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More SIMD preparations in the FE calculations
2020-01-29
Magnus
L
u
n
dbor
g
More SIMD
p
r
epar
a
ti
o
ns
i
n
t
he FE calculati
o
n
s
commit
|
commitdiff
|
tree
2020-01-29
Paul Bauer
Add
replaceme
n
t f
o
r
s
ymb
o
l ta
b
l
e
commit
|
commitdiff
|
tree
2020-01-27
Ma
r
k Abraham
Remo
v
e
eleme
n
t-size membe
r
fields
commit
|
commitdiff
|
tree
2020-01-27
Mark Abraham
Make Nbnx
n
Gpu cla
s
s wit
h
constructor
commit
|
commitdiff
|
tree
2020-01-24
Sz
i
l
á
rd Páll
A
d
d targ
e
t
f
or offline PME OpenCL compil
a
t
ion
commit
|
commitdiff
|
tree
2020-01-24
Magn
u
s Lun
d
bo
r
g
Removed SC
R
Powe
r
48 from
F
EP ker
n
el
commit
|
commitdiff
|
tree
2020-01-17
Ma
r
k
A
braham
Regu
l
arize nbnxm
m
odule dox
y
gen
commit
|
commitdiff
|
tree
2020-01-09
Mark Abrah
a
m
Cl
e
an up ewald module intern
a
ls
commit
|
commitdiff
|
tree
2020-01-09
Mark Abraham
Split lines w
i
th man
y
copyr
i
g
ht year
s
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eri
c
I
rrgan
g
Remove transitiona
l
links fo
r
onlin
e
g
m
xapi Py
t
hon
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
Paul
Bauer
GROMACS
2
020 release
commit
|
commitdiff
|
tree
2020-01-01
Erik L
i
nda
h
l
Add
link to p
a
per explaining GROMOS twin-
r
a
n
ge i
s
su
e
s
.
commit
|
commitdiff
|
tree
2019-12-31
Mark Abraham
Avoid
3
86 O3 codegen bug even m
o
re
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Inform us
e
r why
f
orcing GPU upda
t
e is not possible
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
em Zhmurov
A
d
d des
c
ription o
f
GM
X
_FORCE_
U
PDATE_DEFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmu
r
ov
Fix gpu
u
pdate
m
atrix
commit
|
commitdiff
|
tree
2019-12-28
A
rtem Zhmurov
Change
the beh
a
vior of the GPU update UI
commit
|
commitdiff
|
tree
2019-12-28
Mark Abraham
Merge "M
e
rge origin/re
l
ea
s
e-2019 in
t
o relea
s
e-2020
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
P
aul Ba
u
er
Remove membed from
f
eatures
commit
|
commitdiff
|
tree
2019-12-28
Mark A
b
rah
a
m
Remove su
p
port for
ARMv
7
commit
|
commitdiff
|
tree
2019-12-28
Mark
A
braham
S
t
op testing AR
M
v7
commit
|
commitdiff
|
tree
2019-12-20
Szilárd
Páll
E
n
able
b
uffer ops when
G
MX_GP
U
_
D
D_COM
M
S
is set
commit
|
commitdiff
|
tree
2019-12-19
Pa
u
l Bauer
Fix reg
r
e
s
siontests failing
w
it
h
ctes
t
commit
|
commitdiff
|
tree
2019-12-18
Paul B
a
uer
I
gn
o
re build host for CI b
u
ilds
commit
|
commitdiff
|
tree
2019-12-17
M
a
rk Abraham
Fi
x
that tests i
n
tended for multiple r
a
nks run that way
commit
|
commitdiff
|
tree
2019-12-16
Szilár
d
Páll
Fix
the GPU bond
e
d st
r
eam
with 1 PP +
1
P
M
E rank
commit
|
commitdiff
|
tree
2019-12-16
Be
r
k Hess
Use ListOf
L
ists in gmx_
m
top_t
a
n
d gmx_localt
o
p_t
commit
|
commitdiff
|
tree
2019-12-15
Christian Blau
Fix densit
y
f
i
t
t
ing s
t
a
l
l
i
ng and energies
commit
|
commitdiff
|
tree
2019-12-14
Ma
r
k Abraham
Simplify gmxapi RPATH handling
commit
|
commitdiff
|
tree
2019-12-12
Mark Abraham
Merge "Merg
e
branch 'origin/release-
2
0
2
0' into m
a
s
ter"
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
A
llow using
G
PU updat
e
with DD and
u
p
date
g
roups
commit
|
commitdiff
|
tree
2019-12-11
Mark Abraham
Document DOM
A
I
NDECOMP(cr) co
r
rectly
commit
|
commitdiff
|
tree
2019-12-11
Paul Bauer
Tes
t
parallel mpi o
n
ly with openmp
commit
|
commitdiff
|
tree
2019-12-04
Mar
k
Abraham
Add
e
d OpenCL build
t
o re
l
ease
m
atrix
commit
|
commitdiff
|
tree
2019-12-04
Mark Abr
a
h
a
m
R
e
moved un
n
ecessary link_director
i
e
s
command for gtest
commit
|
commitdiff
|
tree
2019-11-29
Paul Bauer
Fix build error without thread or regul
a
r mpi
commit
|
commitdiff
|
tree
2019-11-29
Mark Abraham
Merge branc
h
relea
s
e
-2019 into
release-20
2
0
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmurov
Ren
a
m
e
some variables i
n
GPU U
p
date
commit
|
commitdiff
|
tree
2019-11-28
Pa
u
l B
a
u
er
C
h
e
c
k for using correc
t
h
w
loc headers and runtime
commit
|
commitdiff
|
tree
2019-11-28
Ar
t
em Zhmurov
Clear dev
i
ce force buffer if i
t
was reallocated
commit
|
commitdiff
|
tree
2019-11-27
A
r
tem Zhmurov
Ad
d
method
for coord
i
nates scaling into GPU u
p
date
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eri
c
Irrgang
Add gmxapi_exte
n
sion tests to 't
e
s
t
s
' tar
g
et
.
commit
|
commitdiff
|
tree
2019-11-27
Alan Gray
Event-b
a
s
e
d De
p
ende
n
c
y for GPU
F
o
rce
H
a
lo Exch
a
ng
e
commit
|
commitdiff
|
tree
2019-11-26
Mark Abra
h
a
m
Improve handl
i
ng of task-ass
i
gnment
exceptions
commit
|
commitdiff
|
tree
2019-11-25
Alan G
r
a
y
Fix race condition
in GPU
X halo exchange with GPU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
Christian Bl
a
u
InMemorySerializer with e
n
dianess swap
.
commit
|
commitdiff
|
tree
2019-11-21
M
ark Abra
h
am
Mer
g
e b
r
a
n
c
h
r
ele
a
se-2020
commit
|
commitdiff
|
tree
2019-11-21
Mark Abraham
New cool q
u
ote
commit
|
commitdiff
|
tree
2019-11-20
Artem
Z
hmurov
Add D2H copies
for t
h
e checkp
o
in
t
ing
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
Move the copy of the velocities for the out
p
ut closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
Berk Hess
Quiet pdb2gmx and
use gmx_fat
a
l
commit
|
commitdiff
|
tree
2019-11-20
M
.
Er
i
c Irrgang
Remove stub con
t
ent from gmxapi docs
.
commit
|
commitdiff
|
tree
2019-11-16
Mark Abraham
Relaxed listed forces
t
e
st
t
o
l
era
n
ces
commit
|
commitdiff
|
tree
2019-11-06
Be
r
k Hess
Depre
c
ated sc-r-po
w
er=48
commit
|
commitdiff
|
tree
2019-11-04
P
a
ul Bau
e
r
A
dd
b
uild for clang-form
a
t
commit
|
commitdiff
|
tree
2019-11-04
Pa
u
l
Bauer
Split up source code formatting s
c
ripts
commit
|
commitdiff
|
tree
2019-11-04
Tee
m
u Murtola
Update clan
g
-format config
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
ric Irrgan
g
Impro
v
e
unifor
m
ity
of OS X C
M
ake configuration
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgan
g
Restore CMake
c
o
n
venience targ
e
t
s
for sample_re
s
train
t
.
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
R
e
mo
v
e
d
ead code for n
b
nxm H2D coordin
a
t
e
copy event
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
Bug fix for
e
v
e
n
t
passed to GPU comm fe
a
tures
commit
|
commitdiff
|
tree
2019-10-31
P
ascal Merz
Ch
e
c
k for contradicting
environment variab
l
es (modula
r
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Mark
A
brah
a
m
Te
s
ts for
v
a
lid periodic actions
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric
I
rrgang
Disab
l
e i
t
s tests when
s
a
m
ple_restraint i
s
not the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Ir
r
g
ang
Decrease the ma
x
imum allowed Python version for gmxa
p
i
.
commit
|
commitdiff
|
tree
2019-10-29
A
r
tem Zhmuro
v
Disabl
e
GP
U
update when coordin
a
tes swa
p
ping is enable
d
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add
bool useDomai
n
Decom
p
osition in mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add gmx_m
t
op_interaction_
c
o
unt
(
)
commit
|
commitdiff
|
tree
2019-10-23
ej
j
or
d
an
M
ake
t_nextnb an implementation
d
etail
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Correct f
o
r skewed box before domain decomposition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Alan Gray
Enabl
e
GPU Peer Access in
GPU Utilities
commit
|
commitdiff
|
tree
2019-10-22
e
j
j
ordan
Rem
o
ve unused functions from gmxpre
p
rocess
commit
|
commitdiff
|
tree
2019-10-22
B
e
rk Hess
R
equire -ei for e
s
sential dynamics
commit
|
commitdiff
|
tree
2019-10-22
ejjordan
Remove unused functi
o
n
g
enerate
_
excls and make clean_excls
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Berk
Hess
Const cor
r
ec
t
ne
s
s for
genhy
d
r
o
commit
|
commitdiff
|
tree
2019-10-15
Pau
l
Bauer
F
i
x bug in preprocessing
commit
|
commitdiff
|
tree
2019-10-14
M
.
E
r
i
c Irrgang
Fix
l
o
gi
c
error in g
m
xapi
.
version
.
api_is_at_leas
t
()
.
commit
|
commitdiff
|
tree
2019-10-13
Mark Ab
r
a
ham
Ensure environment
v
ariable
use
d
oes not
g
i
v
e warn
i
ngs
commit
|
commitdiff
|
tree
2019-10-12
Berk
H
ess
Add cl
a
ss Fix
e
dCap
a
cityVec
t
or
commit
|
commitdiff
|
tree
2019-10-12
Art
e
m Zhmurov
Centralize ma
n
agement of coord
i
n
a
t
e
s ready on GPU eve
n
t
commit
|
commitdiff
|
tree
2019-10-08
P
r
ashanth Kanduri
Fused two
if br
a
nches with the
same conditional
commit
|
commitdiff
|
tree
2019-10-02
Ca
r
sten Kutzne
r
Update the www
l
in
k
to the D
o
xygen documen
t
ation
i
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
B
erk Hess
Fix harmless OpenM
P
wri
t
e r
a
ce
commit
|
commitdiff
|
tree
2019-10-02
Mark Abraham
Improve PME testing
commit
|
commitdiff
|
tree
2019-10-01
B
er
k
Hess
Use gmx::Ra
n
ge
i
n domdec
commit
|
commitdiff
|
tree
2019-10-01
Artem Zhmurov
StatePropagatorDataGpu obje
c
t
to manag
e
GPU f
o
rces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Ma
r
k Abraham
F
i
x icc warnings
commit
|
commitdiff
|
tree
2019-10-01
Berk
H
ess
Com
p
lete
l
y rem
o
ve charg
e
grou
p
s
commit
|
commitdiff
|
tree
2019-10-01
Pau
l
Bauer
F
i
x
chai
n
ID ha
n
dling in mak
e
_nd
x
commit
|
commitdiff
|
tree
2019-10-01
Chr
i
s
toph
J
ungha
n
s
c
m
ake: add
m
issing header to l
e
gacy api
commit
|
commitdiff
|
tree
2019-10-01
Mark
Abraham
Removed d
e
pendenc
y
o
n commrec o
f
mdrun setup
commit
|
commitdiff
|
tree
2019-09-30
Carsten Kutzner
Mo
v
e Force
P
roviders cla
s
s in
t
o t
h
e gmx na
m
espace
commit
|
commitdiff
|
tree
2019-09-30
Mark Ab
r
ah
a
m
M
a
k
e
a
b
uilder for DD
commit
|
commitdiff
|
tree
2019-09-30
Berk
Hess
R
e
move charg
e
group code from forcerec
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Páll
Make th
e
wait
o
n
PME GPU results conditio
n
a
l
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Improve M
i
MiC test impleme
n
ta
t
ion
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraha
m
Fix gro file output with inde
x
gr
o
ups
commit
|
commitdiff
|
tree
2019-09-27
Mark
Abraham
Fix gro fil
e
output with index groups
commit
|
commitdiff
|
tree
2019-09-27
Ma
r
k Abr
a
ham
Remove leftover sup
p
ort for
pre-9
.
0
C
UDA
commit
|
commitdiff
|
tree
2019-09-24
Paul Baue
r
Add tes
t
f
o
r
n
o
app
e
nd
commit
|
commitdiff
|
tree
next