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Fixed thread_mpi's Makefile.am to not include removed file.
2011-04-21
S
a
nder P
r
o
n
k
Fixed thread_mpi's
M
akefile
.
a
m
to not include
removed
.
.
.
commit
|
commitdiff
|
tree
2011-04-21
Sander Pro
n
k
Added
p
rotot
y
pes f
o
r functio
n
s
i
n
md_sup
p
ort
.
c
to mdrun
.
h
commit
|
commitdiff
|
tree
2011-04-20
Sander Pronk
Revert
"
NUMA a
w
a
re mem
o
r
y allocators
get called (for
.
.
.
commit
|
commitdiff
|
tree
2011-04-20
S
ander Pronk
NUMA aw
a
re memory allocators get called (for Wind
o
ws)
.
commit
|
commitdiff
|
tree
2011-04-20
Sander Pronk
New thread_mp
i
libr
a
ry, with NUMA aw
a
re allo
c
ator for
.
.
.
commit
|
commitdiff
|
tree
2011-04-01
Sa
n
der
P
ronk
Fi
x
ed g_pme_er
r
or
t
o use MP
I
, but no
t
thre
a
ds
.
commit
|
commitdiff
|
tree
2011-03-25
Sander
Pronk
Fixed d
e
allocation b
u
g in en
e
rgy history checkpoint
commit
|
commitdiff
|
tree
2011-03-21
Sander P
r
onk
The -
v
ersion flag now p
r
ints more information
.
commit
|
commitdiff
|
tree
2011-03-21
Sa
n
d
er
P
r
o
nk
Fixe
d
re
a
l
/
double i
s
sue in gmx_de
n
sity
commit
|
commitdiff
|
tree
2011-03-17
Sande
r
P
ro
n
k
Various f
i
x
e
s for Windo
w
s buil
d
s
.
commit
|
commitdiff
|
tree
2011-03-16
Sand
e
r Pronk
m
d
run -
m
ulti,
m
ultidir and replica
exchange now exchange
.
.
.
commit
|
commitdiff
|
tree
2011-03-15
Sand
e
r Pronk
Multisim
simulations now all stop when th
e
first one
.
.
.
commit
|
commitdiff
|
tree
2011-03-11
S
a
n
der Pronk
M
e
rge branch 'rel
e
as
e
-4-5-p
a
tc
h
es' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-03-10
Sand
e
r
P
ronk
More allocation
fixes for NUMA
allocator
.
commit
|
commitdiff
|
tree
2011-03-10
San
d
er Pr
o
nk
Add
e
d doc
u
menta
t
ion for multidir
.
commit
|
commitdiff
|
tree
2011-03-10
Sand
e
r Pron
k
Ad
d
ed more
sup
p
ort for mul
t
idir
.
commit
|
commitdiff
|
tree
2011-03-03
Sa
n
der Pronk
R
e
p
lac
e
d st
r
d
ups with gmx_strdups so tha
t
they can
.
.
.
commit
|
commitdiff
|
tree
2011-02-20
Sande
r
Pron
k
M
inor
fix
f
or wh
e
n write_d
h
dl_file=false an
d
delt
a
_lambda
.
.
.
commit
|
commitdiff
|
tree
2011-02-10
Sander Pr
o
nk
Fixed a
bug in g_energy -odh
commit
|
commitdiff
|
tree
2010-11-19
Sander P
r
o
n
k
F
i
xed TMPI_WAIT_FOR_NO_ONE deadlock
.
commit
|
commitdiff
|
tree
2010-11-02
Sander Pronk
Fixed double pre
c
i
sion energy file reading +
box matri
x
.
.
.
commit
|
commitdiff
|
tree
2010-10-30
Sander Pronk
A
d
ded Windows mac
r
o
f
or snp
r
intf
.
commit
|
commitdiff
|
tree
2010-10-20
Sander Pr
o
nk
file r
e
ading err
o
r messages in
g_bar less confusing
.
commit
|
commitdiff
|
tree
2010-10-18
Sander Pronk
Tries recovery during errors in
.
edr fil
e
s
.
commit
|
commitdiff
|
tree
2010-10-18
Sander Pronk
Bette
r
time checks
i
n
.
edrs wihtout
v
ersio
n
numbers
.
commit
|
commitdiff
|
tree
2010-10-18
San
d
er Pronk
More
s
t
ri
n
gent
.
edr
f
i
l
e data checks
.
commit
|
commitdiff
|
tree
2010-10-08
S
ander
Pronk
N
ow
r
e
a
l
l
y fixed lo
c
king of
l
og file
.
commit
|
commitdiff
|
tree
2010-10-07
Sand
e
r Pronk
cmake LIB environment v
a
riable c
h
eck, and GM
X
RC check
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
Sander Pronk
Modified FO
R
TRAN a
n
d
t
h
reads warni
n
g
.
commit
|
commitdiff
|
tree
2010-09-30
Sander Pronk
Error
m
essage
on enabling FOR
T
RAN and threads
.
commit
|
commitdiff
|
tree
2010-09-22
Sander
P
ronk
A
d
ded
m
issing in
c
l
u
des to
gmx_tune_pme
.
c
commit
|
commitdiff
|
tree
2010-09-17
Sander P
r
onk
Fixed more checkpointing issues
w
ith
.
edr dh data
.
commit
|
commitdiff
|
tree
2010-09-17
S
ander Pro
n
k
Ch
e
ckpoint
s
backward-compa
t
ibl
e
+ more consisten
c
y
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Sander Pronk
Fixed checkpointing
bug
with
g
_b
a
r energi
e
s
commit
|
commitdiff
|
tree
2010-09-16
Sander Pro
n
k
eneconv now warns when throwing a
w
ay b
l
ocks w
i
th
d
H
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
Sander P
r
on
k
Improved pe
r
formance of g_b
a
r whi
l
e rea
d
ing
.
edr
f
iles
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
San
d
er Pronk
Mo
r
e scheduler-friendly loc
k
s
fo
r
gmxfio
commit
|
commitdiff
|
tree
2010-09-09
S
a
nder Pronk
Fixed a deadlock while closing file
s
.
commit
|
commitdiff
|
tree
2010-09-09
S
an
d
er Pronk
F
ixed se
g
v i
n
trajana due to wrong cell
index ca
l
culati
o
n
.
commit
|
commitdiff
|
tree
2010-09-08
San
d
er Pr
o
nk
Fix
e
d
s
egv whil
e
reading ove
r
ly lo
n
g lines
i
n
xvgr
.
c
commit
|
commitdiff
|
tree
2010-09-07
Sander
Pronk
Fixed segfault in g_ba
r
with une
q
ua
l
ly di
s
tribut
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-09-06
Sand
e
r Pronk
Merge bra
n
ch
'release-4-5-patches
'
o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-09-06
Sander Pronk
F
i
x
ed re
a
di
n
g
of older
.
xv
g
file formats in g_bar
commit
|
commitdiff
|
tree
2010-09-06
Sander Pronk
Fixed misin
t
erpretation of -b and
-e in g_bar
.
commit
|
commitdiff
|
tree
2010-09-03
Sand
e
r
P
ronk
Add
e
d
missi
n
g
wi
n
dows th
r
ead fil
e
s to dist
r
ibution
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Sander Pronk
Shared libraries
o
ff by default on
Windows
.
commit
|
commitdiff
|
tree
2010-09-01
Sand
e
r Pronk
Added sup
p
ort for PGI atomics i
n
thread_mpi
.
commit
|
commitdiff
|
tree
2010-09-01
Sander Pronk
Fi
n
al
thread_
m
pi fixes (ppc works,
n
o deadlocks on
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Sander Pronk
Code reorg in thre
a
d_mpi
commit
|
commitdiff
|
tree
2010-08-31
Sander Pronk
Merge branch 'rel
e
ase-4-5-patches'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Sander
Pron
k
Fixe
d
memory ord
e
ring
i
ssue
o
n ppc with gcc&xlc
.
commit
|
commitdiff
|
tree
2010-08-31
Sander Pronk
thread
_
mp
i
fixes
:
gcc works on power7
,
xl
c
s
till does
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
San
d
er Pronk
Fixe
d
war
n
i
n
g in gmx_e
n
ergy
commit
|
commitdiff
|
tree
2010-08-30
Sande
r
Pron
k
grompp calculates output si
z
e with
d
h dat
a
estimate
.
commit
|
commitdiff
|
tree
2010-08-30
Sander
Pronk
C
l
earer
e
r
ro
r
messages in g_energy
.
commit
|
commitdiff
|
tree
2010-08-30
San
d
er Pro
n
k
Fi
x
ed the g_energy
-odh option to be le
s
s
confusi
n
g
.
commit
|
commitdiff
|
tree
2010-08-29
S
ander Pr
o
nk
Made th
e
dhdl_derivatives option d
o
somethi
n
g when
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Sander Pro
n
k
Fixed beg
i
n
a
n
d end times in g_bar
.
commit
|
commitdiff
|
tree
2010-08-27
S
an
d
er Pronk
More doc
u
men
t
ation for g_
b
ar
.
commit
|
commitdiff
|
tree
2010-08-27
Sander Pron
k
Some documentation changes
.
commit
|
commitdiff
|
tree
2010-08-27
Sander Pr
o
nk
Some docu
m
entation chan
g
es
.
commit
|
commitdiff
|
tree
2010-08-26
Sander
Pronk
gmx_
b
ar now works wi
t
h der
i
v
ati
v
e histogr
a
m sets
.
commit
|
commitdiff
|
tree
2010-08-26
S
a
nder
Pronk
Free
e
nergy histogram bu
g
fix
e
s
.
commit
|
commitdiff
|
tree
2010-08-26
Sand
e
r
P
ronk
de
r
iva
t
i
ve histograms ar
e
now written in bo
t
h p
o
sitive
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
S
a
nder P
r
onk
g_bar rea
d
s dhdl
.
xvg files withou
t
de
r
ivati
v
es
.
commit
|
commitdiff
|
tree
2010-08-26
Sander Pronk
Free energy wri
t
ing to ener
.
edr
a
nd four new
o
pt
i
ons
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
San
d
er Pronk
Another try w
i
t
h xlc/ppc ato
m
ics
.
.
commit
|
commitdiff
|
tree
2010-08-23
Sand
e
r Pronk
Modified m
e
mory b
a
r
r
ier on ppc/xlc
.
commit
|
commitdiff
|
tree
2010-08-23
Sa
n
der Pronk
Enabled gcc at
o
mic intrins
i
c
s
f
or
g
c
c on ppc
.
commit
|
commitdiff
|
tree
2010-08-23
Sander Pro
n
k
More xlc ppc c
h
anges t
o
thread_mpi
commit
|
commitdiff
|
tree
2010-08-23
Sande
r
Pronk
Comple
t
ely remo
v
ed all
occurren
c
es of '
i
nline'
f
or
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Sander Pronk
Added support fo
r
new mdp
option
s
c
ontrolling free
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Sand
e
r Pronk
Fixed
g
et_libd
i
r()
P
AT
H
search
.
commit
|
commitdiff
|
tree
2010-08-18
Sa
n
d
e
r Pronk
Cmake tests for SIGUSR1
commit
|
commitdiff
|
tree
2010-08-17
Sander Pronk
Fix
e
d thread_mpi inline
a
ss
e
m
bly
issue and non-optimized
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Sander Pronk
fsync fix for
F
A
H core
.
commit
|
commitdiff
|
tree
2010-08-16
Sa
n
der Pr
o
nk
Fixed x
d
r3dfcoord thread safety i
s
sues
.
commit
|
commitdiff
|
tree
2010-08-16
Sander Pronk
Moved the
OS-dependent part of gmx_fio_fsync() to futil
.
c
commit
|
commitdiff
|
tree
2010-08-14
Sander P
r
onk
Fixed an issue wi
t
h gm
x
_copy_file t
h
at would allow
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Sand
e
r Pronk
C++
t
ype
fi
x
es in
thread_m
p
i atomi
c
s
.
commit
|
commitdiff
|
tree
2010-08-11
Sander Pronk
Cma
k
e now
h
ono
r
s CFLAGS/CXX
F
LAGS
a
s much as
it can
.
commit
|
commitdiff
|
tree
2010-08-09
Sa
n
der P
r
onk
S
mall
f
i
x to deal
wit
h
po
s
sib
l
e overflows i
n
dh
b
inni
n
g
.
commit
|
commitdiff
|
tree
2010-08-09
Sander Pr
o
nk
Now cor
r
ectly c
h
ec
k
points
o
n d
h
dl histograms/l
i
sts
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Sander Pronk
BAR calcul
a
tions can now store energy histo
g
ram
s
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Sander P
r
onk
Added
an uninstall target t
o
CMake bui
l
d
s
.
commit
|
commitdiff
|
tree
2010-08-02
Sander Pronk
A
d
ded missi
n
g
.
h file
.
commit
|
commitdiff
|
tree
2010-08-02
Sander Pronk
Fi
x
ed s
h
ared libra
r
y build b
y
r
emoving references to
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Sander
Pronk
M
o
re
o
nerous locki
n
g of ope
n
_files
in gmx_fio
.
commit
|
commitdiff
|
tree
2010-07-30
Sander Pro
n
k
Fixed
f
f
c
lose b
u
g
i
n futil
.
c, g
m
x_fio_c
l
ose
n
ow c
h
ecks
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Sande
r
P
r
onk
Me
r
ge branch
'
master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-30
Sander Pro
n
k
Fix
e
d
a potential mutex pro
b
l
e
m
in gm
x
_fio
.
c
commit
|
commitdiff
|
tree
2010-07-29
Sa
n
der
P
r
onk
.
edr
block gmxd
u
mp fixes
.
commit
|
commitdiff
|
tree
2010-07-27
Sa
n
der Pronk
Re-added sched
.
h de
f
ine in config
.
h
.
cma
k
e
in
.
commit
|
commitdiff
|
tree
2010-07-26
S
ander Pronk
Merg
e
branch 'm
a
ster' of git
.
g
r
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-26
Sander Pr
o
nk
Added support for Windows _fseeki6
4
.
commit
|
commitdiff
|
tree
2010-07-26
Sander Pronk
Wind
o
ws fi
x
es
.
commit
|
commitdiff
|
tree
2010-07-26
San
d
er Pronk
M
erg
e
br
a
n
ch
'
maste
r
'
of gi
t
.
gr
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-26
Sander Pronk
Fixed more thread_m
p
i
i
nstall
a
tion
issues
.
commit
|
commitdiff
|
tree
2010-07-26
Sande
r
Pr
o
nk
M
erge bran
c
h 'm
a
ster' of
g
i
t
.
g
romacs
.
org
:
gro
m
a
c
s
commit
|
commitdiff
|
tree
2010-07-26
S
a
nder Pronk
Fixed
thread_
m
pi distribution issue
s
.
commit
|
commitdiff
|
tree
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