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Always run the essential dynamics tests
2018-02-08
Aleksei
Iupinov
Always run the e
s
s
e
nt
i
al dynam
i
cs
t
e
s
t
s
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
Merge branch 'r
e
l
e
ase-2018' into ma
s
ter
commit
|
commitdiff
|
tree
2018-02-06
A
l
eksei
Iupin
o
v
R
e
m
o
v
e unnecessary includes from domd
e
c
.
h
commit
|
commitdiff
|
tree
2018-02-06
Aleks
e
i Iupinov
Zero
u
nused valu
e
s to silence the
w
arning
commit
|
commitdiff
|
tree
2018-02-06
Mark Abraham
Use
i
sf
i
nite una
m
biguou
s
ly
commit
|
commitdiff
|
tree
2018-02-05
Aleks
e
i Iupinov
Make ndx
f
iles
optiona
l
in Si
m
u
l
atio
n
Runner
commit
|
commitdiff
|
tree
2018-02-05
Aleksei I
u
pinov
Remove m
d
pInputFileNa
m
e_ from
Simulation
R
unn
e
r, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupino
v
Fix inp
u
t
M
DP
c
onte
n
ts f
o
r
s
w
ap and IMD tes
t
s
commit
|
commitdiff
|
tree
2018-02-01
Aleksei
I
u
p
ino
v
Che
c
k for
G
TEST_IS_THR
E
AD
S
AFE bein
g
defined
commit
|
commitdiff
|
tree
2018-01-30
Mark Abraham
Up
d
at
e
GoogleTest to
1
.
8
.
0
commit
|
commitdiff
|
tree
2018-01-30
B
e
rk Hess
Remove
d
u
n
u
sed flag PCA_CAN_R
E
AD
_
NODE
commit
|
commitdiff
|
tree
2018-01-24
Aleksei I
u
p
ino
v
Re
m
ove unused fields per TODO
commit
|
commitdiff
|
tree
2018-01-23
Alek
s
ei Iupino
v
Test the mixed mode PME wi
t
h w
a
l
l
s a
n
d box scaling
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i
Iupin
o
v
Mov
e
t
h
e
temporary
f
ile MPI workaround into
t
he base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Merge b
r
an
c
h 'relea
s
e-2018' into master
commit
|
commitdiff
|
tree
2018-01-18
Mark Abraham
Port thread
-
MP
I
t
o
comp
i
le as C
+
+
commit
|
commitdiff
|
tree
2018-01-17
A
leksei
Iup
i
nov
Me
r
ge
b
ranch 'rel
e
ase-2018' into m
a
ster
commit
|
commitdiff
|
tree
2018-01-16
Alek
s
ei Iupinov
A
lways write the input MDP file
for
t
e
s
t
in
g
j
ust bef
o
re
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
A
leksei Iupinov
Move O
c
tan
e
Sand
w
ich
.
mdp and spc2-IMD
.
mdp into strings
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iup
i
nov
Re
m
ove
u
nused
alani
n
e_vsit
e
.
mdp
commit
|
commitdiff
|
tree
2018-01-11
M
ark A
b
ra
h
a
m
Remove contrib di
r
ec
t
ory
commit
|
commitdiff
|
tree
2018-01-03
Erik
L
indahl
Re
m
ove
d
uplication
s
in GMXLIB search paths
commit
|
commitdiff
|
tree
2017-12-27
Mark A
b
raham
Silence POWE
R
8
co
m
piler w
a
rnin
g
s
commit
|
commitdiff
|
tree
2017-12-21
Mar
k
Ab
r
a
ham
Version 5
.
1
.
5
commit
|
commitdiff
|
tree
2017-12-20
Aleksei
Iupinov
Set GMX_GPU_
A
UTO to
FALSE with GMX_GPU defined
commit
|
commitdiff
|
tree
2017-12-11
M
ark Abraham
Con
s
ume any error prod
u
ced d
u
rin
g
G
PU
d
e
tection
commit
|
commitdiff
|
tree
2017-12-08
Berk He
s
s
A
d
d Viveca Lindahl as
c
o
n
trib
u
tor
commit
|
commitdiff
|
tree
2017-12-03
Be
r
k He
s
s
Tighten B-spli
n
e moduli single prec
i
sion test
tolera
n
ce
.
.
.
commit
|
commitdiff
|
tree
2017-11-28
A
l
eksei Iupinov
Replac
e
of pm
e
GPU variabl
e
name wit
h
p
m
eG
p
u
commit
|
commitdiff
|
tree
2017-11-28
Sz
i
lárd Páll
Separate local GPU NB wait from e
m
u
l
ation la
u
nch
commit
|
commitdiff
|
tree
2017-11-28
Sz
i
lárd Pá
l
l
Refac
t
or
GPU rol
l
ing pr
u
ne lau
n
ch
commit
|
commitdiff
|
tree
2017-11-27
Aleksei I
u
pinov
Add tests for PME tuni
n
g an
d
fix mixed PME mode
w
ith
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupin
o
v
D
e
stroy PME G
P
U
context
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iup
i
no
v
Do
n
o
t call
m
ix
e
d CPU+GPU PME m
o
de "Hyb
r
id"
commit
|
commitdiff
|
tree
2017-11-24
B
e
rk Hess
Disab
l
ed CUDA
t
imings
commit
|
commitdiff
|
tree
2017-11-24
M
a
rk Ab
r
aham
Se
p
arat
e
management o
f
GPU cont
e
xts from modul
e
s
commit
|
commitdiff
|
tree
2017-11-23
Szil
á
rd Páll
M
ove
G
PU FFT
/
gather laun
c
h after GPU nonbo
n
de
d
s
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupinov
Fix CUD
A
re
l
ease
b
uild warning
commit
|
commitdiff
|
tree
2017-11-21
Aleks
e
i Iupinov
Fix pinned memory st
a
tus checker tests
commit
|
commitdiff
|
tree
2017-11-20
Berk Hes
s
Prevent PME tuning excessive grid scaling
commit
|
commitdiff
|
tree
2017-11-19
M
a
r
k Abraham
Fix Fin
d
C
U
D
A
.
cmake for
-
Wundef
commit
|
commitdiff
|
tree
2017-11-17
Aleksei
I
up
i
nov
Make
gpu_uti
l
s
-test buil
d
with GMX_CLANG_CUDA
commit
|
commitdiff
|
tree
2017-10-31
Mark
A
b
r
aham
Updat
e
treat
m
ent of GPU compati
b
ilit
y
data structur
e
commit
|
commitdiff
|
tree
2017-10-31
S
zilárd Páll
F
i
x
nstlist increase w
a
rning
p
ri
n
t
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Use
n
e
w
/delete fo
r
gmx_
p
me_t
commit
|
commitdiff
|
tree
2017-10-30
Aleksei
Iupi
n
ov
Simplify
P
ME data handling in runner
commit
|
commitdiff
|
tree
2017-10-29
Ale
k
s
ei Iupinov
Ma
k
e
P
ME tu
n
ing logic more readab
l
e
commit
|
commitdiff
|
tree
2017-10-27
Aleksei Iup
i
no
v
Replace a few assert
s
with GMX
_
A
S
S
ERT's
commit
|
commitdiff
|
tree
2017-10-27
Al
e
ks
e
i Iup
i
nov
Re
m
o
v
e
defunct
PME
i
nitialization error c
o
de
r
eturn
commit
|
commitdiff
|
tree
2017-10-26
Mark Abrah
a
m
M
a
ke release
m
atri
x
work ag
a
in
commit
|
commitdiff
|
tree
2017-10-24
Aleksei Iupinov
Remove duplicate/
o
u
t
dated funct
i
on dec
l
aration
commit
|
commitdiff
|
tree
2017-10-23
Aleksei Iupi
n
o
v
Correct the pa
g
e al
l
ocator des
c
ription
commit
|
commitdiff
|
tree
2017-10-23
S
z
i
lárd Páll
Elimin
a
te so
m
e OCL/CUDA code
co
d
e
dupli
c
at
i
on
commit
|
commitdiff
|
tree
2017-10-22
Ale
k
s
e
i Iupi
n
ov
Change PM
E
GPU gather
red
u
ction a
r
gument from boolean
.
.
.
commit
|
commitdiff
|
tree
2017-10-21
A
l
eksei Iupinov
Add
c
alls
t
o the
P
M
E GPU stag
e
s
commit
|
commitdiff
|
tree
2017-10-19
Szi
l
ár
d
Pá
l
l
Remo
v
e unised OpenCL
debugging
h
e
lpers
commit
|
commitdiff
|
tree
2017-10-12
Aleksei Iupinov
Remove useless
extern
C
UDA texture reference de
c
lar
a
ti
o
n
s
.
.
.
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
CUDA 9/Volta support for PME
commit
|
commitdiff
|
tree
2017-10-11
Al
e
ksei Iupinov
Drop
NB_ f
r
o
m
G
MX_C
U
DA_NB_SING
L
E_COMPILATION_UN
I
T cmake
.
.
.
commit
|
commitdiff
|
tree
2017-10-09
A
le
k
sei
I
u
pinov
R
e
move
s
ome unnecessary includes from P
M
E
commit
|
commitdiff
|
tree
2017-10-04
Aleksei Iupinov
Remove GPU tim
i
ng fun
c
tions supersed
e
d
b
y G
p
uRegi
o
n
T
imer
commit
|
commitdiff
|
tree
2017-10-03
Szilár
d
Páll
Move E
w
ald splitting
-
related code
to e
w
ald-utils
commit
|
commitdiff
|
tree
2017-10-03
A
l
e
ksei
Iupi
n
o
v
Bri
n
g
C
UDA textu
r
e
ge
t
ters
documentatio
n
up-to-d
a
te
commit
|
commitdiff
|
tree
2017-10-03
A
l
eks
e
i Iupinov
A
dd Wi
n
A
PI page
si
z
e
quer
y
for
a
llocator p
u
rposes
commit
|
commitdiff
|
tree
2017-09-22
A
l
eksei Iu
p
inov
Tem
p
la
t
e the CUDA text
u
re setup
c
ode on raw value type T
commit
|
commitdiff
|
tree
2017-09-21
Aleksei Iupinov
Eliminate unu
s
ed Cou
l
o
m
b correction
table s
i
ze co
u
l
omb_tab_size
commit
|
commitdiff
|
tree
2017-09-21
Aleksei Iup
i
nov
El
i
minat
e
duplicat
e
CUDA t
e
xture
s
et
u
p code
commit
|
commitdiff
|
tree
2017-09-19
Rolan
d
S
c
hulz
IC
C
: Disabl
e
in
c
lu
d
e path warning
commit
|
commitdiff
|
tree
2017-09-19
Mark Abraham
Upda
t
e t
e
stin
g
m
a
trices to
t
est with (
l
a
t
est) i
c
c-
1
8
commit
|
commitdiff
|
tree
2017-09-12
Aleksei
I
upinov
Pr
e
vent
refer
e
nce
X
ML reader s
e
gfault on nullptr
e
rror
.
.
.
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Fix exception i
n
SI
M
D LJ P
M
E sol
v
e
commit
|
commitdiff
|
tree
2017-09-08
R
oland Sch
u
lz
Fix compiler
warning
commit
|
commitdiff
|
tree
2017-09-04
Aleksei Iupinov
Merge "M
e
r
ge branch release-5-1 into rel
e
ase-2
0
16"
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Aleksei
Iupin
o
v
B
ring back
s
p
a
ce lost in comm
i
t e43
e
83b
f
commit
|
commitdiff
|
tree
2017-08-29
Ale
k
sei Iup
i
nov
Allow passing optio
n
al width argument
into CUDA shuffle
.
.
.
commit
|
commitdiff
|
tree
2017-08-28
Berk Hess
Av
o
id bonded forces loops/timers on inputs with no
.
.
.
commit
|
commitdiff
|
tree
2017-08-21
Aleksei
I
upinov
PME
solvin
g
tests
commit
|
commitdiff
|
tree
2017-08-17
Aleks
e
i Iupin
o
v
Merg
e
"
Merge branch release
-
5-1 in
t
o releas
e
-201
6
"
.
.
.
commit
|
commitdiff
|
tree
2017-07-06
Mar
k
Abraham
Simp
l
if
y
gmx_
g
pu_opt_t
commit
|
commitdiff
|
tree
2017-07-03
B
e
rk Hess
R
emove gm
x
_constexpr
commit
|
commitdiff
|
tree
2017-06-30
Alekse
i
I
u
pinov
Remove outdated cm
a
ke
n
vcc logic
commit
|
commitdiff
|
tree
2017-06-30
M
.
Er
i
c Irrgang
Mark unmodified
i
n
p
u
t
parameter
as co
n
st
.
commit
|
commitdiff
|
tree
2017-06-07
Vedran Mile
t
ić
Exp
a
n
d
Performa
n
ce
s
ect
i
on of
t
he user guide
commit
|
commitdiff
|
tree
2017-06-07
Szilárd Páll
Supp
r
es
s
sm_2x depre
c
ati
o
n wa
r
n
in
g
with
C
UDA 8
.
0
commit
|
commitdiff
|
tree
2017-04-18
Berk Hess
Suppre
s
s
two compile
r
warnings
commit
|
commitdiff
|
tree
2017-04-06
Teemu Murtola
Fix memory access issues in g
m
x solvate
commit
|
commitdiff
|
tree
2017-04-06
T
eemu Murtola
C
o
n
s
istent na
m
ing for
g
mx
a
na tests
commit
|
commitdiff
|
tree
2017-04-04
Tee
m
u
Mur
t
ola
Utility functions for formatting s
t
r
i
n
g
values
commit
|
commitdiff
|
tree
2017-03-29
Mark Abraham
Fix
parameter descrip
t
io
n
for di
h
e
d
ral_restraint
s
commit
|
commitdiff
|
tree
2017-03-29
Szi
l
árd Pá
l
l
Add CUDA u
t
il
f
unction fo
r
constant loads
commit
|
commitdiff
|
tree
2017-03-25
Szilárd Pá
l
l
Conditi
o
nal
twe
a
k in the non
b
onded G
P
U
k
e
rnels
commit
|
commitdiff
|
tree
2017-03-17
Ale
k
s
e
i Iupinov
Fix dereferenc
i
ng nullptr in PME
solve work destr
u
ctor
commit
|
commitdiff
|
tree
2017-03-09
Ma
r
k Abra
h
am
R
efactor G
P
U
selec
t
ion handli
n
g
commit
|
commitdiff
|
tree
2017-02-21
Al
e
ks
e
i Iup
i
nov
R
e
m
o
ve
u
nused function
c
u_synchs
t
ream_atd
a
t()
commit
|
commitdiff
|
tree
2017-02-09
A
leksei Iupinov
Fix
ty
p
o (D
i
hed
a
rl
-
> Dihedral)
commit
|
commitdiff
|
tree
2017-02-02
Berk Hes
s
Fix array of compl
e
x in cross_co
r
r
commit
|
commitdiff
|
tree
2017-01-19
Ale
k
sei Iupinov
Simpl
i
fy gmx_count_gpu_dev_
u
niqu
e
()
commit
|
commitdiff
|
tree
2017-01-05
Aleksei
I
upinov
Fix compi
l
ation with CMAKE_CX
X
_
F
LAGS
=
"
-
W
a
ll -Werror"
commit
|
commitdiff
|
tree
2016-12-22
A
leksei Iupi
n
ov
Remove
unu
s
ed member thre
a
d
_one
f
rom the PME spline
.
.
.
commit
|
commitdiff
|
tree
2016-12-05
Al
e
ksei Iupinov
Sto
p
includin
g
p
arallel_3dfft
.
h
i
n headers
commit
|
commitdiff
|
tree
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