree
2015-08-12
B
erk
H
es
s
Added const
q
ualifier
s
t
o
core MD routines
commit
|
commitdiff
|
tree
2015-07-06
Be
r
k Hess
Fix t
o
o small GPU pair count est
i
mates
commit
|
commitdiff
|
tree
2015-07-06
Berk He
s
s
Fix bug in GPU
l
ist b
a
lanci
n
g
commit
|
commitdiff
|
tree
2015-07-05
B
e
rk Hess
Fix DD DLB state
issue
commit
|
commitdiff
|
tree
2015-07-05
Berk
Hess
Fix bug i
n
GP
U
lis
t
balancin
g
commit
|
commitdiff
|
tree
2015-07-04
Berk He
s
s
O
bey OpenMP t
h
r
e
a
d
count limit with tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
Fix two PME DL
B
trig
g
er issu
e
s
commit
|
commitdiff
|
tree
2015-07-03
B
e
r
k
H
e
ss
Corr
e
ct gr
o
mpp pull warning message
commit
|
commitdiff
|
tree
2015-06-30
Be
r
k Hess
Fix inc
o
nsiste
n
t OpenMP automation
commit
|
commitdiff
|
tree
2015-06-30
Berk Hes
s
e
nable
d
1 PP + 1 PME node
commit
|
commitdiff
|
tree
2015-06-30
Be
r
k
Hess
Add
checks
f
or inefficient resource usage
commit
|
commitdiff
|
tree
2015-06-29
Berk Hess
Improve DLB
+
PME tuning
w
ith GP
U
s
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk Hess
Impro
v
e pa
i
r
s
earch th
r
ead load
balance
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk Hess
Impr
o
v
ed
t
h
e in
t
ra
-
GPU load
b
alancing
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk Hess
Re
d
uce the
u
s
e of n
b
n
xn_consts
.
h
commit
|
commitdiff
|
tree
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