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Unify CUDA and OpenCL lookup-table creation
2020-05-05
A
r
tem Zhmurov
U
n
ify
CUDA and Op
e
nCL lookup-table
c
reation
commit
|
commitdiff
|
tree
2020-05-04
Ar
t
em Zhmur
o
v
Unify CUDA and OpenCL lookup-tabl
e
c
r
eation
commit
|
commitdiff
|
tree
2020-04-30
ejjordan
Add EOF newlines
t
o eliminate compi
l
er warnings
commit
|
commitdiff
|
tree
2020-04-30
ej
j
ordan
Remov
e
cmak
e
logic
t
hat is outdated
b
y r
e
quiring cma
k
e
.
.
.
commit
|
commitdiff
|
tree
2020-04-27
Artem
Z
hmurov
Move PBC setu
p
out of the l
a
u
nchKer
n
el(
.
.
.
)
i
n
GPU
.
.
.
commit
|
commitdiff
|
tree
2020-04-23
Pa
u
l Ba
u
er
Use branch point also for
f
ormat and copyrigh
t
check
commit
|
commitdiff
|
tree
2020-04-23
M
a
rk A
b
ra
h
am
Mark HWLOC cma
k
e cac
h
e v
a
riabl
e
a
s
ad
v
anced
commit
|
commitdiff
|
tree
2020-04-22
Pascal
M
erz
Make init
_
dires i
n
depend
e
n
t
of
t
_
commrec
commit
|
commitdiff
|
tree
2020-04-21
Mark
Abraham
Fix war
n
i
n
g
s with c
l
ang 9
commit
|
commitdiff
|
tree
2020-04-20
Artem Zh
m
urov
Fix the number of
s
teps c
h
eck when
checkp
o
int is loaded
commit
|
commitdiff
|
tree
2020-04-20
Paul
B
auer
M
ake tests che
c
k code for warn
i
ngs same
a
s the
main
.
.
.
commit
|
commitdiff
|
tree
2020-04-16
A
r
tem Zhmu
r
ov
Unif
y
C
UDA and O
p
enCL loo
k
up-table
creation
commit
|
commitdiff
|
tree
2020-04-14
Pascal Merz
M
ake bonded
i
nterac
t
ion checking more robust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-13
Mark Abraham
F
ix warnings for
n
o-mpi build
commit
|
commitdiff
|
tree
2020-04-12
Mark Abraham
R
e
moved unused variabl
e
in force table gene
r
ation
commit
|
commitdiff
|
tree
2020-04-11
Paul Bauer
A
d
d Ima
g
e
f
o
r
GCC 7 and A
M
D Op
e
nCL
commit
|
commitdiff
|
tree
2020-04-07
Mark Abrah
a
m
Replace EnumOption
w
ith Enumerati
o
nArray
O
ption
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eric
I
rrgang
Pr
e
pare Python en
v
iro
n
ments for Git
L
ab CI
p
ipel
i
ne
.
commit
|
commitdiff
|
tree
2020-04-07
Pascal Me
r
z
Mak
e
global
t
o
pology constant in energyOutpu
t
.
printAnne
a
ling
.
.
.
commit
|
commitdiff
|
tree
2020-04-06
Ber
k
H
es
s
M
o
ve force buff
e
r resizing to m
d
s
e
tu
p
commit
|
commitdiff
|
tree
2020-04-06
Pascal Merz
Make
b
onded
i
nteraction ch
e
ck
i
n
g
more
r
obust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric I
r
rga
n
g
Impr
o
ve gmx
a
pi Python pa
c
k
ag
e
dependency reso
l
ut
i
on
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric I
r
rgang
P
run
e
c
hange-man
a
g
e
me
n
t
.
rst and update
l
inks
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eri
c
Irrg
a
ng
Prepare
Python
en
v
ir
o
nments
for GitLab CI
pipeli
n
e
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
E
r
i
c
Irrga
n
g
Require Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-23
Arte
m
Zhmurov
Introd
u
ce DeviceStreamManage
r
commit
|
commitdiff
|
tree
2020-03-21
P
a
ul Bauer
Add Doc
u
ment
a
t
i
o
n build to script
commit
|
commitdiff
|
tree
2020-03-19
Paul Ba
u
er
Add sc
r
i
p
t t
o
generate CI Docker files
commit
|
commitdiff
|
tree
2020-03-19
Artem Z
h
murov
P
a
ss DeviceContext instead of GPU runtime data wh
e
n
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
A
dd stub Var
i
ables documentatio
n
to Gi
t
L
ab
C
I doc
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric I
r
rg
a
ng
Define an argparse p
a
rent
parser for
cont
a
iner image
.
.
.
commit
|
commitdiff
|
tree
2020-03-14
M
a
r
k
Abraham
Move testing code to test directory
commit
|
commitdiff
|
tree
2020-03-12
Gilles Gouaillardet
grompp: fix the
-
ref <f
i
le>
o
p
t
ion
commit
|
commitdiff
|
tree
2020-03-10
Artem
Z
h
m
urov
Use ini
t
(
.
.
)
function to bui
l
d
DeviceContext
commit
|
commitdiff
|
tree
2020-03-07
Berk Hess
Make shak
e
w
ork w
i
thout gr
a
ph
commit
|
commitdiff
|
tree
2020-03-04
Mark Abra
h
am
Im
p
rove TPI
h
a
ndling
commit
|
commitdiff
|
tree
2020-03-02
B
e
rk Hess
Fi
x
center of mass motion removal
w
ith
frozen atoms
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmur
o
v
Updat
e
the mes
s
ag
e
on whether
update and constraints
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
P
a
ul Bauer
Remove
froze
n
ato
m
s from VCM g
r
oups
commit
|
commitdiff
|
tree
2020-02-27
Pasc
a
l Merz
Loose
n
gmxapi stopsignaler test
commit
|
commitdiff
|
tree
2020-02-27
Pascal Me
r
z
Ex
t
ract
and expose f
u
nc
t
i
on to d
e
t
er
m
ine w
h
e
ther molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
S
z
i
lárd Páll
R
emove
outdated P
M
E-GPU li
m
itation i
n
user guide
commit
|
commitdiff
|
tree
2020-02-25
Magnus Lundborg
Fi
x
out of sync c
h
eckpo
i
nt
fil
e
s in simu
l
a
t
ions
sha
r
i
ng
.
.
.
commit
|
commitdiff
|
tree
2020-02-24
Paul Baue
r
Fix
cla
n
g-6 image
t
empl
a
te
commit
|
commitdiff
|
tree
2020-02-20
A
rte
m
Zhmurov
U
se CUD
A
float3 vector
t
ype
i
nstea
d
of fvec in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
P
aul Bauer
Workaround for Gitlab archiv
e
size
commit
|
commitdiff
|
tree
2020-01-29
Magnus Lundb
o
rg
More SIMD pr
e
pa
r
ations in the FE calc
u
lations
commit
|
commitdiff
|
tree
2020-01-29
Paul Bauer
Add re
p
lacement
for s
y
m
b
o
l
table
commit
|
commitdiff
|
tree
2020-01-27
Mark Abraham
Remov
e
element-size memb
e
r fields
commit
|
commitdiff
|
tree
2020-01-27
Mark Abraham
Mak
e
NbnxnGpu class with constructor
commit
|
commitdiff
|
tree
2020-01-24
Szilárd Pál
l
A
d
d tar
g
et for
offl
i
ne PME Op
e
nCL compilation
commit
|
commitdiff
|
tree
2020-01-24
Magnus Lu
n
dborg
Remove
d
SC R
P
o
w
er 48
f
rom FEP k
e
rnel
commit
|
commitdiff
|
tree
2020-01-17
Mark Abraham
Regularize nbnxm module dox
y
gen
commit
|
commitdiff
|
tree
2020-01-17
Paul Bauer
Fix ba
d
link in developer docs
commit
|
commitdiff
|
tree
2020-01-17
Berk Hess
A
d
d c
h
e
ck for shells and GPU update
commit
|
commitdiff
|
tree
2020-01-13
Paul Bau
e
r
Re
v
ert "Exclude bui
l
d-system files f
r
om
C
Pack"
commit
|
commitdiff
|
tree
2020-01-13
Christoph Jun
g
hans
gmxMana
g
eMPI
.
cm
a
ke: c
o
nvert MPI FLAGS to lists
commit
|
commitdiff
|
tree
2020-01-09
Mark Abraham
Clea
n
up ewald module inter
n
als
commit
|
commitdiff
|
tree
2020-01-09
Mark
A
br
a
ham
Split lines with many copyright years
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric Irr
g
ang
R
emove t
r
ansitional links for online gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
Paul Bauer
GR
O
MACS 2020 r
e
lease
commit
|
commitdiff
|
tree
2020-01-01
Erik Li
n
dah
l
A
dd link to paper explaining GROMO
S
twin-ra
n
ge issues
.
commit
|
commitdiff
|
tree
2019-12-31
Mark
Abraham
A
v
oid 386
O3 c
o
degen bug even
m
o
r
e
commit
|
commitdiff
|
tree
2019-12-31
Arte
m
Zhmur
o
v
Inform user w
h
y forcing G
P
U update is
not possible
commit
|
commitdiff
|
tree
2019-12-31
Arte
m
Zhmurov
A
d
d
de
s
cription of GMX_FORCE_UPDATE_DEFAULT_GP
U
dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Fix gpuu
p
date matrix
commit
|
commitdiff
|
tree
2019-12-28
Arte
m
Zhmu
r
ov
Change the behavior of the
G
PU update
U
I
commit
|
commitdiff
|
tree
2019-12-28
Mark Ab
r
aham
M
erge "Merge origin/re
l
ease-2019 into rel
e
ase-
2
0
20
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Paul Bauer
Remove me
m
bed
f
ro
m
featu
r
es
commit
|
commitdiff
|
tree
2019-12-28
Mar
k
Abrah
a
m
Remove suppo
r
t for ARM
v
7
commit
|
commitdiff
|
tree
2019-12-28
M
a
rk Abraham
S
t
op te
s
ting ARM
v
7
commit
|
commitdiff
|
tree
2019-12-20
Szilár
d
Páll
Enable
b
uffe
r
ops when
G
M
X
_GPU_DD_
C
OMMS is set
commit
|
commitdiff
|
tree
2019-12-19
P
aul Ba
u
e
r
Fix regress
i
o
n
tests
faili
n
g w
i
th c
t
est
commit
|
commitdiff
|
tree
2019-12-18
Paul Bauer
Igno
r
e build hos
t
f
o
r
CI builds
commit
|
commitdiff
|
tree
2019-12-17
Mar
k
Abraham
F
i
x that tests i
n
tended for multip
l
e ranks
run that way
commit
|
commitdiff
|
tree
2019-12-16
Szi
l
árd Pá
l
l
Fix the G
P
U bonded strea
m
with 1 PP + 1 PME ra
n
k
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
U
s
e ListOfLists in gmx_
m
top_
t
a
nd gmx_
l
ocaltop_t
commit
|
commitdiff
|
tree
2019-12-15
Christia
n
Blau
Fix
d
ensityfitting
s
t
a
ll
i
ng and energi
e
s
commit
|
commitdiff
|
tree
2019-12-14
Mark Abraham
Simpl
i
fy gmxapi
RPATH ha
n
dl
i
ng
commit
|
commitdiff
|
tree
2019-12-12
Mar
k
A
b
raham
Merge "Merge bra
n
ch 'o
r
igin/
r
eleas
e
-2020' i
n
t
o m
a
ster"
commit
|
commitdiff
|
tree
2019-12-12
Arte
m
Zhmurov
A
l
low usi
n
g
G
PU up
d
a
t
e
wit
h
DD and up
d
ate groups
commit
|
commitdiff
|
tree
2019-12-11
Mark Abr
a
ham
D
ocument DOMAINDECOMP(cr) correctly
commit
|
commitdiff
|
tree
2019-12-11
Paul Bauer
Test pa
r
allel mpi on
l
y
w
ith
o
p
enmp
commit
|
commitdiff
|
tree
2019-12-04
Mark Abrah
a
m
Added Ope
n
CL
build to relea
s
e matrix
commit
|
commitdiff
|
tree
2019-12-04
Mark Ab
r
aham
Removed unnecessary
link_
d
irectories
c
o
m
mand for gtest
commit
|
commitdiff
|
tree
2019-11-29
Pau
l
Bauer
Fix
build e
r
r
or wi
t
hout thread or regul
a
r m
p
i
commit
|
commitdiff
|
tree
2019-11-29
Mark Abraha
m
Merge branch release-2019
into release-
2
020
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmuro
v
Renam
e
some variables in GP
U
Update
commit
|
commitdiff
|
tree
2019-11-28
Paul Bauer
Check for using corr
e
ct hwloc headers and runtime
commit
|
commitdiff
|
tree
2019-11-28
Artem
Zhmurov
Clear device force buffer if it was realloc
a
ted
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmur
o
v
Add met
h
od for coo
r
d
i
nates scaling in
t
o
GPU up
d
ate
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric Irr
g
ang
Ad
d
gmxapi_extension tests to
'
tes
t
s' tar
g
et
.
commit
|
commitdiff
|
tree
2019-11-27
A
l
an G
r
ay
Event-based Dependenc
y
for GPU Force
H
alo Exc
h
ange
commit
|
commitdiff
|
tree
2019-11-26
Mark Abraham
Improve han
d
l
i
ng of task-assignment e
x
cep
t
i
ons
commit
|
commitdiff
|
tree
2019-11-25
Al
a
n
G
ray
Fi
x
race conditio
n
in
GPU
X
halo
e
xchange with GPU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
Christian Blau
InM
e
morySerializer with endianess swa
p
.
commit
|
commitdiff
|
tree
2019-11-21
M
a
r
k A
b
raham
M
erge b
r
a
nch
release-20
2
0
commit
|
commitdiff
|
tree
2019-11-21
Mark Abraham
New cool quote
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmuro
v
Add D2H copi
e
s
f
o
r
t
h
e
checkpoint
i
n
g
commit
|
commitdiff
|
tree
2019-11-20
Art
e
m Zhmurov
Move the copy of the
v
e
locities for
the
o
utput cl
o
ser
.
.
.
commit
|
commitdiff
|
tree
next