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Make pull with COM from previous step work with MPI
2018-11-29
Magnus Lund
b
org
Make pull
w
ith COM from pre
v
i
o
us step
w
ork w
i
th
M
PI
commit
|
commitdiff
|
tree
2018-11-29
M
a
rk A
b
raham
Removed erronous manual
v
a
ria
b
le handling
commit
|
commitdiff
|
tree
2018-11-29
Paul B
a
uer
Fix reference m
a
nual image sizes
commit
|
commitdiff
|
tree
2018-11-29
Paul Bauer
F
i
x reference manual do
c
b
u
i
ld
commit
|
commitdiff
|
tree
2018-11-28
Paul Bauer
Fix
g
c
c-
8
war
n
ings
commit
|
commitdiff
|
tree
2018-11-28
Ma
r
k Abraham
I
nt
r
oduce GpuBonde
d
commit
|
commitdiff
|
tree
2018-11-27
Szilárd Páll
Add ARMPL suppor
t
to a
d
min scri
p
t
commit
|
commitdiff
|
tree
2018-11-27
S
z
i
lárd
Páll
Add tweak
s
to support
AR
M
PL for FFTs
commit
|
commitdiff
|
tree
2018-11-26
Paul Bauer
Fi
x
n
ewli
n
e
p
r
inting in -
v
output
commit
|
commitdiff
|
tree
2018-11-20
Mar
k
Abraham
Partial revert of "Fix i
n
effici
e
nt sh
e
ll
m
inimization"
commit
|
commitdiff
|
tree
2018-11-15
Paul Ba
u
er
R
efine Find
S
phinx
commit
|
commitdiff
|
tree
2018-11-15
M
.
Eric
Irrgang
Note GMX_ENA
B
LE
_
CC
A
CHE
in
build s
y
stem docs
.
commit
|
commitdiff
|
tree
2018-11-15
M
a
r
k
Abraham
F
i
x checkpoint re
s
tart
of tpr with infinite step count
commit
|
commitdiff
|
tree
2018-11-15
Pau
l
Baue
r
R
e
wo
r
k GMXAPI tes
t
s
commit
|
commitdiff
|
tree
2018-11-15
M
ark Abraham
Re
l
a
x
arbitr
a
ry tolerance on
r
erun test
commit
|
commitdiff
|
tree
2018-11-14
Mark Abra
h
am
F
ix OpenCL mdrun from installed path
commit
|
commitdiff
|
tree
2018-11-11
Viacheslav Bolny
k
h
Fixin
g
segfaul
t
in parall
e
l MiMiC QM/MM run
s
commit
|
commitdiff
|
tree
2018-11-11
David van der Spoel
Fix entrop
y
calcula
t
ion
i
n gmx an
a
eig
commit
|
commitdiff
|
tree
2018-11-09
Da
v
id van de
r
Spoel
Change get_atom_index to a
l
l
ow
multiple molecules
.
commit
|
commitdiff
|
tree
2018-11-08
Paul Ba
u
er
Is
s
u
e fatal err
o
r if checkpoint doe
s
n
o
t
suit the
.
tp
r
commit
|
commitdiff
|
tree
2018-11-08
Ma
r
k Abraham
Pragma
w
arning suppressin
s
for icc+windows
commit
|
commitdiff
|
tree
2018-11-07
Paul Bauer
Mark new cmake v
a
ri
a
b
l
es
advan
c
e
d
commit
|
commitdiff
|
tree
2018-11-07
Szilárd Páll
Elimi
n
ate ma
c
r
o
that e
x
pand
s
to variable in PME G
P
U
commit
|
commitdiff
|
tree
2018-11-07
Szilárd
P
áll
Ensure minim
u
m exec
widt
h
of the PME Ope
n
C
L
kernels
commit
|
commitdiff
|
tree
2018-11-07
Paul Bauer
A
dd global directory for s
i
mulat
i
on test inp
u
ts
commit
|
commitdiff
|
tree
2018-11-06
Paul Bau
e
r
Fix
w
rong branch for regressi
o
n
t
e
s
t
s
commit
|
commitdiff
|
tree
2018-11-05
Mark Abraham
Mak
e
P
M
E OpenCL en
a
bled on
l
y for AMD devices
commit
|
commitdiff
|
tree
2018-11-05
P
aul Baue
r
Make QM/MM c
o
d
e
always compile
commit
|
commitdiff
|
tree
2018-11-05
Alex
e
y S
h
vetsov
D
i
sable -Wno-missing
-
prototypes
commit
|
commitdiff
|
tree
2018-11-05
Paul Bauer
Give more info when trying to build manual
commit
|
commitdiff
|
tree
2018-11-01
Mark
Ab
r
aham
Disable ccache by
default
commit
|
commitdiff
|
tree
2018-10-31
Berk
Hess
Limit auto assig
n
m
e
nt
of bon
d
ed
s
to GPUs
commit
|
commitdiff
|
tree
2018-10-31
J
o
nathan Vincent
Add CUDA bon
d
ed kernels
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Work aroun
d
expanded en
s
emble
issues
commit
|
commitdiff
|
tree
2018-10-31
B
erk
Hess
Correct VV integrator
nstcalcen
e
rgy use
commit
|
commitdiff
|
tree
2018-10-30
Ma
r
k
A
b
raham
I
m
prove
ccache implementat
i
on
commit
|
commitdiff
|
tree
2018-10-30
Paul
B
a
uer
C
h
ange Table of
contents de
p
th
commit
|
commitdiff
|
tree
2018-10-30
M
a
rk Abra
h
a
m
R
e
n
ame to GMX_OPE
N
C
L_NB_CLUSTER_
S
IZE
commit
|
commitdiff
|
tree
2018-10-26
Mark
Abraham
Merg
e
"M
e
rge branc
h
relea
s
e-2018 into rel
e
ase-2
0
1
9
.
.
.
commit
|
commitdiff
|
tree
2018-10-26
Mark A
b
r
a
h
a
m
M
erge
bran
c
h release-2018 into r
e
le
a
se
-
2019
commit
|
commitdiff
|
tree
2018-10-26
B
er
k
H
e
s
s
Add missing mass term t
o
deltaH
commit
|
commitdiff
|
tree
2018-10-25
Mar
k
Abraham
Introduce ArrayRe
f
WithPadding
commit
|
commitdiff
|
tree
2018-10-25
Paul Bau
e
r
Cha
n
ge doc buil
d
wi
t
hout image conve
r
sion
commit
|
commitdiff
|
tree
2018-10-24
Pa
u
l Bauer
F
i
x MPI w/o MPI_IN_PLACE
commit
|
commitdiff
|
tree
2018-10-21
Berk He
s
s
F
ix mdrun start/end time
p
rint
commit
|
commitdiff
|
tree
2018-10-19
M
.
Eric
Irrgang
Documentation
b
ug in gmxapi/c
o
ntext
.
h
commit
|
commitdiff
|
tree
2018-10-18
Be
r
k Hess
A
dd env
.
v
a
r
.
to disable u
p
date grou
p
s
commit
|
commitdiff
|
tree
2018-10-16
M
a
r
k Ab
r
aham
Eliminat
e
d
t_ifu
n
c
from
t_interaction_function
commit
|
commitdiff
|
tree
2018-10-16
Ma
g
nus Lun
d
borg
Move gm
x
_ffpa
r
ams_t to forc
e
fieldparameters
commit
|
commitdiff
|
tree
2018-10-16
Mar
k
Ab
r
aham
Task assig
n
ment f
o
r bon
d
ed interactions on
C
UDA GPUs
commit
|
commitdiff
|
tree
2018-10-16
Mark Ab
r
ah
a
m
Fix compiler issue
s
commit
|
commitdiff
|
tree
2018-10-16
Mark Abrah
a
m
Removed support for NVIDIA CC 2
.
x devices (codename
.
.
.
commit
|
commitdiff
|
tree
2018-10-15
Mark
Abraham
C
reat
e
ExclusionBlocks
commit
|
commitdiff
|
tree
2018-10-15
Mark A
b
raham
De-duplicating mdrun setup
commit
|
commitdiff
|
tree
2018-10-15
M
a
gn
u
s
Lundb
o
rg
Ena
b
le
o
u
t
p
ut of
averag
e
pull for
c
e and po
s
itions
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
E
r
i
c Ir
r
g
a
ng
Re
s
olve some l
i
n
t
er war
n
in
g
s
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric
I
rrgang
Test
signaling facility th
r
ough
session
resources
.
commit
|
commitdiff
|
tree
2018-10-14
Szilár
d
Páll
Modern
i
z
e
Open
C
L memory allocation f
l
ags
commit
|
commitdiff
|
tree
2018-10-14
M
.
E
ric Irrgang
C
lean up gmxap
i
tes
t
s
u
pport ou
t
put
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Irrgang
gmxapi::UsageEr
r
o
r
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Irrgang
Al
l
ow API access to
s
imulation sign
a
ls
.
commit
|
commitdiff
|
tree
2018-10-13
Aleksei Iupinov
Add and enable
PME OpenCL
commit
|
commitdiff
|
tree
2018-10-12
M
.
Er
i
c
I
r
rgang
A
d
d
A
P
I
for adding
M
DModu
l
es
/ Res
t
raints
.
commit
|
commitdiff
|
tree
2018-10-12
Berk Hess
Implem
e
nt as
s
igning
b
ondeds to
the GPU
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Ir
r
ga
n
g
Ad
d
res
t
rai
n
ts framework
.
commit
|
commitdiff
|
tree
2018-10-12
Viach
e
slav
Bolny
k
h
Implemen
t
ed
Q
M/MM
workflow insid
e
c
o
re GROMACS
commit
|
commitdiff
|
tree
2018-10-12
Mark
Abrah
a
m
Ex
c
lude gmx
a
pi so
u
rce
f
iles
from include sorting
commit
|
commitdiff
|
tree
2018-10-11
Dav
i
d v
a
n de
r
Spoel
Re
i
nstate
d
q
u
a
s
i
h
a
r
monic entr
o
py c
a
lc
u
lation in gmx
.
.
.
commit
|
commitdiff
|
tree
2018-10-11
M
.
E
ric Irrgang
A
d
d gmxapi::Sessio
n
.
commit
|
commitdiff
|
tree
2018-10-11
M
a
r
k Abraham
Fix Padde
d
Vector i
s
s
ues
commit
|
commitdiff
|
tree
2018-10-11
P
aul Bau
e
r
Add shor
t
sec
u
r
ity notice
commit
|
commitdiff
|
tree
2018-10-10
Paul Bauer
Incl
u
d
e doi s
t
rings from zenodo during release
commit
|
commitdiff
|
tree
2018-10-10
M
.
Eric Irr
g
a
ng
gmxapi expec
t
s position
i
n
d
ependent co
d
e
.
commit
|
commitdiff
|
tree
2018-10-10
Szilár
d
P
áll
Swap c
u
stom OpenCL mem
s
et kernel fo
r
c
l
Enq
u
eueFil
l
Buffer
commit
|
commitdiff
|
tree
2018-10-09
Szilárd Páll
U
pdate regressionte
s
t
r
e
f to downl
o
ad
commit
|
commitdiff
|
tree
2018-10-09
V
i
a
cheslav
B
o
lnykh
I
m
p
l
em
e
nted
c
hanges to prepr
o
ce
s
sor
t
o wor
k
with
MiMiC
.
.
.
commit
|
commitdiff
|
tree
2018-10-09
Mark
Abra
h
am
Fix DomdecOption
s
def
a
ult
commit
|
commitdiff
|
tree
2018-10-09
Rolan
d
Schulz
F
i
x MSA
N
e
rror
s
commit
|
commitdiff
|
tree
2018-10-08
Berk He
s
s
Ena
b
le upda
t
e groups
commit
|
commitdiff
|
tree
2018-10-08
Szilárd Pá
l
l
T
weak
F
indFFTW API checks
commit
|
commitdiff
|
tree
2018-10-08
S
z
ilárd P
á
ll
Fix
c
la
n
g-6 warnings
commit
|
commitdiff
|
tree
2018-10-08
Roland Sch
u
lz
OCL
:
Add const to
f
u
n
ction a
r
guments
commit
|
commitdiff
|
tree
2018-10-08
Rolan
d
Schulz
Add
OC
L
ke
r
nel
target
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
Disable F
P
E
e
xplicitly for TPI force calculation
commit
|
commitdiff
|
tree
2018-10-08
Szilárd Páll
Replac
e
som
e
NULL
w
i
th nullptr in
CUDA
code
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
I
mplemen
t
PaddedVector
commit
|
commitdiff
|
tree
2018-10-08
Paul Baue
r
Workaround for IC
C
po
s
ts
u
bm
i
t bug
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
More upd
a
tes to te
s
t matrix
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
Fix make test
commit
|
commitdiff
|
tree
2018-10-07
Mark
A
braham
Test with g
c
c 8 a
n
d cuda 1
0
commit
|
commitdiff
|
tree
2018-10-05
Mark Abraham
Check log and other
f
iles differently during
a
ppend
i
ng
.
.
.
commit
|
commitdiff
|
tree
2018-10-05
Berk Hes
s
Add update g
r
oups to DD atom displacement
commit
|
commitdiff
|
tree
2018-10-05
Mark Abraham
Change to
te
s
t
TSA
N
with clang
a
nd
libomp
commit
|
commitdiff
|
tree
2018-10-05
Rol
a
n
d
S
c
hulz
OCL: Make
va
r
i
a
b
l
e
s const
commit
|
commitdiff
|
tree
2018-10-05
M
.
Eric Irr
g
ang
Add gmxapi::System
.
commit
|
commitdiff
|
tree
2018-10-05
Sz
i
lárd
P
áll
Update test matrices wit
h
new
GPU specifi
e
rs
commit
|
commitdiff
|
tree
2018-10-04
B
erk Hess
Make AVX2 pass TSAN
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Extrac
t
helper functions for preparing for appen
d
i
ng
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Simplify EM usage of mdeb
i
n
commit
|
commitdiff
|
tree
2018-10-03
M
a
rk
Ab
r
aham
Use fast re
t
urns i
n
m
d
5
computation
commit
|
commitdiff
|
tree
next