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grompp: fix the -ref <file> option
2020-03-12
Gilles Gouaillardet
g
ro
m
pp: fix th
e
-ref <file> option
commit
|
commitdiff
|
tree
2020-03-10
Artem Zhm
u
rov
Use
i
nit(
.
.
)
function
t
o buil
d
D
e
viceContext
commit
|
commitdiff
|
tree
2020-03-07
Be
r
k
H
es
s
Make shake
w
ork wi
t
h
o
ut graph
commit
|
commitdiff
|
tree
2020-03-04
Mark Abraha
m
Imp
r
o
v
e
TPI hand
l
in
g
commit
|
commitdiff
|
tree
2020-03-02
Be
r
k Hess
Fix center
o
f
mass
motion removal with frozen atoms
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmur
o
v
Upda
t
e the message on whether u
p
date a
n
d constr
a
ints
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Pau
l
Bauer
Remove f
r
ozen atoms from VCM gr
o
up
s
commit
|
commitdiff
|
tree
2020-02-27
Pascal
M
erz
Loosen gmxap
i
stopsign
a
ler test
commit
|
commitdiff
|
tree
2020-02-27
Pa
s
cal
Merz
Extract and
expose function to dete
r
mine
whether molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
S
z
ilárd Pá
l
l
Rem
o
ve
o
u
tdated PME-GPU limi
t
ation in user guide
commit
|
commitdiff
|
tree
2020-02-25
Magnus Lundb
o
rg
Fix o
u
t of
s
ync checkpoi
n
t files in s
i
m
ulation
s
sharing
.
.
.
commit
|
commitdiff
|
tree
2020-02-24
P
aul
Bauer
Fix clang-6
i
m
age template
commit
|
commitdiff
|
tree
2020-02-20
A
rtem Zhmurov
Use CUDA float3 v
e
c
t
or type instead o
f
fve
c
i
n
G
P
U
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Paul B
a
uer
Worka
r
ound for Git
l
ab archive
s
i
ze
commit
|
commitdiff
|
tree
2020-01-29
Magnus
Lun
d
borg
M
o
re SI
M
D prep
a
rat
i
ons in the FE calculations
commit
|
commitdiff
|
tree
2020-01-29
Paul Bauer
A
d
d
replacement for symbol tabl
e
commit
|
commitdiff
|
tree
2020-01-27
Mark
A
braham
Remo
v
e element-size member fields
commit
|
commitdiff
|
tree
2020-01-27
M
ar
k
Ab
r
aham
Make
N
bnxnGp
u
class
wi
t
h
c
onstructor
commit
|
commitdiff
|
tree
2020-01-24
Szilár
d
Páll
Add target for offline
P
M
E
OpenCL compilation
commit
|
commitdiff
|
tree
2020-01-24
Magnus Lundbo
r
g
Re
m
oved SC RPower 48 from FEP ker
n
el
commit
|
commitdiff
|
tree
2020-01-17
Mark
Abr
a
ham
Reg
u
larize nbnxm module d
o
xyg
e
n
commit
|
commitdiff
|
tree
2020-01-17
Paul Bauer
Fix bad link i
n
developer docs
commit
|
commitdiff
|
tree
2020-01-17
Ber
k
Hess
Add
c
heck for
s
hells and GPU update
commit
|
commitdiff
|
tree
2020-01-13
Paul B
a
uer
Revert "Exc
l
ude buil
d
-sys
t
em files
f
rom C
P
ack"
commit
|
commitdiff
|
tree
2020-01-13
C
h
ristoph J
u
nghans
gmxMa
n
ageMPI
.
cmake: conve
r
t MPI FLAGS to lists
commit
|
commitdiff
|
tree
2020-01-09
M
a
rk
A
braha
m
Clean up ewald mo
d
ule
internals
commit
|
commitdiff
|
tree
2020-01-09
Mark Abra
h
am
Split
lines with man
y
copyright yea
r
s
commit
|
commitdiff
|
tree
2020-01-03
M
.
E
r
ic Irrg
a
ng
Remove transitiona
l
links for online gmxapi
Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
Pa
u
l Bauer
GR
O
MACS 2020 rele
a
se
commit
|
commitdiff
|
tree
2020-01-01
E
r
ik Lindahl
Add
l
i
nk
to
paper exp
l
a
ining GROMOS twin-ran
g
e
issue
s
.
commit
|
commitdiff
|
tree
2019-12-31
Mark Abraham
Avoid 386
O
3 codegen bug
e
ven m
o
re
commit
|
commitdiff
|
tree
2019-12-31
A
r
tem Zhmu
r
ov
Inform user why forcing GP
U
update is not
po
s
sible
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
A
dd description of GMX_FORCE_UP
D
ATE_DEFAULT_
G
PU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
F
i
x gpuupdate
matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmuro
v
Change th
e
b
ehavior of the GPU u
p
date UI
commit
|
commitdiff
|
tree
2019-12-28
Mark A
b
raham
Merge "Merge origin/release-2019 into release-2020
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Paul Bauer
Remove membed from features
commit
|
commitdiff
|
tree
2019-12-28
Mark Abraham
Remove s
u
pport for AR
M
v
7
commit
|
commitdiff
|
tree
2019-12-28
Mark Abra
h
am
Stop testing A
R
Mv7
commit
|
commitdiff
|
tree
2019-12-20
Szilárd Páll
Enable buffer o
p
s when GMX_GPU_DD_COM
M
S is set
commit
|
commitdiff
|
tree
2019-12-19
P
aul Bauer
Fix regressiontests failing
w
ith ct
e
s
t
commit
|
commitdiff
|
tree
2019-12-18
P
a
ul Bauer
Ignore build host for CI builds
commit
|
commitdiff
|
tree
2019-12-17
Mark Abraham
Fix th
a
t te
s
ts i
n
tended fo
r
mu
l
ti
p
le ranks run tha
t
way
commit
|
commitdiff
|
tree
2019-12-16
Szilárd P
á
ll
Fix the
GPU bonded stream
w
ith 1 PP + 1 PME
r
a
n
k
commit
|
commitdiff
|
tree
2019-12-16
Ber
k
H
ess
Use ListOf
L
ists in gmx_mtop_t a
n
d gmx_l
o
caltop_t
commit
|
commitdiff
|
tree
2019-12-15
Ch
r
istian Blau
Fix densityfit
t
ing
st
a
ll
i
ng
and energies
commit
|
commitdiff
|
tree
2019-12-14
Mark Abr
a
ham
Simplify gmxapi RPATH handling
commit
|
commitdiff
|
tree
2019-12-12
Mar
k
Abraha
m
Merge "Merge br
a
nch
'
or
i
gin
/
re
l
ease-2020' into
m
as
t
er"
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
A
llow using GPU update with D
D
and update group
s
commit
|
commitdiff
|
tree
2019-12-11
M
a
rk Abraham
Document DO
M
AINDECOMP
(
c
r) c
o
rrectly
commit
|
commitdiff
|
tree
2019-12-11
Paul B
a
uer
Test
p
ar
a
lle
l
mpi only wit
h
o
penmp
commit
|
commitdiff
|
tree
2019-12-04
Mark Abraham
Added Ope
n
CL build to rel
e
ase
matrix
commit
|
commitdiff
|
tree
2019-12-04
Ma
r
k Abraham
Remov
e
d unn
e
cessary
link_
d
i
r
ectories com
m
and for gtest
commit
|
commitdiff
|
tree
2019-11-29
Paul Bauer
Fix buil
d
error without thread
o
r
regul
a
r
mpi
commit
|
commitdiff
|
tree
2019-11-29
Mark Abraham
Merg
e
branch rel
e
a
s
e
-2019 i
n
t
o
release-
2
0
20
commit
|
commitdiff
|
tree
2019-11-29
Artem
Zhmurov
Rename
some varia
b
l
es in GP
U
Update
commit
|
commitdiff
|
tree
2019-11-28
Paul Bauer
Check
for usi
n
g co
r
rec
t
hwloc
hea
d
e
rs and
r
untime
commit
|
commitdiff
|
tree
2019-11-28
A
r
tem Zhmurov
Cl
e
ar
d
evice force buffer if i
t
w
as real
l
oc
a
ted
commit
|
commitdiff
|
tree
2019-11-27
A
rtem Zhmur
o
v
Add
meth
o
d for coordinates
s
caling int
o
GP
U
update
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eri
c
Irrgan
g
Add gmxapi_extension
tests to 't
e
sts' target
.
commit
|
commitdiff
|
tree
2019-11-27
Ala
n
Gr
a
y
Event-based Dependency for
G
PU Force
Ha
l
o Exch
a
ng
e
commit
|
commitdiff
|
tree
2019-11-26
Mark
Abraham
Improve h
a
nd
l
i
ng of
task-
a
ssignment exc
e
ptio
n
s
commit
|
commitdiff
|
tree
2019-11-25
Alan Gray
Fix race condition in GPU X h
a
lo exchange wi
t
h GP
U
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
Christ
i
an Blau
I
n
M
e
morySerialize
r
with end
i
aness swap
.
commit
|
commitdiff
|
tree
2019-11-21
Mar
k
A
brah
a
m
Merge branch r
e
lease-2020
commit
|
commitdiff
|
tree
2019-11-21
Mark Abrah
a
m
N
ew c
o
ol quote
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhm
u
rov
A
d
d D2H copies fo
r
t
h
e
ch
e
ckpo
i
nting
commit
|
commitdiff
|
tree
2019-11-20
Artem
Z
h
m
u
r
o
v
M
o
ve the copy o
f
the veloc
i
ties for the outpu
t
closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
Berk Hess
Qui
e
t
pdb2g
m
x and use
g
mx_fatal
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric Irrgang
Remove s
t
ub conten
t
from gmxapi docs
.
commit
|
commitdiff
|
tree
2019-11-16
Ma
r
k
A
b
r
a
h
a
m
Relaxe
d
l
isted
forc
e
s test
t
o
l
erances
commit
|
commitdiff
|
tree
2019-11-06
B
erk Hess
Depr
e
c
a
ted sc
-
r-po
w
er=48
commit
|
commitdiff
|
tree
2019-11-04
P
a
u
l Bauer
Add build
f
or clang-form
a
t
commit
|
commitdiff
|
tree
2019-11-04
Paul Bauer
Split up s
o
urc
e
cod
e
formatting sc
r
ipts
commit
|
commitdiff
|
tree
2019-11-04
Teemu Murtola
Update clang-format config
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
Improve
uniformit
y
o
f OS
X
CM
a
ke co
n
figurat
i
on
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
r
ic Irrgan
g
Re
s
tore CMake
conven
i
ence ta
r
gets
f
o
r samp
l
e
_
r
e
str
a
int
.
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
Remove dea
d
code for nbnxm H2D
c
oordinate
copy e
v
ent
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
Bug fi
x
for e
v
e
n
t pa
s
sed
t
o GPU comm feat
u
res
commit
|
commitdiff
|
tree
2019-10-31
Pascal
M
erz
Check
f
or c
o
n
t
r
adi
c
ting environment var
i
ables (modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Mark Abraham
Tests f
o
r va
l
i
d
p
e
riodic actions
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrga
n
g
Dis
a
ble its
tests
when sam
p
l
e_
r
estr
a
int is not th
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
E
ric Ir
r
gang
Decrease the
m
a
ximum
a
l
lowe
d
Python version for
g
mxapi
.
commit
|
commitdiff
|
tree
2019-10-29
Ar
t
em Zhmuro
v
Disable GPU up
d
ate when c
o
or
d
inates swa
p
p
i
ng
is enabled
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add bo
o
l useDo
m
ai
n
Decomposition in md
r
unn
e
r
commit
|
commitdiff
|
tree
2019-10-24
B
erk Hess
Add gmx_
m
top
_
inte
r
acti
o
n_coun
t
()
commit
|
commitdiff
|
tree
2019-10-23
ejjordan
Make
t
_
nextnb an implem
e
ntation deta
i
l
commit
|
commitdiff
|
tree
2019-10-23
Pasc
a
l Merz
Correct for skewed box
b
efore domain decompos
i
tio
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Al
a
n Gray
Enable GPU Pe
e
r A
c
cess in GPU Utili
t
ie
s
commit
|
commitdiff
|
tree
2019-10-22
e
jjordan
Re
m
o
v
e unused fu
n
ct
i
on
s
fr
o
m gmxpreproc
e
s
s
commit
|
commitdiff
|
tree
2019-10-22
B
e
rk Hess
Requi
r
e -ei for ess
e
nt
i
al
dynami
c
s
commit
|
commitdiff
|
tree
2019-10-22
ejjor
d
an
Remove
unused f
u
nct
i
on
g
e
nerate_excls
a
nd
m
a
k
e
c
le
a
n_excls
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
B
e
rk
H
ess
Const
c
orrectness for genhydr
o
commit
|
commitdiff
|
tree
2019-10-15
Paul Bauer
F
i
x
bug in p
r
ep
r
ocessing
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eric
I
rrgang
Fix logic error i
n
gmxapi
.
vers
i
on
.
a
pi_i
s
_at_least()
.
commit
|
commitdiff
|
tree
2019-10-13
M
a
rk Abra
h
am
Ensu
r
e e
n
vironment variable
u
se doe
s
not give warnin
g
s
commit
|
commitdiff
|
tree
2019-10-12
B
e
rk Hess
Add class FixedCapacityVe
c
t
o
r
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhm
u
ro
v
Cen
t
ralize management of coordinates r
e
ady on GPU even
t
commit
|
commitdiff
|
tree
2019-10-08
Prasha
n
t
h Kanduri
Fu
s
e
d two if branches with the same conditional
commit
|
commitdiff
|
tree
2019-10-02
Cars
t
en Kut
z
ner
Upda
t
e the www link
t
o
t
he D
o
xyg
e
n do
c
umentation in
.
.
.
commit
|
commitdiff
|
tree
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