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Extend "Finding out how to run mdrun better" section
2018-03-06
Szilárd Páll
Extend "Fin
d
ing out how
t
o run
m
drun be
t
ter" section
commit
|
commitdiff
|
tree
2018-03-05
Szilárd Páll
A
d
d
to the contributor secti
o
n
commit
|
commitdiff
|
tree
2018-02-21
S
zilárd Páll
Switch
pre-sub
m
it CUDA 8
.
0
test to
9
.
0
commit
|
commitdiff
|
tree
2018-02-20
Szilárd Páll
Avoi
d
aborti
n
g
mdr
u
n when GPU sanity
c
heck detects
.
.
.
commit
|
commitdiff
|
tree
2018-01-12
S
zilárd Páll
Cal
l
GPU
profil
e
r
reset on sep
a
rate PME r
a
nks
commit
|
commitdiff
|
tree
2018-01-10
Szil
á
rd Páll
User guide upd
a
tes to GPU
s
ection
commit
|
commitdiff
|
tree
2018-01-10
S
zil
á
rd Páll
Release no
t
es
tweaks
commit
|
commitdiff
|
tree
2018-01-10
Szil
á
rd Páll
I
n
st
a
ll guide
u
pdat
e
s
commit
|
commitdiff
|
tree
2018-01-10
Szilárd Páll
Environm
e
nt variable doc
s
maintenance
commit
|
commitdiff
|
tree
2017-12-10
Szilárd
P
áll
Disable defaul
t
-
o
n NVM
L
support in CMake
commit
|
commitdiff
|
tree
2017-12-06
Szilárd Pál
l
Implement altern
a
ting
GP
U
wait
commit
|
commitdiff
|
tree
2017-11-28
Szilárd Páll
Separate local GP
U
NB
w
ait from emulation launch
commit
|
commitdiff
|
tree
2017-11-28
Szi
l
árd Páll
Refa
c
tor GPU rolli
n
g
p
rune
l
aunch
commit
|
commitdiff
|
tree
2017-11-27
Szilárd Páll
Time FFT/gat
h
e
r
i
n mixed m
o
de
commit
|
commitdiff
|
tree
2017-11-24
Szilárd Páll
Add GPU sharing pos
t
-
s
ubmit config
commit
|
commitdiff
|
tree
2017-11-23
Szilár
d
Pá
l
l
Move GPU FF
T
/g
a
t
h
e
r
launch a
f
te
r
G
P
U non
b
ondeds
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Us
e
-m
a
vx2
-
m
fma i
n
stead
of -march
with AVX2
commit
|
commitdiff
|
tree
2017-11-07
S
z
i
l
árd Páll
Merge com
m
o
n n
b
nxn CUDA
/
O
penCL G
P
U
w
ait
c
o
d
e-paths
commit
|
commitdiff
|
tree
2017-11-07
S
z
i
l
árd Páll
Add wallcycle tim
e
r for the PME G
P
U F reduction
commit
|
commitdiff
|
tree
2017-11-07
Szilár
d
Páll
Split off nb
n
xn GP
U
tim
i
ng a
n
d staging
r
educti
o
n
commit
|
commitdiff
|
tree
2017-11-07
Szilárd
Páll
Deduplica
t
e CUD
A
and OpenC
L
timer
s
truct
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Fix nst
l
i
s
t
i
n
crea
s
e w
a
rning print
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
C
h
eck
CUD
A
avai
l
a
ble/com
p
iled code compat
i
b
i
li
t
y
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Fix nstlist
i
ncr
e
ase
w
a
rning print
commit
|
commitdiff
|
tree
2017-10-26
Szilárd Páll
R
eorganize PM
E
GPU lau
n
ch
commit
|
commitdiff
|
tree
2017-10-23
Szilárd Páll
Eliminate
s
om
e
OCL/
C
UDA c
o
de code dup
l
icatio
n
commit
|
commitdiff
|
tree
2017-10-19
Szilárd Páll
Disable Open
M
P
with clang
3
.
4 post-submit
con
f
ig
commit
|
commitdiff
|
tree
2017-10-19
Szilárd
P
áll
Remove unised
O
p
enCL
debug
g
ing he
l
pers
commit
|
commitdiff
|
tree
2017-10-12
Szilárd
P
áll
Remov
e
the
size_t
from the P
M
E ga
t
her CUDA ken
e
ls
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Páll
Refactor
scaled box h
a
n
d
l
ing for PME/Ewald
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Páll
F
i
x pair li
s
t array asse
r
tion
commit
|
commitdiff
|
tree
2017-10-05
Szilárd
P
áll
Avoi
d
-
Wmissin
g
-prototypes wa
r
ni
n
gs in
c
lang CUDA build
s
commit
|
commitdiff
|
tree
2017-10-03
Szilárd Páll
Move Ewald s
p
litti
n
g
-
r
elat
e
d code to ewald-util
s
commit
|
commitdiff
|
tree
2017-10-03
S
z
ilárd
P
áll
Enable compiling CUDA device code with c
l
ang
commit
|
commitdiff
|
tree
2017-09-28
Szilárd Páll
Correct mispla
c
ed
CUDA ti
m
i
n
g
e
v
ent record
commit
|
commitdiff
|
tree
2017-09-26
Szilárd Páll
Rename GPU launch/
w
a
it cycle c
o
unters
commit
|
commitdiff
|
tree
2017-09-18
Szilárd
P
ál
l
Minor refactori
n
g o
f
CUDA
non-
b
ond
e
d ke
r
nel
s
commit
|
commitdiff
|
tree
2017-09-14
Szi
l
árd Páll
CUDA 9/Vol
t
a suppo
r
t for the pru
n
ing kern
e
l
commit
|
commitdiff
|
tree
2017-09-12
Szilárd
Pál
l
Merg
e
branch 'release-2016'
commit
|
commitdiff
|
tree
2017-09-11
Szilárd Pál
l
NVIDIA
V
ol
t
a performance
t
weaks
commit
|
commitdiff
|
tree
2017-08-29
Szilárd
P
á
ll
F
ix typo and tweak env var docs
commit
|
commitdiff
|
tree
2017-08-29
Sz
i
l
á
rd P
á
ll
A
v
oid divis
i
on by ze
r
o
is prun
i
n
g
part cal
c
ul
a
ti
o
n
commit
|
commitdiff
|
tree
2017-08-21
Szilárd Páll
A
dd OpenC
L
p
ru
n
ing
kernels and launch/timing logic
commit
|
commitdiff
|
tree
2017-08-18
Szil
á
rd Páll
Improve awkward handling of GMX_CUDA_TA
R
GET* he
l
p
commit
|
commitdiff
|
tree
2017-08-18
S
z
ilár
d
Páll
Add CU
D
A
pr
u
ning
kernels and launch/timi
n
g logic
commit
|
commitdiff
|
tree
2017-07-27
Szilárd Páll
Infor
m
user
s
abou
t
t
he end of ru
n
DLB s
t
a
te
commit
|
commitdiff
|
tree
2017-06-26
Szilárd Páll
Add ARM_NEON_ASIM
D
post-submit t
e
st
commit
|
commitdiff
|
tree
2017-06-21
Szilárd Páll
Re-e
n
abl
e
lost DD war
n
ing + min
o
r code modernization
commit
|
commitdiff
|
tree
2017-06-20
Szilárd P
á
ll
Re
-
enab
l
e accidentally lost DD warning
commit
|
commitdiff
|
tree
2017-06-20
Szi
l
árd Páll
R
e
f
actoring + clarification o
f
D
L
B stat
e
ha
n
dling
commit
|
commitdiff
|
tree
2017-06-15
Sz
i
lárd Pá
l
l
Al
l
ow disabling the explici
t
use
of CUDA text
u
res
commit
|
commitdiff
|
tree
2017-06-07
Szilá
r
d Páll
Suppress
sm_2x depreca
t
ion warning wi
t
h CUDA
8
.
0
commit
|
commitdiff
|
tree
2017-06-05
Sz
i
l
árd Páll
A
d
d CUDA 8
.
0 + S
I
MD pre
-
submit test
commit
|
commitdiff
|
tree
2017-06-02
Szi
l
árd
P
áll
Add ARM_NEON
p
ost-sub
m
it test
commit
|
commitdiff
|
tree
2017-05-29
Szilá
r
d
Páll
Quotes are cool, typo
-
free
ones are even "cooler"
commit
|
commitdiff
|
tree
2017-05-23
S
zilárd Páll
Add
b
asic
doxyg
e
n for th
e
V
erl
e
t non
b
onded mod
u
le
commit
|
commitdiff
|
tree
2017-03-29
Szilá
r
d Páll
Refactor CUDA ker
n
el u
s
e
of tables
commit
|
commitdiff
|
tree
2017-03-29
Szilárd Páll
Add CUDA util
f
unction for c
o
nstant loads
commit
|
commitdiff
|
tree
2017-03-25
Szilárd Páll
Co
n
ditional tweak in the nonb
o
nded GPU
k
ernels
commit
|
commitdiff
|
tree
2017-03-17
Sz
i
lárd Pál
l
A
l
lo
w
byp
a
ssing
Op
e
nCL dev
i
c
e
c
ompatibility ch
e
ck
commit
|
commitdiff
|
tree
2017-03-16
Szil
á
rd Páll
Print code of unkno
w
n OpenC
L
error
commit
|
commitdiff
|
tree
2017-03-09
Szilárd Páll
Fi
x
m
dru
n
h
anging upon ex
i
t wit
h
sep PME ranks
commit
|
commitdiff
|
tree
2017-01-24
S
zil
á
rd Páll
Re
m
ove
unused
a
rgument in GPU kernels
commit
|
commitdiff
|
tree
2016-12-09
S
z
ilárd Páll
Tu
r
n off
hwloc supp
o
r
t
when static lib found
commit
|
commitdiff
|
tree
2016-11-17
Szilárd Páll
C
or
r
ect
k
er
n
el launch bounds
f
or CUDA sm_60
commit
|
commitdiff
|
tree
2016-11-01
Szilárd Páll
Merg
e
"Merge bra
n
ch release-2016"
commit
|
commitdiff
|
tree
2016-10-28
Szilárd Páll
GPU-
r
el
a
te
d
addit
i
ons to the
i
nsta
l
l/user guide
commit
|
commitdiff
|
tree
2016-10-27
S
zilárd Páll
Make -cl-fast-relaxed-math defau
l
t
commit
|
commitdiff
|
tree
2016-10-26
Szilár
d
Pá
l
l
Add
G
M
X
_
DISABLE_GPU_TIMING
env
var
commit
|
commitdiff
|
tree
2016-10-09
S
z
i
lá
r
d Páll
Cor
r
ect
k
er
n
el
launc
h
bo
u
nds for
CUDA sm_60
commit
|
commitdiff
|
tree
2016-08-27
Szilár
d
Páll
M
a
ke AS
A
N/TSA
N
/
M
SAN build types easi
e
r to discover
commit
|
commitdiff
|
tree
2016-07-08
Szilárd Pál
l
Add PDF meta
d
ata to
the
m
anual
commit
|
commitdiff
|
tree
2016-07-08
Szilárd
Páll
User
guide clar
i
ficatio
n
s
commit
|
commitdiff
|
tree
2016-07-07
Szilárd
P
á
ll
Add use
r
g
u
ide info on CUDA
a
pplication cl
o
cks
commit
|
commitdiff
|
tree
2016-07-05
Szilárd Pá
l
l
D
oc
u
me
n
t G
M
X_G
P
U_APPLICATION_CLOCKS
commit
|
commitdiff
|
tree
2016-07-04
Szil
á
rd Páll
Disable NVIDIA JIT cac
h
e with OpenCL
commit
|
commitdiff
|
tree
2016-06-14
Szilárd P
á
ll
Fix C
U
DA bui
l
d with multiple
c
o
m
p
ilation
u
nits
commit
|
commitdiff
|
tree
2016-06-05
Szilárd Páll
A
d
d su
p
port for CU
D
A CC
6
.
0
/
6
.
1
commit
|
commitdiff
|
tree
2016-06-02
Szi
l
á
r
d
Páll
Add env
.
va
r
.
t
o enable
Open
C
L cac
h
ing
commit
|
commitdiff
|
tree
2016-06-02
Szilárd Páll
Fix Open
C
L bi
n
ary cache f
i
le
name gen
e
ratio
n
commit
|
commitdiff
|
tree
2016-05-05
S
z
ilárd Páll
Re
m
o
ve CUDA h
o
st compiler co
n
s
i
stency checks
commit
|
commitdiff
|
tree
2016-04-28
Sz
i
lárd Páll
W
o
rkaround for gcc false positive warnin
g
commit
|
commitdiff
|
tree
2016-04-27
Szi
l
árd P
á
l
l
Fix mult
i
ple MPI r
a
n
k
s
p
e
r
node with
O
p
e
n
C
L
commit
|
commitdiff
|
tree
2016-04-26
Szilárd Páll
Fix
OpenCL as
s
e
r
tion
commit
|
commitdiff
|
tree
2016-04-19
Szi
l
árd
Páll
Move o
u
t CUDA
p
rofiler t
r
iggers from N
B
NXN
commit
|
commitdiff
|
tree
2016-04-13
Szi
l
árd
P
áll
Sp
e
ll
i
ng
fixes
commit
|
commitdiff
|
tree
2016-04-13
S
z
ilárd
P
áll
D
o
n
ot creat
e
empty man/ma
n
7 directory
commit
|
commitdiff
|
tree
2016-04-04
Szil
á
rd Pál
l
Mark more vari
a
bl
e
s as
a
dvanced
commit
|
commitdiff
|
tree
2016-03-31
Szilárd
Pál
l
refacto
r
CUDA
texture-ba
s
ed t
a
ble init
i
alization
commit
|
commitdiff
|
tree
2016-03-31
Szilárd Páll
Fi
x
multipl
e
tM
P
I ranks per
O
penCL d
e
vice
commit
|
commitdiff
|
tree
2016-03-30
Szilárd P
á
ll
LJ combina
t
i
o
n rule kernels for O
p
enCL
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
R
e
-enable i-atom type local mem
p
r
efet
c
h in O
p
en
C
L
commit
|
commitdiff
|
tree
2016-03-30
Szilárd
P
á
ll
Des
c
ribe AMD APPSD
K
3
.
0
issues in
t
h
e guide
commit
|
commitdiff
|
tree
2016-03-17
Szilárd Páll
Fixed Open
C
L
e/
f
shi
f
t cle
a
r kernel first invocation
commit
|
commitdiff
|
tree
2016-02-26
Szilárd Páll
F
i
x leftover load() calls in
the
s
im
d
util he
a
ders
commit
|
commitdiff
|
tree
2016-02-19
Szi
l
á
r
d Páll
F
i
x OpenCL tabl
e
interpolatio
n
s
of
Ewald correction
commit
|
commitdiff
|
tree
2016-02-17
Szilárd Páll
reintroduce super
c
l
i
nteract
i
on mask constant
commit
|
commitdiff
|
tree
2016-02-17
Szil
á
rd Páll
change macros to constants
in GPU code
commit
|
commitdiff
|
tree
2016-02-15
Szilárd Pá
l
l
Allow GM
X
_NB_MIN_CI=0 to be passed
commit
|
commitdiff
|
tree
2016-02-11
Szilár
d
Páll
Re-ena
b
le LJ-PME + Lorentz-Ber
t
helot
o
n GPUs
commit
|
commitdiff
|
tree
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