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Support 4 sized cluster for GPU NBL search
2018-05-02
Roland Sch
u
lz
Support 4
s
ize
d
cluster fo
r
GP
U
N
B
L search
commit
|
commitdiff
|
tree
2018-04-27
Be
r
k Hess
Remove
pull M
P
I code duplicatio
n
commit
|
commitdiff
|
tree
2018-04-26
Paul B
a
uer
Reorganize file
s
for refere
n
ce manu
a
l
commit
|
commitdiff
|
tree
2018-04-26
Pau
l
Ba
u
er
Split up analysis chapter in reference manual
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
Spl
i
t
up spe
c
ial topics
secti
o
n in man
u
al
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
A
dd page
b
reaks in re
f
erenc
e
manual
commit
|
commitdiff
|
tree
2018-04-25
Paul
B
auer
S
p
l
it up Interactio
n
functions manual page
commit
|
commitdiff
|
tree
2018-04-25
Mark Abraham
Refactor SD update
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
C
hange im
a
g
e conversion to only
b
e
b
uild once
commit
|
commitdiff
|
tree
2018-04-23
Ale
k
sei Iupinov
Dev
i
c
e
Buffe
r
headers are a
d
ded
commit
|
commitdiff
|
tree
2018-04-23
Szilárd Páll
Fix icc warning in post-submit
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Páll
Ad
d
post-submit with
ARM HPC Tool
c
h
a
in
commit
|
commitdiff
|
tree
2018-04-21
S
z
i
lá
r
d Páll
Tweak PM
E
run mo
d
e
checks
commit
|
commitdiff
|
tree
2018-04-21
Paul
Baue
r
C
onvert m
a
nual from LaT
e
X to Mark
u
p
commit
|
commitdiff
|
tree
2018-04-21
Paul
B
auer
Second ch
a
nge
t
racking co
m
mi
t
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Intermediate commit to t
r
ack changes to manual
commit
|
commitdiff
|
tree
2018-04-17
Vi
v
eca Lindahl
Disa
l
low -ski
p
values <= 0 for gmx trjconv
.
commit
|
commitdiff
|
tree
2018-04-17
P
aul Bauer
Fix legacy topology memo
r
y e
r
r
or
commit
|
commitdiff
|
tree
2018-04-17
Mark Abra
h
am
Shif
t
per-ste
p
contr
o
l lo
g
ic to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark Ab
r
aham
Bre
a
k
apart update_co
n
straints
commit
|
commitdiff
|
tree
2018-04-16
Szilár
d
Páll
Add post-submit test with hwloc
o
f
f
commit
|
commitdiff
|
tree
2018-04-16
B
e
rk Hess
Mov
e
nato
m
s_
m
ol out
of
g
mx_molb
l
ock_t
commit
|
commitdiff
|
tree
2018-04-16
Mark
A
braham
Updat
e
d mdr
u
n
comp
a
rison infra
s
t
r
ucture
commit
|
commitdiff
|
tree
2018-04-13
Mark Abraham
Clea
n
u
p
constraints cod
e
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Remove use of where(),
if DEB
U
G etc
.
commit
|
commitdiff
|
tree
2018-04-12
M
a
rk
A
braham
Re
o
rganize ene
r
gy evaluation for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei
I
upi
n
ov
Prevent OpenCL timing memory leak
commit
|
commitdiff
|
tree
2018-04-09
Berk
H
ess
Co
n
vert gmx
_
molblock_t to C+
+
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Si
m
plified h
a
n
d
l
ing of
simu
l
atio
n
runners
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Create
gromacs/mdrun module and
m
ove
code
t
h
ere
commit
|
commitdiff
|
tree
2018-04-05
Szi
l
ár
d
Páll
Refactor cj
p
relo
a
d in
the nonbonded
OpenC
L
ke
r
n
els
commit
|
commitdiff
|
tree
2018-04-04
Mark
A
b
raham
Quiet ch
e
ckpoint rea
d
i
n
g
commit
|
commitdiff
|
tree
2018-04-04
Pascal Mer
z
Mo
v
e checkN
u
mberOfBonded
I
nteractions
commit
|
commitdiff
|
tree
2018-04-03
Berk H
e
ss
C
onvert gmx_mtop_t to
C
++
commit
|
commitdiff
|
tree
2018-04-03
M
ark Abraham
R
emo
v
e leftover menti
o
n of twin-ra
n
ge s
c
h
eme
commit
|
commitdiff
|
tree
2018-04-03
Mark Ab
r
a
ham
Merge
"
Merge
b
r
a
nch
r
e
lease-2018"
commit
|
commitdiff
|
tree
2018-03-29
B
erk Hess
Mov
e
fi
l
e o
p
e
nin
g
out o
f
ini
t
_p
u
ll()
commit
|
commitdiff
|
tree
2018-03-29
Szilárd
Páll
Tweak/ena
b
le icc
1
8
post-submit tests
commit
|
commitdiff
|
tree
2018-03-29
Magnus L
u
ndb
o
rg
Improv
e
d
c
heck of
i
f
on
l
y forces ar
e
compute
d
in
d
o_pai
r
s()
commit
|
commitdiff
|
tree
2018-03-29
Paul Bauer
Fix
cmak
e
Sphinx
detectio
n
for versions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
S
z
ilárd P
á
ll
Switch
C
UDA 9
.
0
/
gcc 5 t
e
s
t t
o
CUD
A
9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
B
e
r
k H
e
s
s
M
o
dul
a
rize p
u
ll_coord_wor
k
_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
F
r
ee more mem
o
ry in
g
rompp and m
d
r
un
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Remo
v
e mols from
g
mx_
m
to
p
_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraha
m
M
e
r
g
e
b
ranch release-
2
018
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
C
larified mdp options relating to bonds
commit
|
commitdiff
|
tree
2018-03-27
M
a
rk
A
b
raham
More
g
cc-
8
f
ixes for POWER
commit
|
commitdiff
|
tree
2018-03-21
D
a
vid van der Spoel
Renamed entropy
.
* to
thermochemi
s
try
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Ver
s
ion 201
8
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark
Abrah
a
m
Merge "Merge
branch re
l
ease-20
1
6 into
r
elease-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark A
b
raha
m
U
p
date release notes for 2
0
18
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark
Abr
a
ha
m
Merge branch rel
e
a
se-2016 i
n
to
r
ele
a
s
e-
2
018
commit
|
commitdiff
|
tree
2018-03-20
M
ark Ab
r
aham
Update use
o
f
gp
u
_id in
J
enkins
commit
|
commitdiff
|
tree
2018-03-20
Berk Hes
s
Disallow single simulation wit
h
m
ultisim
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
A
b
rah
a
m
U
pdate
u
se of g
p
u_id i
n
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abra
h
am
U
pdate use o
f
gpu_id i
n
J
enkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
A
d
d
helper functio
n
to make a v
e
ctor from an ArrayRef
commit
|
commitdiff
|
tree
2018-03-19
M
ark Abraham
Fix VSX SIMD wit
h
g
cc 8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
Only free t
o
pology wh
e
n a
l
located
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct PMF sign err
o
r in AWH
bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk He
s
s
I
mpro
v
e inter
-
sim
u
lation signaling
commit
|
commitdiff
|
tree
2018-03-14
M
ark Abrah
a
m
Make a p
e
rsistent phy
s
ical node communic
a
tor
commit
|
commitdiff
|
tree
2018-03-14
Berk He
s
s
F
i
x md
r
un si
g
nalling with AWH b
i
as
s
haring
commit
|
commitdiff
|
tree
2018-03-13
Ber
k
Hess
A
dd AWH fi
x
es to
release notes
commit
|
commitdiff
|
tree
2018-03-13
Szilá
r
d Páll
R
e
q
u
i
r
e
OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ensemble checkp
o
in
t
in
g
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH deconvoluti
o
n when shari
n
g a bias
commit
|
commitdiff
|
tree
2018-03-13
Mark Ab
r
aham
I
ntroduce constrain_shake
commit
|
commitdiff
|
tree
2018-03-13
Szil
á
rd Páll
Fix clang 6
.
0 with CUDA
9
.
0
commit
|
commitdiff
|
tree
2018-03-13
M
ark
A
b
r
a
ham
M
e
r
g
e
"
Merge
b
r
anch rel
e
as
e
-2018"
commit
|
commitdiff
|
tree
2018-03-09
B
e
rk Hess
Correct pdb2gmx -missing option
commit
|
commitdiff
|
tree
2018-03-06
Berk Hes
s
Convert t_f
i
lenm to C
+
+
commit
|
commitdiff
|
tree
2018-03-06
Ma
r
k A
b
raham
M
e
rge branch release-2018
commit
|
commitdiff
|
tree
2018-03-06
M
a
rk Abra
h
am
Fixed
d
vd
l
am
b
d
a f
o
r
SHAK
E
+ FE
commit
|
commitdiff
|
tree
2018-03-05
Szi
l
árd Páll
A
d
d to
t
he contributor se
c
tion
commit
|
commitdiff
|
tree
2018-03-01
B
e
rk Hes
s
Detect
A
MD SMT topology
commit
|
commitdiff
|
tree
2018-02-28
Mark Abraham
Moved and removed
c
onstrai
n
t code
commit
|
commitdiff
|
tree
2018-02-28
Mark Abraham
R
e
or
g
anize
d
constraint code
commit
|
commitdiff
|
tree
2018-02-27
Mark Abraha
m
Fix G
P
U utils test
commit
|
commitdiff
|
tree
2018-02-26
Paul B
a
uer
Chan
g
e TNG file opening
commit
|
commitdiff
|
tree
2018-02-26
Mark
A
braham
P
e
r
mi
t
define
.
m
dp f
i
eld
to a
s
s
ign val
u
es
commit
|
commitdiff
|
tree
2018-02-26
Aleksei Iupinov
Advice users on in
f
inite outp
u
t of TPI
commit
|
commitdiff
|
tree
2018-02-26
Mark A
b
ra
h
am
Orga
n
iz
e
for r
e
cording 2016-era release n
o
tes and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Berk H
e
ss
Fix
m
d integrator with Nose-Hoover cou
p
l
ing
commit
|
commitdiff
|
tree
2018-02-21
Mark
A
braham
Enhanced docs of pimpl pointer
h
elper
commit
|
commitdiff
|
tree
2018-02-16
Mark Abrah
a
m
Mer
g
e b
r
anch release
-
2
016 into release-2018
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
B
umped patc
h
ver
s
ion f
o
r next r
e
lease
commit
|
commitdiff
|
tree
2018-02-16
B
e
r
k
Hess
C
orr
e
ct multisi
m
MPI barrier
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
M
erge branch release-2018 into
m
as
t
er
commit
|
commitdiff
|
tree
2018-02-16
M
a
rk Abraham
V
ersion 2016
.
5
commit
|
commitdiff
|
tree
2018-02-15
Mark A
b
r
aham
Use
s
truct for
chec
k
point header conte
n
ts
commit
|
commitdiff
|
tree
2018-02-15
A
leks
e
i Iupinov
Update F
F
T
W
build
to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Remove read_check
p
o
i
nt_st
a
te
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Rem
o
ve sup
p
ort for tpx version b
e
fore 58/g
m
x
4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Use s
t
d::vector f
o
r
checkpoint o
u
t
p
utfiles
commit
|
commitdiff
|
tree
2018-02-14
Mark Abra
h
a
m
M
e
r
g
e
branch release-2016 into
release-2018
commit
|
commitdiff
|
tree
2018-02-14
Berk
H
e
ss
F
i
x range bug in add_
s
election_groups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Aleksei
I
up
i
nov
Replace the remaining
E
XPECT_DEATH with
EXPECT_DEATH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
A
l
e
ksei Iupinov
Ad
d
DeviceBuffe
r
as a typedef for cl
_
me
m
/device p
o
nter
commit
|
commitdiff
|
tree
2018-02-14
S
z
ilárd Páll
R
emove ba
r
riers prev
e
ntin
g
t
extu
r
e re
f
erence rac
e
s
commit
|
commitdiff
|
tree
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