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Separate job script files for gmxapi package versions.
2020-05-24
P
aul Bauer
A
dd conversion fro
m
new to
l
egacy symtab
commit
|
commitdiff
|
tree
2020-05-24
Kevi
n
Boyd
Clean
up g
r
ompp mem
o
ry leaks in
ro
t
at
i
on and pull s
t
r
uctures
.
commit
|
commitdiff
|
tree
2020-05-24
Paul Bauer
Avo
i
d parsing
of fatalerror
.
cpp
a
s lint
f
ailu
r
e
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgang
Enab
l
e MPI
ensemble te
s
ting for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-22
Artem Zhmurov
Remove depen
d
ence of
c
o
nstraints
on t_
m
d
atoms
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c
I
r
rg
a
ng
U
p
dat
e
docker imag
e
build scripts
f
o
r
master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Make
sure C
I
script ca
n
c
al
l
/bi
n
/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Irrgan
g
Minor clean up to buildal
l
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irr
g
a
ng
A
l
low llvm
o
ption already used in buildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-05-13
P
a
ul Bauer
Fix chec
k
s
ource error parsing
commit
|
commitdiff
|
tree
2020-05-11
Arte
m
Zh
m
uro
v
Unify CUDA and OpenC
L
l
o
okup-table creation
commit
|
commitdiff
|
tree
2020-05-05
Art
e
m Zh
m
ur
o
v
Unify C
U
D
A and Op
e
nC
L
lookup-table c
r
eation
commit
|
commitdiff
|
tree
2020-05-04
Paul Bauer
Fix
c
make
e
rror:
Mixed s
t
y
l
e
s of t
a
r
g
e
t_link_libr
a
ries
.
.
.
commit
|
commitdiff
|
tree
2020-05-04
Artem Zh
m
u
r
o
v
Un
i
fy CU
D
A and Open
C
L lookup-table creatio
n
commit
|
commitdiff
|
tree
2020-04-30
ejjor
d
an
Add EOF newl
i
nes t
o
eliminate compiler war
n
ings
commit
|
commitdiff
|
tree
2020-04-30
ejjorda
n
R
em
o
v
e c
m
ake l
o
gic that is outdated by requiri
n
g
cm
a
k
e
.
.
.
commit
|
commitdiff
|
tree
2020-04-28
Roland Schu
l
z
Add clang
WA
commit
|
commitdiff
|
tree
2020-04-28
Roland Schulz
F
i
x M
S
VC 20
1
9 test failures
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmurov
Fix the
r
emoval of C
O
M
veloc
i
ty in case of
G
P
U update
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmu
r
ov
Mo
v
e P
B
C setup ou
t
of
t
h
e
launch
K
ernel(
.
.
.
)
in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-04-27
Paul Bauer
Fi
x
segmentatio
n
fault i
n
do_ds
s
p
commit
|
commitdiff
|
tree
2020-04-25
Mark Abraham
M
ove co
n
fig
u
ration of global header
s
commit
|
commitdiff
|
tree
2020-04-25
Pau
l
Bauer
Fix copyr
i
gh
t
h
eader
commit
|
commitdiff
|
tree
2020-04-25
Roland Sc
h
ulz
Fix MSVC 2
0
19 warnin
g
s
commit
|
commitdiff
|
tree
2020-04-23
Paul Bauer
Use br
a
nch point a
l
so for format and copyright
c
h
e
ck
commit
|
commitdiff
|
tree
2020-04-23
Mark
A
braham
Mark HWLOC cmake c
a
che variable as advanced
commit
|
commitdiff
|
tree
2020-04-22
Pascal Mer
z
M
a
k
e
i
nit_dires independen
t
of
t
_
c
o
m
m
rec
commit
|
commitdiff
|
tree
2020-04-21
Mark
Abraham
F
i
x warning
s
w
i
th clang 9
commit
|
commitdiff
|
tree
2020-04-20
Ar
t
em Zhmu
r
ov
Fix
the numb
e
r of steps check when
c
h
eckpo
i
n
t is loaded
commit
|
commitdiff
|
tree
2020-04-20
Paul Ba
u
er
Make t
e
sts check code for warning
s
s
a
me as the main
.
.
.
commit
|
commitdiff
|
tree
2020-04-16
Artem Zhmurov
Un
i
fy
CUDA and O
p
enCL l
o
okup-table crea
t
ion
commit
|
commitdiff
|
tree
2020-04-14
Pascal M
e
rz
M
a
ke
bo
n
de
d
in
t
eractio
n
ch
e
ckin
g
m
ore robust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-13
Mark A
b
rah
a
m
F
i
x
w
arning
s
for
no-mpi bu
i
ld
commit
|
commitdiff
|
tree
2020-04-12
Mark Ab
r
a
h
am
Rem
o
v
e
d
u
nused variable
i
n force t
a
ble generation
commit
|
commitdiff
|
tree
2020-04-11
P
a
u
l
Bauer
Add Ima
g
e for
GCC 7
and AMD OpenCL
commit
|
commitdiff
|
tree
2020-04-07
Ma
r
k Abrah
a
m
Repl
a
ce EnumOption wit
h
Enume
r
ationArrayOption
commit
|
commitdiff
|
tree
2020-04-07
M
.
E
r
ic
I
r
r
gan
g
Prepare Python environments for
G
itLab CI pipeline
.
commit
|
commitdiff
|
tree
2020-04-07
Pa
s
cal Merz
Mak
e
global
topology
co
n
s
tant in
e
nerg
y
Output
.
pr
i
n
tAnn
e
aling
.
.
.
commit
|
commitdiff
|
tree
2020-04-06
Berk Hess
Move force
buffer re
s
izing to mdsetup
commit
|
commitdiff
|
tree
2020-04-06
Pas
c
al M
e
rz
Make bonded interaction checking more robust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
E
r
i
c Ir
r
gan
g
Im
p
r
o
v
e
gmxapi Python
p
ackag
e
dependency
r
esolu
t
ion
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Ir
r
gang
Pru
n
e
c
ha
n
ge-mana
g
e
m
ent
.
rst and update
l
inks
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric
Irrg
a
n
g
Prepare Python environmen
t
s for Gi
t
Lab CI pip
e
l
ine
.
commit
|
commitdiff
|
tree
2020-03-30
Mark A
b
raham
S
e
t
buffer
s
approp
r
iat
e
ly so
.
xpm files c
a
n be read
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Irrg
a
ng
R
e
quire Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-23
Artem Z
h
m
urov
Introduce Devic
e
StreamMa
n
ager
commit
|
commitdiff
|
tree
2020-03-21
Paul
Ba
u
er
A
d
d Docume
n
ta
t
ion build
to scr
i
pt
commit
|
commitdiff
|
tree
2020-03-19
Paul Ba
u
e
r
Add scri
p
t
t
o generate CI Docker file
s
commit
|
commitdiff
|
tree
2020-03-19
Art
e
m
Zhmu
r
o
v
Pas
s
DeviceCo
n
te
x
t
inste
a
d of GP
U
r
u
nt
i
me data when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric
Irrg
a
ng
Add stub Varia
b
les
d
ocument
a
tion t
o
G
i
tLab CI doc
.
commit
|
commitdiff
|
tree
2020-03-17
Ber
k
Hess
Disa
b
le Ewal
d
dipole correct
i
o
n withou
t
DD
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
D
e
fine an argparse parent parser f
o
r c
o
n
t
ainer ima
g
e
.
.
.
commit
|
commitdiff
|
tree
2020-03-14
Mark Ab
r
aham
Move
testing code to test directory
commit
|
commitdiff
|
tree
2020-03-12
Gille
s
Gouaillarde
t
grompp: fix the
-ref <file>
option
commit
|
commitdiff
|
tree
2020-03-10
Artem Zhmurov
Use init(
.
.
)
f
u
nction to
build
DeviceContext
commit
|
commitdiff
|
tree
2020-03-07
Ber
k
He
s
s
Make shak
e
work with
o
ut g
r
aph
commit
|
commitdiff
|
tree
2020-03-04
M
a
r
k
Abraham
Improve
TPI handling
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix
cen
t
er of mass motion removal
wit
h
fro
z
en atoms
commit
|
commitdiff
|
tree
2020-03-02
Arte
m
Zhmurov
Update the message
on whether up
d
ate and constraints
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Paul Bauer
Remove frozen atom
s
from VCM groups
commit
|
commitdiff
|
tree
2020-02-27
Pascal M
e
rz
Loosen
g
m
xa
p
i stopsignale
r
test
commit
|
commitdiff
|
tree
2020-02-27
P
ascal Me
r
z
Ex
t
r
a
ct and expose function to dete
r
mine
w
h
ether molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
S
zil
á
rd Páll
Remov
e
outdated P
M
E
-GPU l
i
mitatio
n
i
n user guide
commit
|
commitdiff
|
tree
2020-02-25
Magnus Lundborg
Fix out
of syn
c
checkpo
i
nt files in simulations sharing
.
.
.
commit
|
commitdiff
|
tree
2020-02-24
Paul Bauer
F
ix clang-6 ima
g
e temp
l
a
t
e
commit
|
commitdiff
|
tree
2020-02-20
Artem
Z
h
murov
U
s
e
CU
D
A
f
loat3 vector t
y
pe
i
n
s
tead of fvec in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
P
aul Bauer
Workaround for G
i
tlab
archive size
commit
|
commitdiff
|
tree
2020-01-29
Magnus Lundborg
More SI
M
D p
r
ep
a
rations in
t
he FE calculations
commit
|
commitdiff
|
tree
2020-01-29
Paul Bauer
Add replacement for symb
o
l table
commit
|
commitdiff
|
tree
2020-01-27
Mark Abraham
Remove element-size me
m
ber fields
commit
|
commitdiff
|
tree
2020-01-27
M
ar
k
Ab
r
aham
Make NbnxnGpu class with constructor
commit
|
commitdiff
|
tree
2020-01-24
Szilárd
P
áll
Add t
a
rget for offli
n
e
PME Op
e
nCL compilation
commit
|
commitdiff
|
tree
2020-01-24
Magnus
L
undb
o
rg
Removed SC RPow
e
r 48 from FEP kernel
commit
|
commitdiff
|
tree
2020-01-17
Mark A
b
rah
a
m
Regula
r
i
ze nbnxm module
d
oxygen
commit
|
commitdiff
|
tree
2020-01-17
Paul Bauer
Fix
b
ad l
i
n
k in d
e
ve
l
oper docs
commit
|
commitdiff
|
tree
2020-01-17
Berk Hess
Add che
c
k for shells
an
d
GPU update
commit
|
commitdiff
|
tree
2020-01-13
Paul Bau
e
r
Revert "Excl
u
de
b
u
ild-syst
e
m f
i
les
from CPack"
commit
|
commitdiff
|
tree
2020-01-13
C
h
r
ist
o
ph Ju
n
g
h
ans
g
m
x
M
a
nageMPI
.
c
m
ake:
convert MPI FLAGS
t
o lis
t
s
commit
|
commitdiff
|
tree
2020-01-09
M
ar
k
Abraham
Cle
a
n
u
p
ewald module i
n
ternals
commit
|
commitdiff
|
tree
2020-01-09
Mar
k
Abraham
Spli
t
lines with many copyright years
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric Irrgang
Remove
t
ran
s
itional links for onli
n
e
g
mxapi Py
t
hon
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
P
a
u
l
Bau
e
r
GROMAC
S
2
020 relea
s
e
commit
|
commitdiff
|
tree
2020-01-01
E
r
ik Li
n
d
ahl
Add link
to paper explaining
G
R
O
M
OS twin-r
a
nge issues
.
commit
|
commitdiff
|
tree
2019-12-31
M
a
r
k
A
braham
Avoid 386 O
3
codeg
e
n bug even more
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Inform us
e
r why forcing GPU
update is
n
o
t possib
l
e
commit
|
commitdiff
|
tree
2019-12-31
A
r
tem Zhmurov
Add descriptio
n
of GMX_FOR
C
E_UP
D
ATE_DEFAULT_GP
U
dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Z
h
murov
Fix gpuupdate matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zh
m
urov
Change the behavior of the GPU up
d
ate
U
I
commit
|
commitdiff
|
tree
2019-12-28
Mar
k
Abr
a
h
a
m
Me
r
ge "Me
r
ge origin/release-2019 into release-2020
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Pa
u
l
Bauer
Remove mem
b
ed fro
m
features
commit
|
commitdiff
|
tree
2019-12-28
M
a
rk Abraham
Re
m
ove support
f
or ARMv7
commit
|
commitdiff
|
tree
2019-12-28
Mark Abraham
Stop
t
e
sting ARMv7
commit
|
commitdiff
|
tree
2019-12-20
Szi
l
árd Pá
l
l
E
n
able buffer ops when
G
MX_GPU_DD_COMMS is set
commit
|
commitdiff
|
tree
2019-12-19
Paul B
a
uer
Fix regressiontests failing with
c
t
est
commit
|
commitdiff
|
tree
2019-12-18
Paul Ba
u
er
Ignore build host for
C
I builds
commit
|
commitdiff
|
tree
2019-12-17
M
ark Abra
h
am
Fix that tes
t
s
in
t
ended f
o
r
multiple ranks run tha
t
wa
y
commit
|
commitdiff
|
tree
2019-12-16
Szilár
d
Páll
F
ix
t
h
e GPU bonde
d
stre
a
m
w
it
h
1
PP +
1
P
M
E ran
k
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
Use L
i
stOfLis
t
s in gmx_m
t
op
_
t an
d
gmx_loc
a
ltop_t
commit
|
commitdiff
|
tree
2019-12-15
Christian Bl
a
u
F
ix densityfitting s
t
alli
n
g
and en
e
rgies
commit
|
commitdiff
|
tree
2019-12-14
Mark Abraham
Simpli
f
y gmxa
p
i RPA
T
H
hand
l
i
n
g
commit
|
commitdiff
|
tree
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