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Use legacy code path for t_graph (modular simulator)
2020-02-27
P
a
scal
M
erz
Use lega
c
y code path for t
_
g
r
aph (modular simulator)
commit
|
commitdiff
|
tree
2020-02-25
S
z
ilár
d
Páll
Improve G
P
U
u
pdate tasks
as
s
i
gnment consist
e
ncy
commit
|
commitdiff
|
tree
2020-02-25
Paul
Baue
r
Avoi
d
i
n
teger overflow in dispersion correction
commit
|
commitdiff
|
tree
2020-02-25
Paul Bauer
Rever
t
"Expose
v
site co
u
nting"
commit
|
commitdiff
|
tree
2020-02-21
M
.
Eric Irrgang
Simplify GitLab CI D
o
cker
f
i
l
es
.
commit
|
commitdiff
|
tree
2020-02-10
Sz
i
l
á
r
d Páll
A
v
oid
d
e
v
fl
a
gs
in tr
i
ggeri
n
g gpuupda
t
e nightly m
a
trix
commit
|
commitdiff
|
tree
2020-02-10
S
zilár
d
Pá
l
l
Avoid (re)i
n
itializing
GPU updat
e
without DD
commit
|
commitdiff
|
tree
2020-01-24
P
au
l
B
a
u
e
r
Use u
t
f
-
8 for pyt
h
on
file
r
eading
commit
|
commitdiff
|
tree
2020-01-23
Berk
Hess
Fix DD rank count prime check
commit
|
commitdiff
|
tree
2020-01-23
Artem Zhmurov
Fix
a couple of c
o
mmas in cool quote
s
commit
|
commitdiff
|
tree
2020-01-23
Gaurav Ga
r
g
Fix PME
ch
e
cks in GPU update assignment decision
commit
|
commitdiff
|
tree
2020-01-21
P
a
ul
Bauer
F
ix docu
m
entat
i
on er
r
or with d
o
x
y
gen
>
1
.
8
.
1
6
commit
|
commitdiff
|
tree
2020-01-17
Paul B
a
uer
Actually f
i
x
Gitlab doc build
commit
|
commitdiff
|
tree
2020-01-16
Szil
á
rd Pá
l
l
Fix PME run m
o
de wi
t
h
o
ut P
M
E
commit
|
commitdiff
|
tree
2020-01-16
Paul Bauer
Fix nightly build
fail
u
re on Gitl
a
b
commit
|
commitdiff
|
tree
2020-01-08
Roland Schul
z
Merge release
-
2
019 into release-2020
commit
|
commitdiff
|
tree
2020-01-01
Paul Bauer
Prepare f
o
r 2020
.
1
commit
|
commitdiff
|
tree
2020-01-01
Paul Ba
u
e
r
GROMACS 2020 release
commit
|
commitdiff
|
tree
2020-01-01
Paul Bauer
Revert "GROMACS 2020 release"
commit
|
commitdiff
|
tree
2019-12-30
Pau
l
Bauer
Fix bui
l
d error wit
h
wr
o
ng name
from cached cmake file
commit
|
commitdiff
|
tree
2019-12-29
Er
i
k Li
n
dahl
Write TP
R
b
o
dy
a
s opaque XDR data
in big-endian format
commit
|
commitdiff
|
tree
2019-12-28
M
.
Er
i
c
Irrg
a
ng
Reso
l
ve CM
a
ke am
b
iguities for gm
x
api Python packag
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
P
aul Bauer
Chan
g
e releng
t
o give infor
m
a
t
i
on about Gitlab
commit
|
commitdiff
|
tree
2019-12-28
Paul Bauer
Extend infor
m
ation for GPU update
commit
|
commitdiff
|
tree
2019-12-28
Paul B
a
uer
Exclude build-sys
t
e
m
f
iles
fr
o
m
CPack
commit
|
commitdiff
|
tree
2019-12-28
Paul Ba
u
er
De
p
r
ecate s
u
ppo
r
t fo
r
Arm
v
7
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
Add
a
no
t
e
to the log file wh
e
n -update gpu wa
s
s
et
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Paul Bauer
Add co
p
y
righ
t
che
c
k and i
m
prove cache usa
g
e
commit
|
commitdiff
|
tree
2019-12-27
P
a
ul Bau
e
r
Merg
e
or
i
gin/release-2
0
19 into rel
e
ase
-
2020
commit
|
commitdiff
|
tree
2019-12-27
Art
e
m
Zh
m
urov
Cle
a
n bad auto-format in d
e
cidegpuu
s
age doxygen comments
commit
|
commitdiff
|
tree
2019-12-23
Paul Bauer
A
d
d
f
iles fo
r
Gitlab CI
commit
|
commitdiff
|
tree
2019-12-23
Paul Bauer
P
r
epare for GROMACS 2019
.
6
commit
|
commitdiff
|
tree
2019-12-23
Paul
Bauer
GROMACS version
2
0
19
.
5
commit
|
commitdiff
|
tree
2019-12-23
Paul
Ba
u
e
r
R
e
ve
r
t "Fix that
t
es
t
s intended for multiple ranks
.
.
.
commit
|
commitdiff
|
tree
2019-12-20
Paul Ba
u
er
G
R
OMACS 2020 release candidate
commit
|
commitdiff
|
tree
2019-12-19
Alan Gray
Fix PME tuning issue when P
M
E-PP communi
c
ations are
.
.
.
commit
|
commitdiff
|
tree
2019-12-19
Szilárd
P
ál
l
PP-PM
E
load balancing improv
e
m
e
nts
commit
|
commitdiff
|
tree
2019-12-18
Szil
á
r
d
Páll
A
llow x
D
2H to ove
r
lap
with GPU force co
m
p
ut
e
commit
|
commitdiff
|
tree
2019-12-18
Berk Hess
Change grompp dec
o
upling SD warnin
g
to note
commit
|
commitdiff
|
tree
2019-12-18
P
a
ul Bauer
Add ab
i
l
ity to s
e
t
O
MP a
n
d
tMPI thread for cte
s
t
commit
|
commitdiff
|
tree
2019-12-13
Paul Bauer
Check f
o
r using correct hwloc header
s
a
n
d runtime
commit
|
commitdiff
|
tree
2019-12-11
Ar
t
em
Zhmurov
Cl
a
r
ify
w
hat setting zero to so
m
e output mdp o
p
ti
o
ns
.
.
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Ir
r
gang
gmxapi
l
anding page upd
a
te
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
Eric Irrgang
Fin
a
lize gm
x
api 0
.
1
commit
|
commitdiff
|
tree
2019-12-06
Mar
k
Abraha
m
Avoid 386 O3 codegen bug
commit
|
commitdiff
|
tree
2019-12-06
M
.
E
r
ic I
r
rgang
Add notes on M
P
I with
gmxapi Pyth
o
n p
a
ckage
.
commit
|
commitdiff
|
tree
2019-12-06
Ar
t
e
m
Zhmurov
Pass a
r
ray ref instead of casting to basic a
r
ray in
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Christ
i
an Blau
C
h
an
g
e arbitrary
u
n
i
ts to coun
t
s in RM
S
D distance
distributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Mark A
b
raham
Provide more f
e
ed
b
ack
when listed
f
or
c
es tes
t
s
fail
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrg
a
ng
gmxapi Pyth
o
n pa
c
kage usage pros
e
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
E
ric Ir
r
gang
Im
p
rove pytest fixtures for directory manag
e
m
ent
.
commit
|
commitdiff
|
tree
2019-12-05
Chri
s
tian Blau
Relax cross-correla
t
ion test precision
commit
|
commitdiff
|
tree
2019-12-03
Paul Ba
u
er
Third beta release of GROMA
C
S
2020
commit
|
commitdiff
|
tree
2019-12-03
Paul
B
aue
r
Rever
t
"Ena
b
l
e GP
U
upda
t
e wi
t
h DD
w
hen
G
P
U comm features
.
.
.
commit
|
commitdiff
|
tree
2019-12-03
Paul Bauer
Fix nightly build by correctly defining severa
l
commit
|
commitdiff
|
tree
2019-12-03
Alan Gray
Enable GPU upd
a
te with DD when GPU comm fe
a
tures
a
re
.
.
.
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
Add check for cou
p
led constraints for C
U
D
A u
p
date
commit
|
commitdiff
|
tree
2019-12-02
Berk
Hess
Ext
r
act LI
N
CS CUDA helper funct
i
o
n
s
commit
|
commitdiff
|
tree
2019-12-01
Paul Baue
r
Use DOI for citing
i
n
r
eferenc
e
m
a
nual
s
ectio
n
commit
|
commitdiff
|
tree
2019-12-01
Mark Abrah
a
m
Furt
h
er im
p
rove ta
s
k
assignm
e
nt except
i
on handlin
g
commit
|
commitdiff
|
tree
2019-11-29
P
aul Bauer
F
i
x unalign
e
d access wi
t
h A
V
X512
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmu
r
ov
Print Op
e
n
C
L error info in
ca
s
e o
f
failed assertion
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Paul
Ba
u
er
Fix post
s
ubmit
commit
|
commitdiff
|
tree
2019-11-28
Ch
r
i
stian Bla
u
Fix che
c
k-pointing for density guided simulati
o
ns
commit
|
commitdiff
|
tree
2019-11-26
Mark Abraham
Relax
t
oleran
c
e for bd t
e
st
s
commit
|
commitdiff
|
tree
2019-11-26
Paul Bauer
Fix unused variable warnin
g
in ewald code
commit
|
commitdiff
|
tree
2019-11-26
Berk Hess
Fix
i
ss
u
es with AWH with periodic
pul
l
in
g
commit
|
commitdiff
|
tree
2019-11-25
Christian
Blau
Fi
x
duplicate
C
ONNECT records in pdb files
commit
|
commitdiff
|
tree
2019-11-25
Artem
Z
hmurov
U
se same matrix for Parrinello-R
a
hman
a
nd B
e
rendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
Read mrc den
s
ity map form
a
t with al
l
endian
e
sses
.
commit
|
commitdiff
|
tree
2019-11-25
Chr
i
stian Blau
Check mr
c
head
e
r f
o
r sanity
commit
|
commitdiff
|
tree
2019-11-25
Artem
Zhmurov
Fix
index m
a
pping
i
ssue with LINCS o
n
GPU
commit
|
commitdiff
|
tree
2019-11-20
Paul Ba
u
er
Merge
'
origin/re
l
e
a
s
e
-
2019' in
t
o release-2020
commit
|
commitdiff
|
tree
2019-11-20
Mark Abraha
m
Q
u
iet uni
n
itialized v
a
riable warning with clang
9
commit
|
commitdiff
|
tree
2019-11-17
S
zilárd Páll
Trigger
ocl_nbnxm_kernels targe
t
w
i
th clang-tid
y
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
ric Irrgang
Remove extraneous fi
l
e
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrga
n
g
Add transitional link
s
f
o
r online gmxapi
P
ython pa
c
kag
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric
I
rrgang
Improve gm
x
api Doc
k
erfiles
.
commit
|
commitdiff
|
tree
2019-11-17
Szi
l
á
rd P
á
ll
Fix clang
-
tidy 8
warnings in OpenCL nbnxm kernels
commit
|
commitdiff
|
tree
2019-11-16
M
a
rk Abraham
Stop t
e
sting that hwlo
c
cache-
s
ize de
t
ecti
o
n wor
k
s
.
.
.
commit
|
commitdiff
|
tree
2019-11-14
Paul Bauer
Fix for
m
atting error
commit
|
commitdiff
|
tree
2019-11-13
E
r
i
k
Lind
a
hl
Updated physical constant
s
to CODATA 201
8
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric I
r
rgang
Achieve gmxa
p
i fr1
5
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
E
ric Irrgang
Up
d
ates to gmxapi F
R
15
acceptance test
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrga
n
g
Update no
t
es
a
nd tes
t
s regardi
n
g gmx
a
pi acc
e
ptance
.
.
.
commit
|
commitdiff
|
tree
2019-11-09
A
la
n
Gray
Moderniz
e
naming in GPU
b
uff
e
r ops k
e
rnels
commit
|
commitdiff
|
tree
2019-11-09
ejjordan
F
ix mdp
p
arameter
ha
n
dling in mdrun
tests
commit
|
commitdiff
|
tree
2019-11-08
M
.
Eric
Irr
g
ang
Fi
x
bug
i
ntroduced by cl
a
ng-format
r
e
format
.
commit
|
commitdiff
|
tree
2019-11-07
P
aul Bauer
Apply clang-format to so
u
rce tre
e
commit
|
commitdiff
|
tree
2019-11-06
Eri
k
Lindahl
Work around broken
A
pple compiler
s
i
n Mac OS 10
.
15
commit
|
commitdiff
|
tree
2019-11-04
M
.
Eric Irrgang
U
pdat
e
g
m
xapi Py
t
ho
n
d
ocument
a
tion
i
nstructions
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric Irrgan
g
Upda
t
e Sp
h
inx link
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Er
i
c Irrgan
g
F
ix
t
ypos
.
commit
|
commitdiff
|
tree
2019-11-01
P
a
u
l Bauer
Second beta release
o
f
GROMACS
2
020
commit
|
commitdiff
|
tree
2019-11-01
Christian
Blau
Fi
x
c
r
o
s
s-correlation calculation insta
b
ility
commit
|
commitdiff
|
tree
2019-11-01
Szi
l
ár
d
Páll
R
e
n
a
me r
e
ference che
c
ksum generati
n
g
t
arget
commit
|
commitdiff
|
tree
2019-11-01
Szilárd P
á
l
l
U
s
e "-" in checksum-rel
a
te
d
version suffix
commit
|
commitdiff
|
tree
2019-11-01
Szilárd
P
á
l
l
Improve workload data s
t
ructu
r
es'
d
ocs
commit
|
commitdiff
|
tree
2019-11-01
Alan Gray
Remove energy step de
p
endence o
n
GPU force buffe
r
ops
commit
|
commitdiff
|
tree
2019-11-01
B
erk Hess
A
dd ha
v
eEwaldSurfaceContr
i
b
u
tion to Simu
l
ationWorklo
a
d
commit
|
commitdiff
|
tree
next