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Set buffers appropriately so .xpm files can be read.
2020-03-30
Mark Abr
a
h
a
m
Se
t
b
uffers appropriately so
.
x
p
m f
i
les can be read
.
commit
|
commitdiff
|
tree
2020-03-17
B
erk Hess
Disable
E
wald dipole correction without DD
commit
|
commitdiff
|
tree
2020-03-02
Berk
H
e
s
s
Fix center of ma
s
s
motion removal w
i
th froz
e
n atoms
commit
|
commitdiff
|
tree
2020-03-02
A
r
t
em Z
h
m
u
rov
Upd
a
t
e
the
message
o
n w
h
ether upd
a
te an
d
c
onstraints
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
P
a
ul Bauer
Remove frozen
atoms fr
o
m VCM group
s
commit
|
commitdiff
|
tree
2020-02-27
P
ascal
M
erz
Loosen
g
m
xapi stopsi
g
n
aler test
commit
|
commitdiff
|
tree
2020-02-27
Pascal Merz
Extract and
e
xpose fun
c
tio
n
to d
e
termi
n
e w
h
ether molecul
e
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Szilárd Pál
l
Remove
outdated
P
ME-GPU limitation in u
s
er gu
i
d
e
commit
|
commitdiff
|
tree
2020-02-25
M
a
gnus Lundborg
Fix out of sync ch
e
ckpoin
t
file
s
in simulati
o
ns sharing
.
.
.
commit
|
commitdiff
|
tree
2020-02-24
Pa
u
l Bauer
Fix cla
n
g-6 image t
e
mp
l
ate
commit
|
commitdiff
|
tree
2020-01-29
Paul Bauer
W
o
rkaround for Git
l
ab
archive s
i
ze
commit
|
commitdiff
|
tree
2020-01-17
Paul Ba
u
er
Fix bad link
i
n dev
e
loper do
c
s
commit
|
commitdiff
|
tree
2020-01-17
B
e
r
k H
e
ss
Add chec
k
f
or shells and
GPU update
commit
|
commitdiff
|
tree
2020-01-13
Paul
Bauer
Rever
t
"Exclude build-system files from CPack"
commit
|
commitdiff
|
tree
2020-01-13
Christ
o
ph Jungha
n
s
gmxManageMPI
.
cmake:
co
n
v
ert MPI F
L
AGS
t
o lists
commit
|
commitdiff
|
tree
2020-01-03
M
.
E
r
ic I
r
rgan
g
Re
m
ove
t
r
a
n
sitional li
n
ks for
o
nlin
e
g
m
xapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
Paul Bauer
GROMACS
20
2
0 release
commit
|
commitdiff
|
tree
2020-01-01
Erik L
i
ndahl
Add
link to paper e
x
plaining GROMOS t
w
in-range i
s
sues
.
commit
|
commitdiff
|
tree
2019-12-31
Mark
A
braham
Avoid 386 O
3
codegen bug even more
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Inform user why forcin
g
GPU update is not
p
os
s
ible
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
e
m Zh
m
ur
o
v
A
dd
d
escripti
o
n
o
f GMX_F
O
RCE
_
UP
D
A
T
E_DEFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
e
m
Z
hmurov
Fix
gpuupdate
matri
x
commit
|
commitdiff
|
tree
2019-12-28
A
r
te
m
Zhmurov
C
han
g
e
the
b
ehavior of t
h
e GPU
u
pdate UI
commit
|
commitdiff
|
tree
2019-12-28
M
ark Abraham
M
e
rge "Mer
g
e origin/
r
e
leas
e
-
2
019
i
n
to release-20
2
0
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
P
a
ul Bauer
Remove membed
f
r
om features
commit
|
commitdiff
|
tree
2019-12-20
Szi
l
árd Pá
l
l
Enable buf
f
er op
s
when GMX_GPU_DD_COMMS is
s
et
commit
|
commitdiff
|
tree
2019-12-19
Paul Ba
u
e
r
Fix
regres
s
ion
t
ests
failing with ctest
commit
|
commitdiff
|
tree
2019-12-18
Paul
B
auer
Ignore bui
l
d
ho
s
t
f
or C
I
b
uilds
commit
|
commitdiff
|
tree
2019-12-17
Mark Abraha
m
Fix t
h
at tests intended for multi
p
l
e ranks run tha
t
way
commit
|
commitdiff
|
tree
2019-12-16
Szilá
r
d P
á
ll
Fix the G
P
U
bonde
d
s
t
ream with 1 PP
+
1 PME rank
commit
|
commitdiff
|
tree
2019-12-15
Christian Bla
u
Fix densityfitting
stalling and ene
r
g
i
es
commit
|
commitdiff
|
tree
2019-12-14
Mark Abr
a
ham
Simplify gmxapi
RPATH handling
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmu
r
ov
A
l
low using GPU upd
a
te
with DD and updat
e
groups
commit
|
commitdiff
|
tree
2019-12-11
Mark Abrah
a
m
Docume
n
t DOMAINDE
C
OM
P
(cr
)
corr
e
ctly
commit
|
commitdiff
|
tree
2019-12-04
M
a
rk Abr
a
ham
Added OpenCL
build
to release matr
i
x
commit
|
commitdiff
|
tree
2019-12-04
Mark A
b
raham
R
e
m
o
ved unnecessary link_directo
r
ies comma
n
d for gtest
commit
|
commitdiff
|
tree
2019-11-29
Pa
u
l Ba
u
er
F
i
x
b
u
ild erro
r
without thr
e
ad or r
e
gu
l
ar mpi
commit
|
commitdiff
|
tree
2019-11-29
Mark Abraham
Merge branch r
e
lease-2019 in
t
o
rele
a
se-
2
020
commit
|
commitdiff
|
tree
2019-11-29
Artem Zh
m
ur
o
v
Re
n
ame
some variables i
n
GPU Update
commit
|
commitdiff
|
tree
2019-11-28
Paul Bauer
Check f
o
r usi
n
g
correct h
w
loc hea
d
ers and ru
n
ti
m
e
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmur
o
v
Clear device
force buffer if it was reallocated
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmur
o
v
Add m
e
thod fo
r
coordinates scaling
i
n
to GPU
u
pdate
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric Irr
g
ang
A
dd gmxapi_extension tes
t
s
t
o 'tests' t
a
rget
.
commit
|
commitdiff
|
tree
2019-11-27
A
l
an
G
ra
y
Ev
e
nt-based Dep
e
ndenc
y
for GPU Force Halo
E
xchange
commit
|
commitdiff
|
tree
2019-11-26
Mark Abraham
I
m
prov
e
handlin
g
of t
a
sk-
a
ssignment exception
s
commit
|
commitdiff
|
tree
2019-11-25
Alan
G
r
a
y
Fix r
a
ce condition in GPU X ha
l
o exchange with
G
PU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
C
hristian B
l
au
I
nMe
m
orySe
r
ializer with endiane
s
s swap
.
commit
|
commitdiff
|
tree
2019-11-21
Mark
A
braham
N
e
w cool quote
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
Add D2H co
p
ies for the checkpointing
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
Move
t
he
copy
o
f
the
v
elocities for the ou
t
put cl
o
ser
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
Ber
k
Hes
s
Quiet pdb2gm
x
and u
s
e gmx
_
fatal
commit
|
commitdiff
|
tree
2019-11-20
M
.
E
r
i
c Irrgan
g
Remove stub
cont
e
nt from
g
m
xapi d
o
cs
.
commit
|
commitdiff
|
tree
2019-11-16
Ma
r
k
A
b
rah
a
m
R
elaxed listed forc
e
s test tolerance
s
commit
|
commitdiff
|
tree
2019-11-06
B
erk Hess
Depre
c
ated sc-r-p
o
wer
=
48
commit
|
commitdiff
|
tree
2019-11-04
P
a
ul Bauer
A
dd build for clang-format
commit
|
commitdiff
|
tree
2019-11-04
P
a
ul
Bauer
Split up source
code formatting s
c
ri
p
t
s
commit
|
commitdiff
|
tree
2019-11-04
T
eemu
Murtola
Update
clang-format config
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Ir
r
gang
Improve u
n
iformity of
O
S X
CMake configuration
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
r
ic
Irrg
a
ng
Res
t
o
r
e CMake co
n
venie
n
ce targets
f
or sample
_
r
e
str
a
int
.
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
Re
m
ove d
e
ad code for nbnxm H
2
D coordinate
c
o
p
y event
commit
|
commitdiff
|
tree
2019-10-31
A
l
a
n Gray
Bug
f
ix fo
r
event passed to GPU c
o
mm features
commit
|
commitdiff
|
tree
2019-10-31
Pascal Merz
Check for contradicting en
v
ir
o
n
ment variabl
e
s (m
o
dular
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Mark Abraham
Tests f
o
r valid per
i
o
dic actions
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irr
g
ang
D
isab
l
e its te
s
t
s
when samp
l
e_restraint is
not the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eri
c
Irrgang
D
ecrease th
e
maximum al
l
owed Python versi
o
n for gmxapi
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmurov
Disable GPU update when co
o
rdinates swapping is en
a
bled
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add bool useDomainDecompos
i
tion
i
n mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Berk He
s
s
Add gmx_mtop
_
interactio
n
_cou
n
t()
commit
|
commitdiff
|
tree
2019-10-23
ejjorda
n
Make
t
_n
e
xtn
b
a
n
i
mp
l
eme
n
ta
t
io
n
detail
commit
|
commitdiff
|
tree
2019-10-23
Pas
c
al Merz
Correct
f
or skewed box
b
e
fore dom
a
in
decomposition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Alan Gra
y
Enable GPU
P
eer Access
i
n GPU U
t
iliti
e
s
commit
|
commitdiff
|
tree
2019-10-22
ejjordan
Re
m
ove unuse
d
fu
n
ctions
from gmxpreprocess
commit
|
commitdiff
|
tree
2019-10-22
Berk Hes
s
R
e
quire -ei
f
or
e
s
sent
i
al dy
n
amics
commit
|
commitdiff
|
tree
2019-10-22
ejjordan
Remove
u
n
use
d
functi
o
n
g
enerate_e
x
cl
s
and make clean_excl
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Berk
Hess
Con
s
t
correctness for gen
h
y
dro
commit
|
commitdiff
|
tree
2019-10-15
P
a
ul B
a
uer
F
i
x bug in prepro
c
essing
commit
|
commitdiff
|
tree
2019-10-14
M
.
E
r
ic
Irrgang
Fix logic erro
r
in
g
mxapi
.
vers
i
on
.
a
pi_
i
s_at_
l
east(
)
.
commit
|
commitdiff
|
tree
2019-10-13
Mark Abraham
Ensure environ
m
ent variable
u
s
e
does not give warnings
commit
|
commitdiff
|
tree
2019-10-12
B
erk H
e
ss
Add class
F
ixedCapacityVector
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhm
u
r
o
v
Centralize
m
anagem
e
n
t of coordina
t
es ready
o
n GPU
event
commit
|
commitdiff
|
tree
2019-10-08
Prashanth Kand
u
ri
Fu
s
ed two if bra
n
ches with t
h
e
s
ame conditional
commit
|
commitdiff
|
tree
2019-10-02
Carsten Kut
z
ner
Update
the www link
to the Doxyge
n
d
ocumentati
o
n in
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
Berk He
s
s
F
i
x h
a
r
mless
O
penMP
w
rite race
commit
|
commitdiff
|
tree
2019-10-02
Mark Abraham
Improve PME tes
t
ing
commit
|
commitdiff
|
tree
2019-10-01
Berk Hes
s
Use
g
m
x::Range in domd
e
c
commit
|
commitdiff
|
tree
2019-10-01
Ar
t
em
Z
h
mu
r
ov
StatePropagatorDataGpu
o
bject to manage GP
U
forces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
M
ark A
b
raham
F
i
x icc warn
i
ngs
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Comp
l
etel
y
re
m
ov
e
ch
a
rge
group
s
commit
|
commitdiff
|
tree
2019-10-01
Paul Bauer
Fix
c
h
a
in ID handling in m
a
k
e
_n
d
x
commit
|
commitdiff
|
tree
2019-10-01
Christoph Jun
g
h
a
n
s
c
make: a
d
d
m
issing
header to legacy
a
pi
commit
|
commitdiff
|
tree
2019-10-01
Mark
A
braham
Removed
d
ependenc
y
on commrec of mdrun s
e
tup
commit
|
commitdiff
|
tree
2019-09-30
Carsten Kutzne
r
Move ForcePr
o
v
i
d
e
r
s class i
n
to the gmx
namesp
a
ce
commit
|
commitdiff
|
tree
2019-09-30
Mark A
b
ra
h
am
M
a
k
e
a
bu
i
lder for DD
commit
|
commitdiff
|
tree
2019-09-30
Berk H
e
ss
Remove charge group code from for
c
erec
commit
|
commitdiff
|
tree
2019-09-30
Szilárd P
á
ll
Make the
wait
o
n
PM
E
GPU r
e
su
l
ts conditional
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
I
m
pro
v
e
MiMiC te
s
t impl
e
ment
a
tion
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
F
ix
gro file output with
i
nde
x
groups
commit
|
commitdiff
|
tree
2019-09-27
Mark Abr
a
ham
Fix g
r
o fi
l
e output wi
t
h ind
e
x gr
o
ups
commit
|
commitdiff
|
tree
2019-09-27
Mar
k
Abraham
R
e
m
ove leftover support for pre-9
.
0 CUDA
commit
|
commitdiff
|
tree
2019-09-24
Paul Bauer
Add test
f
or noappend
commit
|
commitdiff
|
tree
next