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Reduce hwloc & cpuid test requirements
2016-07-07
Erik L
i
ndah
l
Red
u
ce hwloc & cpuid
t
est requirem
e
nts
commit
|
commitdiff
|
tree
2016-07-07
Teemu Murt
o
la
C
hang
e
han
d
ling for
missing re
l
eng do
c
s
commit
|
commitdiff
|
tree
2016-07-07
Szil
á
r
d
Páll
A
d
d user g
u
ide
info
on CU
D
A
appl
i
cat
i
on clocks
commit
|
commitdiff
|
tree
2016-07-07
M
ark A
b
rah
a
m
Fix build if libcuda is found but nvcc is
not
commit
|
commitdiff
|
tree
2016-06-07
Semen Y
e
s
ylevskyy
Added m
a
n
u
al section abo
u
t embe
d
ding
p
r
o
teins to membranes
.
commit
|
commitdiff
|
tree
2016-06-05
Szilárd P
á
ll
A
d
d sup
p
ort for
CUDA CC 6
.
0/6
.
1
commit
|
commitdiff
|
tree
2016-06-03
Berk Hes
s
Han
d
le
partially frozen an
d
c
o
ns
t
rained atoms
commit
|
commitdiff
|
tree
2016-06-02
Szilárd Páll
Add env
.
va
r
.
to en
a
ble Op
e
n
C
L
cachin
g
commit
|
commitdiff
|
tree
2016-06-02
Sz
i
l
árd
Páll
Fix OpenCL
bi
n
ary cache fi
l
e
n
ame gen
e
ration
commit
|
commitdiff
|
tree
2016-06-02
Rola
n
d Sc
h
ulz
Fix
I
C
C 16u3 build
commit
|
commitdiff
|
tree
2016-06-02
Patrick Welche
Ensur
e
IMD
in
c
lude de
p
endencies
work
commit
|
commitdiff
|
tree
2016-05-29
Mark Abraham
Simplif
i
e
d
and updated Open
C
L compilat
i
on
commit
|
commitdiff
|
tree
2016-05-23
Berk H
e
ss
Fix bug in v-rescale t
h
ermo
s
tat &
r
eplica exchang
e
commit
|
commitdiff
|
tree
2016-05-10
Erik Li
n
da
h
l
F
i
xed large f
i
le issue on 32
-
b
i
t
p
latf
o
rms
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
Upd
a
t
e mdrun terminat
i
on info
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
Corre
c
t nrdf for 1D/2D systems
commit
|
commitdiff
|
tree
2015-12-24
E
rik Lindah
l
E
x
t
e
n
ded SIMD, implem
e
ntation for IBM Pow
e
r7/8 VSX
commit
|
commitdiff
|
tree
2015-12-21
E
r
ik Lin
d
ahl
E
xten
d
ed SIMD, im
p
l
ementatio
n
for BlueGene/Q
commit
|
commitdiff
|
tree
2015-12-21
Erik Lindahl
E
x
tended
SIMD impl
e
mentation for
2
56-bit AVX an
d
A
VX2
commit
|
commitdiff
|
tree
2015-12-16
Erik
Lind
a
hl
Next
-
ge
n
e
ration
S
IMD mo
d
u
l
e,
r
eference implementa
t
io
n
commit
|
commitdiff
|
tree
2015-10-30
Eri
k
Linda
h
l
Br
e
ak d
e
pendence of group k
e
rnels on simd module
commit
|
commitdiff
|
tree
2015-09-30
Roland Schulz
Requ
i
re
C++11
commit
|
commitdiff
|
tree
2015-08-13
Mark Abraham
Re-enable multi-G
P
U support in OpenCL for thread MPI
commit
|
commitdiff
|
tree
2015-08-05
Erik Lindahl
Fix
P
GI compile
r
flag
commit
|
commitdiff
|
tree
2015-07-27
Er
i
k Lindahl
Mo
v
ed
a
ddi
t
ional
g
mxlib sou
r
ces to
C++
commit
|
commitdiff
|
tree
2015-07-26
Mark Abrah
a
m
Convert some mdrun utility cod
e
to C+
+
commit
|
commitdiff
|
tree
2015-07-26
Erik
Lindahl
Merge b
r
a
n
ch re
l
ease-5-1
commit
|
commitdiff
|
tree
2015-07-07
E
r
ik Lindahl
Move QMMM source to C++
commit
|
commitdiff
|
tree
2015-07-05
Berk
H
e
ss
Fix
DD DLB
s
tate
i
ss
u
e
commit
|
commitdiff
|
tree
2015-06-27
Er
i
k
Lindahl
Fix s
i
n
gle-p
r
ec
.
softcore i
s
sue i
n
4
.
6
b
ranc
h
commit
|
commitdiff
|
tree
2015-02-20
Eri
k
Lindahl
Famous
qu
o
te from Colleen McCullough
commit
|
commitdiff
|
tree
2015-02-20
Er
i
k Lindahl
Ad
d
ed
t
w
o pop-culture quot
e
s
from A
n
dy Warhol
.
commit
|
commitdiff
|
tree
2014-09-20
Erik L
i
nd
a
hl
Fix RelW
i
t
hDebInf
o
n
am
e
bug
s
,
a
n
d
use f
u
ll optimizat
i
on
.
commit
|
commitdiff
|
tree
2014-09-02
Eri
k
Lindahl
Fixed string
var expans
i
o
n in CMake du
e
to CMP005
3
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindahl
Make internal BL
A
S/LAPACK messages l
e
ss
n
oisy
commit
|
commitdiff
|
tree
2014-07-28
Rol
a
nd Schulz
A
dd unit test
for ran
d
o
m
/Threefry
commit
|
commitdiff
|
tree
2014-07-27
Erik Lin
d
ahl
Fix
s
el
e
cti
o
n
of xtc gr
o
u
p
s
n
o
t
starting at
i
n
d
ex 0
commit
|
commitdiff
|
tree
2014-07-11
E
r
i
k Li
n
dahl
Make AV
X
2 che
c
k more robust
commit
|
commitdiff
|
tree
2014-06-24
Eri
k
Li
n
d
ahl
F
ixed
r
ecent b
u
g w
i
th disp
.
corr
.
and vdwtype
=
shift
commit
|
commitdiff
|
tree
2014-06-23
E
r
ik Li
n
dahl
Ena
b
l
e
termin
u
s-sp
e
c
i
fic atom
t
r
a
ns
l
ation
commit
|
commitdiff
|
tree
2014-06-22
Eri
k
L
indahl
Make lo
g
file opt
i
on listing
s
imilar to mdp
n
ames
commit
|
commitdiff
|
tree
2014-06-21
Eri
k
Lindahl
Make sure mas
s
es
are copied from ter
m
ini databa
s
e
s
commit
|
commitdiff
|
tree
2014-03-31
Teemu
M
urtola
Mov
e
s
o
me
m
a
th
headers away from legacyheaders/
commit
|
commitdiff
|
tree
2014-03-16
Erik
L
indahl
Use
a
constant instead of sizeof(int) for
S
SE
2
immediate
.
.
.
commit
|
commitdiff
|
tree
2014-02-01
Erik Lindahl
Use p
s
eu
d
o-rando
m
in
s
tead of random
s
tr
e
ams to intialize
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland Schu
l
z
Re
m
ove
u
nne
c
e
s
sar
y
I
CC
flags
a
ffecting
p
erformance
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindahl
Fixes SSE/A
V
X comp
i
lation under Windows
commit
|
commitdiff
|
tree
2013-01-09
Erik Li
n
dahl
Added work-
a
roun
d
for gcc bu
g
in AVX int
r
ins
i
ncs
formal
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
Eri
k
Lindahl
Fixed GMXRC so we are no
t
po
l
l
uting s
t
andard shell
.
.
.
commit
|
commitdiff
|
tree
2012-12-27
Erik Lin
d
ahl
Fixed er
r
or message for z
w
i
t
terion residues
commit
|
commitdiff
|
tree
2012-12-20
Erik Lindahl
Fix
e
d
A
VX256 dou
b
le-preci
s
i
on ke
r
nels
for gcc
commit
|
commitdiff
|
tree
2012-11-22
Erik Lindahl
Fix
for icc 1
3
o
p
t
imizatio
n
-
related issue and
TIP4P
.
.
.
commit
|
commitdiff
|
tree
2012-11-22
E
r
i
k
Lindahl
Implemented RMS-base
d
forc
e
tole
r
ance in gmxcheck
commit
|
commitdiff
|
tree
2012-11-22
E
r
ik Lindahl
Fi
x
e
d
LJ-1
4
error in free energy
commit
|
commitdiff
|
tree
2012-11-09
Erik Lin
d
ahl
Removed old (now unused) blu
e
gene
k
er
n
els
.
commit
|
commitdiff
|
tree
2012-11-09
E
rik Lindahl
Removed unused ol
d
kernel gener
a
tor
commit
|
commitdiff
|
tree
2012-11-09
E
rik Lindahl
Removal of
stale Fortran/Powe
r
6 kernels
commit
|
commitdiff
|
tree
2012-11-09
Erik Lindahl
R
emoval of stale Fortr
a
n kernels
commit
|
commitdiff
|
tree
2012-11-08
Er
i
k Lindahl
Fixed bu
g
in the new switch-modif
i
ed
i
n
teractions in
.
.
.
commit
|
commitdiff
|
tree
2012-11-08
Erik Lind
a
h
l
Allow rc
o
ulom
b
=
rlistlong f
o
r PM
E
with
nstc
a
l
cl
r
=
1
commit
|
commitdiff
|
tree
2012-06-21
Erik
L
indahl
Fi
x
e
d
gcc inli
n
e as
s
embly issue with P
I
C
and
older
.
.
.
commit
|
commitdiff
|
tree
2012-06-16
Er
i
k
L
i
n
dahl
Ne
w
CPU
det
e
c
tio
n
& AV
X
/SSE code, remove
d
raw assembly
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
E
r
i
k
L
indahl
Intro
d
uced different option
s
f
or p
d
b2gmx termi
n
i int
r
oductio
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Erik
Li
n
dahl
Fixed
i
ncorre
c
t
i
on AmberGS
f
orce fi
e
ld
(
redmine
#7
2
8)
commit
|
commitdiff
|
tree
2011-05-05
E
rik
Lin
d
a
h
l
Merge branch 'release-4-5-patches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-05-05
Erik Lindahl
Update
d
oc
t
o clarify th
a
t
A
mber nuc
l
eic params ar
e
.
.
.
commit
|
commitdiff
|
tree
2011-05-05
Eri
k
Li
n
dahl
Me
r
ge
b
ranc
h
'maste
r
' of
g
it
.
g
r
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2011-05-05
Erik
L
indahl
Update doc
to c
l
arify that
A
m
b
er nucleic params are
.
.
.
commit
|
commitdiff
|
tree
2011-01-30
Erik Li
n
dahl
I
m
pr
o
ved PBC h
a
nd
l
i
n
g
for large mo
l
ecules during
cluster P
B
C
commit
|
commitdiff
|
tree
2011-01-30
Erik Lin
d
ahl
Fixed t
h
e pbc cluster
o
ption of trjconv by switching
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Erik Lindahl
Merge branch 'release-4-5-pat
c
hes' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Eri
k
Lin
d
ahl
F
ixed uni
n
iti
a
lized
v
ariable
warning in grompp
.
c
commit
|
commitdiff
|
tree
2010-09-01
Erik Lindahl
R
e
m
o
ved lot
s
of
u
n
n
e
c
e
ssa
r
y mes
s
a
g
es to stdout from
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
E
r
ik Li
n
dahl
Added Gerr
i
t to the
l
i
s
t of authors
.
So
r
ry for for
g
et
t
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindah
l
Mad
e
the optio
n
s program for
the
l
atex manua
l
compile
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Linda
h
l
Fixe
d
typo in
s
rc/contri
b
/M
a
ke
f
ile
.
a
m
commit
|
commitdiff
|
tree
2010-08-31
E
r
i
k
L
i
n
dahl
F
ixed i
n
c
orr
e
ct call
to gmx_finalize(
)
in gmx_pme_error()
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Add
e
d final newline to avoid compil
e
r
w
arning in s
f
actor
.
h
commit
|
commitdiff
|
tree
2010-08-31
Er
i
k
L
indahl
Merge br
a
nch 'r
e
lease-4-
5
-pa
t
che
s
' o
f
git
.
gro
m
acs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lind
a
hl
Added C
p
ack s
u
p
p
or
t
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Add
e
d
label writing ca
p
a
bility to e
d
i
t
conf when use
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik L
i
ndahl
Added
c
heck for
<2
fram
e
s when
a
u
t
ocorrelation is
r
equeste
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik
L
i
n
d
a
hl
Mo
v
ed buggy
and uns
u
pport
e
d
g_
s
df
t
o con
t
r
i
b directory
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
Erik Lin
d
ahl
Improved handling of include pa
t
hs in gmxcp
p
from Teem
u
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Lindah
l
Me
r
g
e
bran
c
h 'release-4-5-patches'
commit
|
commitdiff
|
tree
2010-08-27
Erik L
i
n
d
ahl
Added
longer li
s
t of auth
o
r
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
ri
k
Lindahl
M
e
r
ge branc
h
'r
e
lease-4
-
5-patc
h
es' of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lind
a
hl
Added che
c
k for
SSE2 support to
u
se generalized
b
orn
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
i
k
Lindahl
R
esolved merge
c
o
n
f
lict in gmx_membe
d
.
c
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Lindahl
Merge b
r
a
nch 'release-4-5-
p
atches' of
g
it
.
grom
a
cs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik L
i
nda
h
l
Fixed gmxcpp to alwa
y
s use unix path
sep
a
ra
t
ors
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
M
e
rge
b
ran
c
h 'release
-
4-
5
-patches' of git
.
g
romacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
L
i
nd
a
hl
Fixe
d
anot
h
er u
n
initialized va
r
ia
b
le war
n
ing in gmx_energy
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik Lind
a
hl
A
d
d current path (
.
/) to topo
l
.
top
includ
e
when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
indahl
Dont writ
e
EOF warnings
to stdout ever
y
ti
m
e we checkpoi
n
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
rik Li
n
dahl
Merge branch 'release-4-5-patches' of
g
it
.
gro
m
acs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
F
i
xed
f
irst st
a
temement
occu
r
ing bef
o
re variable declara
t
ion
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindah
l
Added t
r
jconv
check
for topology
prescence, see bug
z
illa 526
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Linda
h
l
Mer
g
e b
r
an
c
h
'
release-4-5-p
a
tches' of g
i
t
.
g
r
omac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
indahl
M
o
d
i
f
ied
pdb2gmx to automatical
l
y pick the
f
orce field
.
.
.
commit
|
commitdiff
|
tree
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