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Removed unused variable in force table generation
2020-04-12
Ma
r
k Abr
a
ham
Removed unuse
d
variable in force table
generation
commit
|
commitdiff
|
tree
2020-04-11
Paul Baue
r
Add Imag
e
for GCC 7 and
AMD O
p
enCL
commit
|
commitdiff
|
tree
2020-04-07
Mark Abr
a
ham
R
eplace EnumOption
w
ith Enum
e
ra
t
ionArrayOption
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eri
c
Irrgang
P
r
epar
e
P
y
thon
e
nviron
m
e
n
ts for GitLab CI pipeli
n
e
.
commit
|
commitdiff
|
tree
2020-04-07
Pascal Merz
Make glob
a
l topology constant in energ
y
Outpu
t
.
printA
n
nealing
.
.
.
commit
|
commitdiff
|
tree
2020-04-06
Berk Hes
s
M
ove force
b
uf
f
er re
s
izing to m
d
setup
commit
|
commitdiff
|
tree
2020-04-06
P
a
scal Merz
Make bonded interaction check
i
ng m
o
r
e
robust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irrga
n
g
Improve gmxapi Pyth
o
n pa
c
k
age
d
e
p
endency res
o
l
ution
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric
I
r
r
gang
Prune change-man
a
gement
.
rst and update l
i
n
ks
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgang
Prepare
Pyt
h
o
n
environments for Gi
t
L
a
b C
I
p
ipeline
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Irrgang
Require Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-23
Ar
t
em Zhmurov
I
n
trodu
c
e De
v
iceStream
M
anager
commit
|
commitdiff
|
tree
2020-03-21
Pa
u
l Bauer
Add Documentat
i
on build to s
c
ript
commit
|
commitdiff
|
tree
2020-03-19
Paul Bauer
Add scr
i
pt to
generate CI Doc
k
er files
commit
|
commitdiff
|
tree
2020-03-19
Artem Zhmurov
P
a
ss De
v
ice
C
ontext ins
t
ead of GPU
r
u
ntime data when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
ric I
r
r
gang
Add stu
b
V
a
ri
a
bles do
c
umentatio
n
to
G
i
tLab
C
I
do
c
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
i
c Irrgang
D
e
f
ine
an
a
rgparse
p
are
n
t parser for contai
n
er imag
e
.
.
.
commit
|
commitdiff
|
tree
2020-03-14
Mark
A
b
r
aham
Move testi
n
g code to test dir
e
ctory
commit
|
commitdiff
|
tree
2020-03-12
Gille
s
Gouaillardet
gromp
p
:
fix the -ref <file> option
commit
|
commitdiff
|
tree
2020-03-10
Artem Z
h
murov
Use
i
n
it(
.
.
)
function to build DeviceContext
commit
|
commitdiff
|
tree
2020-03-07
Berk Hess
M
ake shake work without graph
commit
|
commitdiff
|
tree
2020-03-04
Mark Abraha
m
Improve TPI handling
commit
|
commitdiff
|
tree
2020-03-02
B
erk
H
ess
Fix center of m
a
ss motion removal
w
ith froz
e
n atom
s
commit
|
commitdiff
|
tree
2020-03-02
A
r
tem Zhmurov
U
p
date th
e
mes
s
age on w
h
ethe
r
upda
t
e and con
s
tr
a
ints
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
P
au
l
Bauer
Remove fro
z
e
n atoms
f
rom VCM groups
commit
|
commitdiff
|
tree
2020-02-27
Pa
s
cal Merz
Loosen gmxapi stopsignaler test
commit
|
commitdiff
|
tree
2020-02-27
Pascal
M
erz
Extract and expose f
u
nc
t
ion to determine whether
molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Szilárd
P
áll
Rem
o
ve outdated
P
ME-
G
PU
l
imi
t
a
tion in u
s
er guide
commit
|
commitdiff
|
tree
2020-02-25
M
a
gnus Lundborg
Fix out
o
f
sync c
h
ec
k
po
i
nt files
i
n si
m
u
lations sha
r
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2020-02-24
Paul Bauer
Fix c
l
ang-6 i
m
age template
commit
|
commitdiff
|
tree
2020-02-20
Arte
m
Zhmur
o
v
Us
e
CUDA float3 vector type instead of fvec i
n
GP
U
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
P
a
ul
Bauer
Workaroun
d
fo
r
Git
l
ab archi
v
e
size
commit
|
commitdiff
|
tree
2020-01-29
Magnus Lund
b
org
More SIMD prepa
r
ati
o
ns in t
h
e F
E
calculat
i
ons
commit
|
commitdiff
|
tree
2020-01-29
Pau
l
Bauer
Add replacem
e
nt for sym
b
o
l
tab
l
e
commit
|
commitdiff
|
tree
2020-01-27
Mark Abraha
m
Remove ele
m
ent-size member fields
commit
|
commitdiff
|
tree
2020-01-27
Mark
Abraham
M
a
ke Nbn
x
n
Gpu cla
s
s with con
s
tru
c
tor
commit
|
commitdiff
|
tree
2020-01-24
Szilárd Páll
Add
tar
g
et
f
or
o
ffline PME O
p
enCL comp
i
latio
n
commit
|
commitdiff
|
tree
2020-01-24
Magnus Lundborg
Rem
o
ved SC R
P
ower 4
8
from FEP kernel
commit
|
commitdiff
|
tree
2020-01-17
Mark Abraham
R
e
g
ula
r
ize nbnxm module doxygen
commit
|
commitdiff
|
tree
2020-01-17
P
a
ul B
a
uer
Fix bad link in developer docs
commit
|
commitdiff
|
tree
2020-01-17
Berk Hess
Add check for shell
s
and GPU upda
t
e
commit
|
commitdiff
|
tree
2020-01-13
Paul Bauer
Rever
t
"E
x
clude
build-syst
e
m files
from CPack"
commit
|
commitdiff
|
tree
2020-01-13
Christoph Jungh
a
ns
gmx
M
anageMPI
.
cmake: convert MPI FLAGS to
l
is
t
s
commit
|
commitdiff
|
tree
2020-01-09
M
a
rk Abraham
Clean
u
p
ewald mod
u
le internals
commit
|
commitdiff
|
tree
2020-01-09
Mark
A
braham
Split lines with many cop
y
right years
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric Irr
g
ang
Remove
transition
a
l li
n
ks for
online gmxapi P
y
thon
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
P
a
ul Bauer
GROMACS 2020 rel
e
ase
commit
|
commitdiff
|
tree
2020-01-01
Erik
Lindah
l
Add link to p
a
per
explaining GR
O
MOS t
w
in-rang
e
i
s
s
ues
.
commit
|
commitdiff
|
tree
2019-12-31
Mark
A
b
raham
Avoi
d
38
6
O3 code
g
e
n bug even more
commit
|
commitdiff
|
tree
2019-12-31
Artem
Z
hmurov
I
nfor
m
u
s
er why forcin
g
GPU upd
a
t
e is
n
ot possible
commit
|
commitdiff
|
tree
2019-12-31
A
rtem Zhmurov
Add desc
r
i
ption of GM
X
_FOR
C
E_U
P
DATE_DEFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhm
u
r
o
v
Fix
g
p
uup
d
ate
m
atri
x
commit
|
commitdiff
|
tree
2019-12-28
Arte
m
Zhmurov
Change the behavior
o
f
t
he GPU u
p
date U
I
commit
|
commitdiff
|
tree
2019-12-28
Mark
Ab
r
aham
M
e
rge "Merge origin/
r
elease-201
9
into relea
s
e-2020
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Paul Baue
r
Remove me
m
bed from
f
eatures
commit
|
commitdiff
|
tree
2019-12-28
Ma
r
k
A
braham
Remove support
f
o
r
ARM
v
7
commit
|
commitdiff
|
tree
2019-12-28
Mark A
b
ra
h
a
m
Stop testing ARMv7
commit
|
commitdiff
|
tree
2019-12-20
S
z
ilárd Páll
Enable buffer o
p
s
w
hen GMX_GPU_DD_COMM
S
is set
commit
|
commitdiff
|
tree
2019-12-19
P
a
u
l Bauer
Fix re
g
ressionte
s
t
s
f
a
iling
w
ith ctest
commit
|
commitdiff
|
tree
2019-12-18
Paul Ba
u
e
r
Igno
r
e build host
f
o
r
CI builds
commit
|
commitdiff
|
tree
2019-12-17
M
ar
k
Abrah
a
m
Fix that tests intended for multiple rank
s
r
u
n that way
commit
|
commitdiff
|
tree
2019-12-16
Szilárd
Páll
Fix the GPU
b
onded stream with 1
PP +
1 PM
E
r
a
nk
commit
|
commitdiff
|
tree
2019-12-16
Be
r
k Hess
Use L
i
st
O
f
L
ists in gm
x
_mtop_t and
g
mx_localtop_
t
commit
|
commitdiff
|
tree
2019-12-15
Chris
t
ian
Blau
Fix dens
i
tyfitti
n
g st
a
l
l
i
ng and energies
commit
|
commitdiff
|
tree
2019-12-14
M
a
rk
A
brah
a
m
Simplify gmxapi RPATH handling
commit
|
commitdiff
|
tree
2019-12-12
Mark Abraham
Merge "Merge branch 'o
r
i
g
in
/
release
-
2020' in
t
o master
"
commit
|
commitdiff
|
tree
2019-12-12
Artem
Z
hmu
r
o
v
A
llo
w
using GPU update
with DD and update
g
roups
commit
|
commitdiff
|
tree
2019-12-11
Ma
r
k Abraham
Document DOMAINDECOMP(cr) correctly
commit
|
commitdiff
|
tree
2019-12-11
Paul Bauer
Test parallel mpi only with o
p
enmp
commit
|
commitdiff
|
tree
2019-12-04
Mark
A
braham
Ad
d
e
d OpenCL bu
i
ld to r
e
lease matrix
commit
|
commitdiff
|
tree
2019-12-04
Mark Abraha
m
Removed
unnecessary link_directori
e
s c
o
mmand for gtest
commit
|
commitdiff
|
tree
2019-11-29
Paul Bauer
Fix build
e
r
ror witho
u
t thread
or
r
egula
r
mpi
commit
|
commitdiff
|
tree
2019-11-29
Ma
r
k
A
b
raha
m
Merge branch release-
2
019 into release-2020
commit
|
commitdiff
|
tree
2019-11-29
Artem
Zh
m
u
r
o
v
Rename some variables in GPU
Update
commit
|
commitdiff
|
tree
2019-11-28
P
a
ul Ba
u
er
Chec
k
for using c
o
r
r
e
c
t
hwloc
headers
and run
t
ime
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Clea
r
device force buffer if
it was re
a
lloca
t
ed
commit
|
commitdiff
|
tree
2019-11-27
Arte
m
Zhmurov
Add method for coordi
n
a
t
e
s
scaling into GP
U
u
p
date
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric
I
rrgang
A
dd
g
m
x
api_extension tes
t
s
t
o 'tes
t
s' target
.
commit
|
commitdiff
|
tree
2019-11-27
A
l
an Gray
E
vent-bas
e
d D
e
pendency for GPU Force Halo Exc
h
a
n
ge
commit
|
commitdiff
|
tree
2019-11-26
Mark Abrah
a
m
Improve handling of
t
ask-
a
ssig
n
ment exceptions
commit
|
commitdiff
|
tree
2019-11-25
Alan G
r
ay
Fix
r
ace condition in
GPU X ha
l
o exchange with GPU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
Christian
Blau
I
nM
e
morySerialize
r
with endianess swap
.
commit
|
commitdiff
|
tree
2019-11-21
Mark Abraham
M
erge
branch releas
e
-2020
commit
|
commitdiff
|
tree
2019-11-21
Mark Abraham
New coo
l
quote
commit
|
commitdiff
|
tree
2019-11-20
Artem Z
h
murov
Add D2H copies
for the checkpointing
commit
|
commitdiff
|
tree
2019-11-20
Art
e
m Zhmurov
Move
t
he copy of the velocitie
s
for th
e
ou
t
put c
l
o
s
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
Berk He
s
s
Quiet
p
db2gmx a
n
d use gmx_fatal
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric Irr
g
ang
Remove
s
tub co
n
tent f
r
om gmxapi
d
ocs
.
commit
|
commitdiff
|
tree
2019-11-16
Mark Abraha
m
Rela
x
ed listed
f
orces te
s
t toleranc
e
s
commit
|
commitdiff
|
tree
2019-11-06
B
er
k
Hess
De
p
r
ecate
d
sc-r-power=48
commit
|
commitdiff
|
tree
2019-11-04
Paul Bauer
Ad
d
build for clang-format
commit
|
commitdiff
|
tree
2019-11-04
P
aul Bauer
Spli
t
up source code formatting scripts
commit
|
commitdiff
|
tree
2019-11-04
Teemu Mu
r
tola
Update clang-format confi
g
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irr
g
a
ng
Imp
r
ove uni
f
ormity of OS X CMake conf
i
g
u
r
ation
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
Restore CMake c
o
n
ve
n
ience targ
e
ts for s
a
m
ple_restraint
.
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
Remove
d
ead code for nbnxm H2D coordi
n
a
t
e copy
event
commit
|
commitdiff
|
tree
2019-10-31
A
lan Gray
Bug fix for event passed
to GPU comm f
e
atures
commit
|
commitdiff
|
tree
2019-10-31
Pas
c
a
l Merz
Ch
e
ck
f
or contradicting
environmen
t
var
i
ables (modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Ma
r
k Abraham
Tests fo
r
valid periodic a
c
tions
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irr
g
ang
Dis
a
ble
its tests wh
e
n
sample_r
e
st
r
aint is n
o
t the
.
.
.
commit
|
commitdiff
|
tree
next