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Mark HWLOC cmake cache variable as advanced
2020-04-23
Ma
r
k Abraham
Mark HW
L
OC c
m
a
ke c
a
ch
e
variable as
advan
c
ed
commit
|
commitdiff
|
tree
2020-04-22
P
a
s
cal
M
e
rz
M
a
ke init_dires in
d
epend
e
n
t of t_com
m
rec
commit
|
commitdiff
|
tree
2020-04-21
Mark Abrah
a
m
Fix
wa
r
ning
s
with cla
n
g 9
commit
|
commitdiff
|
tree
2020-04-20
Ar
t
e
m
Z
h
m
u
rov
Fix the
num
b
e
r of steps ch
e
ck when checkpoint is lo
a
d
e
d
commit
|
commitdiff
|
tree
2020-04-20
Pau
l
Bauer
Make t
e
sts check code for warnings sam
e
as t
h
e main
.
.
.
commit
|
commitdiff
|
tree
2020-04-16
Artem
Z
hmur
o
v
Unify CUDA
a
nd OpenCL
l
ookup-tab
l
e
c
re
a
tio
n
commit
|
commitdiff
|
tree
2020-04-14
Pasca
l
Merz
Make bond
e
d interaction c
h
ecki
n
g
more r
o
bus
t
(modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-13
Mark Abraham
Fix warnings f
o
r no-mpi build
commit
|
commitdiff
|
tree
2020-04-12
Mark Abraha
m
Remove
d
unused vari
a
ble in force tab
l
e generation
commit
|
commitdiff
|
tree
2020-04-11
Paul Bauer
Add I
m
a
g
e for GCC 7 and AMD OpenCL
commit
|
commitdiff
|
tree
2020-04-07
Mark
Abr
a
ham
Replace EnumOp
t
ion with EnumerationArray
O
ption
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eri
c
Irrgang
Prepare Python
environments for GitLab CI pipeline
.
commit
|
commitdiff
|
tree
2020-04-07
P
a
scal
Merz
Make global
topology constant in energyOutput
.
printAnneali
n
g
.
.
.
commit
|
commitdiff
|
tree
2020-04-06
Berk Hess
M
o
v
e
force b
u
ffer
r
e
s
izing to m
d
setup
commit
|
commitdiff
|
tree
2020-04-06
Pascal Merz
Make
bon
d
ed interac
t
ion ch
e
cking more ro
b
u
s
t (mo
d
ular
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric
I
rrgang
I
m
p
rove gm
x
api Python package d
e
pendency resolution
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irrg
a
ng
Prune
c
h
a
n
g
e
-manage
m
e
nt
.
rst and u
p
date links
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric
I
rrgang
Prepare Py
t
hon envir
o
n
men
t
s for GitLab CI pipe
l
ine
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Er
i
c
I
rrgang
Require Pyt
h
o
n
3
.
6
.
commit
|
commitdiff
|
tree
2020-03-23
Arte
m
Zh
m
ur
o
v
Intr
o
duce
D
ev
i
ceStreamM
a
n
a
ger
commit
|
commitdiff
|
tree
2020-03-21
Paul
B
auer
Add Document
a
tion build to script
commit
|
commitdiff
|
tree
2020-03-19
P
aul
B
auer
Add
s
c
ript to generate CI
Docke
r
f
i
les
commit
|
commitdiff
|
tree
2020-03-19
Art
e
m
Zhmurov
Pass DeviceContext inst
e
ad of G
P
U runtime da
t
a when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
r
ic
I
rr
g
a
n
g
A
d
d
s
tub V
a
riables docume
n
tation to
G
i
t
Lab CI d
o
c
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric
Irrga
n
g
Define an argpa
r
s
e parent
parser fo
r
c
o
nt
a
iner image
.
.
.
commit
|
commitdiff
|
tree
2020-03-14
Mark Abraham
Move te
s
ting code
to t
e
st d
i
rectory
commit
|
commitdiff
|
tree
2020-03-12
Gilles
Gouail
l
a
rdet
gromp
p
:
fix the -ref <file> option
commit
|
commitdiff
|
tree
2020-03-10
A
r
t
em Zh
m
urov
Use init(
.
.
)
f
unction to build DeviceContex
t
commit
|
commitdiff
|
tree
2020-03-07
Berk Hess
Mak
e
shake work
without
g
r
a
ph
commit
|
commitdiff
|
tree
2020-03-04
Mark Abraham
Improve
T
PI h
a
ndling
commit
|
commitdiff
|
tree
2020-03-02
Berk
H
ess
Fix cen
t
er o
f
mass motio
n
re
m
o
v
al with froze
n
atoms
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmurov
Update the me
s
s
a
g
e on whether update and constraints
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Paul Ba
u
e
r
R
emov
e
frozen
a
toms from VCM groups
commit
|
commitdiff
|
tree
2020-02-27
Pa
s
cal Merz
Loo
s
e
n
gmx
a
pi stopsignaler
t
est
commit
|
commitdiff
|
tree
2020-02-27
Pas
c
a
l
Merz
Extract
and expose
f
unction to det
e
rmine whether molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Sz
i
lárd Páll
Remove outda
t
e
d PME
-
GP
U
limita
t
io
n
in
u
ser
g
uide
commit
|
commitdiff
|
tree
2020-02-25
Magnus Lundborg
Fix out of s
y
nc checkpoint fi
l
es in simul
a
tions s
h
aring
.
.
.
commit
|
commitdiff
|
tree
2020-02-24
Paul
Bauer
Fix clang-
6
image tem
p
l
a
te
commit
|
commitdiff
|
tree
2020-02-20
Arte
m
Zhmurov
Use CUDA flo
a
t3 vector type inst
e
ad of fvec in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Pau
l
Bauer
Workarou
n
d
for Gitlab archive size
commit
|
commitdiff
|
tree
2020-01-29
Magnus Lundborg
More SIMD preparations in the F
E
calculati
o
ns
commit
|
commitdiff
|
tree
2020-01-29
Paul
B
auer
Add
repl
a
cement for s
y
mb
o
l
t
a
ble
commit
|
commitdiff
|
tree
2020-01-27
Mark
A
brah
a
m
R
e
mo
v
e element-size membe
r
fields
commit
|
commitdiff
|
tree
2020-01-27
Mark Abr
a
ham
Make
Nbnx
n
Gpu
class with construc
t
or
commit
|
commitdiff
|
tree
2020-01-24
S
zilá
r
d Pá
l
l
Add tar
g
et
for off
l
ine PME OpenCL compilation
commit
|
commitdiff
|
tree
2020-01-24
Magnus Lundborg
Remove
d
SC RPower
4
8 f
r
om FEP kernel
commit
|
commitdiff
|
tree
2020-01-17
Mark Ab
r
aham
Reg
u
larize nb
n
x
m
module do
x
ygen
commit
|
commitdiff
|
tree
2020-01-17
Paul Bauer
Fix
bad link
i
n developer docs
commit
|
commitdiff
|
tree
2020-01-17
Berk Hess
Add c
h
eck for s
h
e
ll
s
an
d
GPU
update
commit
|
commitdiff
|
tree
2020-01-13
Paul Bauer
R
e
v
ert "Ex
c
lude buil
d
-system files fro
m
CPa
c
k"
commit
|
commitdiff
|
tree
2020-01-13
C
hris
t
oph Jungh
a
ns
g
m
xManageMPI
.
cmake: con
v
e
r
t MPI FLAG
S
t
o
lists
commit
|
commitdiff
|
tree
2020-01-09
Mark Abraham
Clea
n
up ewald module internals
commit
|
commitdiff
|
tree
2020-01-09
Mark A
b
raham
Spl
i
t lines with
many
c
o
p
yrigh
t
years
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric I
r
rgang
Remove trans
i
tional links
f
or online gmxapi Pyth
o
n
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
Paul
B
a
u
er
GROM
A
C
S
2020
r
e
lease
commit
|
commitdiff
|
tree
2020-01-01
Eri
k
Lindahl
A
dd link t
o
paper
explaining GROMOS tw
i
n-range iss
u
es
.
commit
|
commitdiff
|
tree
2019-12-31
Mark Abraham
Avoi
d
386 O3 codegen bug e
v
en mo
r
e
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Inform user why forcing GPU update is not possibl
e
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmur
o
v
Add
d
escript
i
on
o
f
GMX_FORCE_UPDATE_DEFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmuro
v
Fix gpu
u
pdate matri
x
commit
|
commitdiff
|
tree
2019-12-28
A
rtem
Z
hmurov
Ch
a
nge
t
h
e
behavior
o
f the GPU update UI
commit
|
commitdiff
|
tree
2019-12-28
M
ark Abraham
M
e
rge "Merge origin/release-2019
i
nto release
-
2
0
20
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Paul
Bauer
Remo
v
e membed from features
commit
|
commitdiff
|
tree
2019-12-28
Mark Abraham
Rem
o
ve supp
o
rt
for ARMv7
commit
|
commitdiff
|
tree
2019-12-28
M
a
rk Abraham
Stop testin
g
ARMv7
commit
|
commitdiff
|
tree
2019-12-20
Szilár
d
Páll
En
a
ble b
u
f
f
er ops
w
h
en
GMX_GP
U
_D
D
_COMMS is set
commit
|
commitdiff
|
tree
2019-12-19
Pa
u
l
Bauer
Fix
r
egressionte
s
ts failing wi
t
h ctest
commit
|
commitdiff
|
tree
2019-12-18
Paul Bauer
Igno
r
e b
u
ild h
o
s
t for CI
b
uilds
commit
|
commitdiff
|
tree
2019-12-17
Mark Abraham
Fi
x
that tests inte
n
ded f
o
r multiple
r
a
nks run that
w
ay
commit
|
commitdiff
|
tree
2019-12-16
Szil
á
r
d Páll
F
i
x
t
he GPU bonde
d
st
r
eam with 1 PP + 1 PM
E
rank
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
Use ListOfLists in gm
x
_mtop_t and g
m
x_localtop_t
commit
|
commitdiff
|
tree
2019-12-15
Christian Blau
F
i
x
d
en
s
ityfitting s
t
alling
and ene
r
gies
commit
|
commitdiff
|
tree
2019-12-14
M
a
rk
A
braham
S
i
m
p
lify gmxap
i
RPAT
H
hand
l
ing
commit
|
commitdiff
|
tree
2019-12-12
Ma
r
k
A
braham
M
e
r
g
e "Merge branch 'origin/release-2020' into mas
t
e
r
"
commit
|
commitdiff
|
tree
2019-12-12
A
rtem Zh
m
ur
o
v
Allo
w
u
sing GPU up
d
ate with DD and update grou
p
s
commit
|
commitdiff
|
tree
2019-12-11
Mark Ab
r
a
ham
D
o
cumen
t
DOM
A
INDECOMP(cr) c
o
rrec
t
ly
commit
|
commitdiff
|
tree
2019-12-11
Paul Bauer
Test parallel mpi only wit
h
openmp
commit
|
commitdiff
|
tree
2019-12-04
Mark
Abraham
Added OpenCL build to
release matrix
commit
|
commitdiff
|
tree
2019-12-04
Mark Abraham
Remove
d
unn
e
cessary link_
d
irectories co
m
ma
n
d for
gtest
commit
|
commitdiff
|
tree
2019-11-29
Paul Bauer
Fix build error without t
h
rea
d
or regular m
p
i
commit
|
commitdiff
|
tree
2019-11-29
M
a
rk Abr
a
h
a
m
Mer
g
e
b
ranch release-2019 i
n
to
r
elease
-
2020
commit
|
commitdiff
|
tree
2019-11-29
Ar
t
em Zhmurov
Re
n
ame some variables in GP
U
Update
commit
|
commitdiff
|
tree
2019-11-28
Paul Bauer
Check
f
o
r using corr
e
ct hwl
o
c hea
d
ers and runtime
commit
|
commitdiff
|
tree
2019-11-28
Artem Z
h
murov
Clear devi
c
e
f
orce bu
f
fer if it was reallocated
commit
|
commitdiff
|
tree
2019-11-27
Ar
t
em Zhmurov
Add method for coord
i
nates sca
l
i
n
g
into
GPU update
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric Irr
g
ang
Add gmxapi_ext
e
nsion test
s
to 'tests' target
.
commit
|
commitdiff
|
tree
2019-11-27
A
la
n
Gra
y
Event-based Depe
n
dency for GPU Forc
e
Hal
o
Ex
c
hang
e
commit
|
commitdiff
|
tree
2019-11-26
Ma
r
k A
b
raham
Improve handl
i
ng
of task-as
s
ig
n
men
t
except
i
ons
commit
|
commitdiff
|
tree
2019-11-25
Alan
G
ray
Fix race
conditio
n
in GPU X halo excha
n
g
e
w
i
th
GPU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
C
hristian Blau
InMemoryS
e
ri
a
lizer with endia
n
e
ss
swap
.
commit
|
commitdiff
|
tree
2019-11-21
Mark Abraham
Merge
bra
n
ch
re
l
ea
s
e-2020
commit
|
commitdiff
|
tree
2019-11-21
Mark Ab
r
aham
New
cool qu
o
t
e
commit
|
commitdiff
|
tree
2019-11-20
Artem
Zhmurov
Add D2H
c
op
i
es for
t
h
e
c
heckpointing
commit
|
commitdiff
|
tree
2019-11-20
Artem
Z
hm
u
ro
v
M
o
ve the copy of the velocities
f
or the output closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
B
e
rk
He
s
s
Q
u
iet pdb2
g
m
x and use
gmx_
f
atal
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric Irrgang
Remove st
u
b content from g
m
xa
p
i docs
.
commit
|
commitdiff
|
tree
2019-11-16
Mark A
b
raha
m
Relaxed listed forc
e
s test tolerance
s
commit
|
commitdiff
|
tree
2019-11-06
Ber
k
Hess
Deprec
a
ted sc-r-power=48
commit
|
commitdiff
|
tree
2019-11-04
Paul Bauer
Add build for clang-f
o
rmat
commit
|
commitdiff
|
tree
2019-11-04
Paul B
a
uer
S
plit u
p
s
o
urc
e
co
d
e form
a
tt
i
ng scri
p
t
s
commit
|
commitdiff
|
tree
next