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SParTA
PuReMD
Commits
efc02992
Commit
efc02992
authored
8 years ago
by
Daniel F Kortemeyer
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Merge branch 'master' of gitlab.msu.edu:SParTA/PuReMD
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b5fb8230
5276c950
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environ/param.gpu.water
+1
-1
1 addition, 1 deletion
environ/param.gpu.water
tools/run_sim.py
+188
-82
188 additions, 82 deletions
tools/run_sim.py
with
189 additions
and
83 deletions
environ/param.gpu.water
+
1
−
1
View file @
efc02992
...
...
@@ -35,7 +35,7 @@ compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5
press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
geo_format 1 ! 0: xyz, 1: pdb, 2: bgf
write_freq
1000
! write trajectory after so many steps
write_freq
0
! write trajectory after so many steps
traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
traj_title WATER_NVT ! (no white spaces)
...
...
This diff is collapsed.
Click to expand it.
tools/run_sim.py
+
188
−
82
View file @
efc02992
#!/usr/bin/env python
from
fileinput
import
input
from
itertools
import
product
from
re
import
sub
from
subprocess
import
Popen
,
PIPE
from
os
import
getcwd
,
environ
,
path
,
re
name
from
os
import
getcwd
,
environ
,
path
,
re
move
,
rename
,
rmdir
from
sys
import
exit
from
tempfile
import
mkdtemp
from
time
import
time
base_dir
=
getcwd
()
control_dir
=
path
.
join
(
base_dir
,
'
environ
'
)
data_dir
=
path
.
join
(
base_dir
,
'
data/benchmarks
'
)
puremd_args
=
[
\
# (path.join(data_dir, 'water/water_6540.pdb'), path.join(data_dir, 'water/ffield.water'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'water/water_78480.pdb'), path.join(data_dir, 'water/ffield.water'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'water/water_327000.geo'), path.join(data_dir, 'water/ffield.water'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'bilayer/bilayer_56800.pdb'), path.join(data_dir, 'bilayer/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
(
path
.
join
(
data_dir
,
'
dna/dna_19733.pdb
'
),
path
.
join
(
data_dir
,
'
dna/ffield-dna
'
),
path
.
join
(
control_dir
,
'
param.gpu.water
'
)),
\
(
path
.
join
(
data_dir
,
'
silica/silica_6000.pdb
'
),
path
.
join
(
data_dir
,
'
silica/ffield-bio
'
),
path
.
join
(
control_dir
,
'
param.gpu.water
'
)),
\
# (path.join(data_dir, 'silica/silica_72000.geo'), path.join(data_dir, 'silica/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'silica/silica_300000.geo'), path.join(data_dir, 'silica/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'petn/petn_48256.pdb'), path.join(data_dir, 'petn/ffield.petn'), path.join(control_dir, 'param.gpu.water')), \
]
header_fmt_str
=
'
{:20}|{:5}|{:5}|{:5}|{:10}|{:10}|{:10}|{:10}|{:10}|{:10}
'
body_fmt_str
=
'
{:20} {:5} {:5} {:5} {:10.6f} {:10.6f} {:10.6f} {:10.6f} {:10} {:10.6f}
'
steps
=
[
'
20
'
]
#['100']
qeq_solver_tol
=
[
'
1e-6
'
]
#['1e-6', '1e-8', '1e-10', '1e-14']
pre_comp_type
=
[
'
2
'
]
#['0', '1', '2']
threads
=
[
'
1
'
,
'
2
'
,
'
4
'
,
'
12
'
,
'
24
'
]
patterns
=
[
\
lambda
l
,
x
:
sub
(
r
'
(?P<key>simulation_name\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
lambda
l
,
x
:
sub
(
r
'
(?P<key>nsteps\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
lambda
l
,
x
:
sub
(
r
'
(?P<key>qeq_solver_q_err\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
lambda
l
,
x
:
sub
(
r
'
(?P<key>pre_comp_type\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
lambda
l
,
x
:
sub
(
r
'
(?P<key>geo_format\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
]
d
=
dict
(
environ
)
print
header_fmt_str
.
format
(
'
Data Set
'
,
'
Steps
'
,
'
Q Tol
'
,
'
Pre T
'
,
'
Pre Comp
'
,
'
Pre App
'
,
'
Iters
'
,
'
SpMV
'
,
'
Threads
'
,
'
Time (s)
'
)
for
i
in
xrange
(
len
(
puremd_args
)):
for
s
in
xrange
(
len
(
steps
)):
for
j
in
xrange
(
len
(
qeq_solver_tol
)):
for
t
in
xrange
(
len
(
pre_comp_type
)):
for
k
in
xrange
(
len
(
threads
)):
for
line
in
input
(
puremd_args
[
i
][
2
],
inplace
=
1
):
line
=
line
.
rstrip
()
line
=
patterns
[
0
](
line
,
path
.
basename
(
puremd_args
[
i
][
0
]).
split
(
'
.
'
)[
0
]
+
'
_
'
+
'
tol
'
+
qeq_solver_tol
[
j
]
+
'
_precomp
'
+
pre_comp_type
[
t
]
+
'
_thread
'
+
threads
[
k
])
line
=
patterns
[
1
](
line
,
steps
[
s
])
line
=
patterns
[
2
](
line
,
qeq_solver_tol
[
j
])
line
=
patterns
[
3
](
line
,
pre_comp_type
[
t
])
print
line
d
[
'
OMP_NUM_THREADS
'
]
=
threads
[
k
]
start
=
time
()
p
=
Popen
([
path
.
join
(
base_dir
,
'
sPuReMD/bin/spuremd
'
)]
+
list
(
puremd_args
[
i
]),
stdout
=
PIPE
,
stderr
=
PIPE
,
env
=
d
)
stdout
,
stderr
=
p
.
communicate
()
stop
=
time
()
iters
=
0.
pre_comp
=
0.
pre_app
=
0.
spmv
=
0.
cnt
=
0
with
open
(
path
.
basename
(
puremd_args
[
i
][
0
]).
split
(
'
.
'
)[
0
]
+
'
_
'
+
'
tol
'
+
qeq_solver_tol
[
j
]
+
'
_precomp
'
+
pre_comp_type
[
t
]
+
'
_thread
'
+
threads
[
k
]
+
'
.log
'
,
'
r
'
)
as
fp
:
for
line
in
fp
:
line
=
line
.
split
()
try
:
iters
=
iters
+
float
(
line
[
7
])
pre_comp
=
pre_comp
+
float
(
line
[
8
])
pre_app
=
pre_app
+
float
(
line
[
9
])
spmv
=
spmv
+
float
(
line
[
10
])
cnt
=
cnt
+
1
except
Exception
:
class
TestCase
():
def
__init__
(
self
,
geo_file
,
ffield_file
,
control_file
,
params
=
{},
result_header_fmt
=
''
,
result_header
=
''
,
result_body_fmt
=
''
,
result_file
=
'
results.txt
'
):
self
.
__geo_file
=
geo_file
self
.
__ffield_file
=
ffield_file
self
.
__control_file
=
control_file
self
.
__param_names
=
sorted
(
params
.
keys
())
self
.
__params
=
params
self
.
__result_header_fmt
=
result_header_fmt
self
.
__result_header
=
result_header
self
.
__result_body_fmt
=
result_body_fmt
self
.
__result_file
=
result_file
self
.
__control_res
=
{
\
'
name
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>simulation_name\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
ensemble_type
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>ensemble_type\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
nsteps
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>nsteps\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
qeq_solver_type
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>qeq_solver_type\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
qeq_solver_q_err
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>qeq_solver_q_err\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
pre_comp_type
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>pre_comp_type\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
pre_comp_refactor
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>pre_comp_refactor\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
pre_comp_sweeps
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>pre_comp_sweeps\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
pre_app_type
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>pre_app_type\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
pre_app_jacobi_iters
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>pre_app_jacobi_iters\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
'
geo_format
'
:
lambda
l
,
x
:
sub
(
r
'
(?P<key>geo_format\s+)\S+(?P<comment>.*)
'
,
r
'
\g<key>%s\g<comment>
'
%
x
,
l
),
\
}
def
_setup
(
self
,
param
,
temp_file
):
fp
=
open
(
self
.
__control_file
,
'
r
'
)
lines
=
fp
.
read
()
fp
.
close
()
for
k
in
self
.
__control_res
.
keys
():
try
:
lines
=
self
.
__control_res
[
k
](
lines
,
param
[
k
])
except
KeyError
:
pass
cnt
=
cnt
-
1
iters
=
iters
/
cnt
pre_comp
=
pre_comp
/
cnt
pre_app
=
pre_app
/
cnt
spmv
=
spmv
/
cnt
print
body_fmt_str
.
format
(
path
.
basename
(
puremd_args
[
i
][
0
]).
split
(
'
.
'
)[
0
],
steps
[
s
],
qeq_solver_tol
[
j
],
pre_comp_type
[
t
],
pre_comp
,
pre_app
,
iters
,
spmv
,
threads
[
k
],
stop
-
start
)
fp_temp
=
open
(
temp_file
,
'
w
'
,
0
)
fp_temp
.
write
(
lines
)
fp_temp
.
close
()
def
run
(
self
,
bin_file
=
'
sPuReMD/bin/spuremd
'
):
base_dir
=
getcwd
()
bin_path
=
path
.
join
(
base_dir
,
bin_file
)
env
=
dict
(
environ
)
write_header
=
True
if
path
.
exists
(
self
.
__result_file
):
write_header
=
False
fout
=
open
(
self
.
__result_file
,
'
a
'
,
0
)
if
write_header
:
fout
.
write
(
self
.
__result_header_fmt
.
format
(
*
self
.
__result_header
))
temp_dir
=
mkdtemp
()
temp_file
=
path
.
join
(
temp_dir
,
path
.
basename
(
self
.
__control_file
))
for
p
in
product
(
*
[
self
.
__params
[
k
]
for
k
in
self
.
__param_names
]):
param_dict
=
dict
((
k
,
v
)
for
(
k
,
v
)
in
zip
(
self
.
__param_names
,
p
))
param_dict
[
'
name
'
]
=
path
.
basename
(
self
.
__geo_file
).
split
(
'
.
'
)[
0
]
\
+
'
_step
'
+
param_dict
[
'
nsteps
'
]
+
'
_tol
'
+
param_dict
[
'
qeq_solver_q_err
'
]
\
+
'
_precomp
'
+
param_dict
[
'
pre_comp_type
'
]
+
'
_thread
'
+
param_dict
[
'
threads
'
]
self
.
_setup
(
param_dict
,
temp_file
)
env
[
'
OMP_NUM_THREADS
'
]
=
param_dict
[
'
threads
'
]
start
=
time
()
proc_handle
=
Popen
([
bin_path
,
self
.
__geo_file
,
self
.
__ffield_file
,
temp_file
],
stdout
=
PIPE
,
stderr
=
PIPE
,
env
=
env
)
#TODO: handle outputs?
stdout
,
stderr
=
proc_handle
.
communicate
()
stop
=
time
()
self
.
_process_result
(
fout
,
stop
-
start
,
param_dict
)
fout
.
close
()
remove
(
temp_file
)
rmdir
(
temp_dir
)
def
_process_result
(
self
,
fout
,
time
,
param
):
qeq
=
0.
iters
=
0.
pre_comp
=
0.
pre_app
=
0.
spmv
=
0.
cnt
=
0
with
open
(
param
[
'
name
'
]
+
'
.log
'
,
'
r
'
)
as
fp
:
for
line
in
fp
:
line
=
line
.
split
()
try
:
qeq
=
qeq
+
float
(
line
[
6
])
iters
=
iters
+
float
(
line
[
7
])
pre_comp
=
pre_comp
+
float
(
line
[
8
])
pre_app
=
pre_app
+
float
(
line
[
9
])
spmv
=
spmv
+
float
(
line
[
10
])
cnt
=
cnt
+
1
except
Exception
:
pass
cnt
=
cnt
-
1
qeq
=
qeq
/
cnt
iters
=
iters
/
cnt
pre_comp
=
pre_comp
/
cnt
pre_app
=
pre_app
/
cnt
spmv
=
spmv
/
cnt
fout
.
write
(
self
.
__result_body_fmt
.
format
(
path
.
basename
(
self
.
__geo_file
).
split
(
'
.
'
)[
0
],
param
[
'
nsteps
'
],
param
[
'
qeq_solver_q_err
'
],
param
[
'
pre_comp_type
'
],
pre_comp
,
pre_app
,
iters
,
spmv
,
qeq
,
param
[
'
threads
'
],
time
))
if
__name__
==
'
__main__
'
:
base_dir
=
getcwd
()
control_dir
=
path
.
join
(
base_dir
,
'
environ
'
)
data_dir
=
path
.
join
(
base_dir
,
'
data/benchmarks
'
)
header_fmt_str
=
'
{:20}|{:5}|{:5}|{:5}|{:10}|{:10}|{:10}|{:10}|{:10}|{:10}|{:10}
\n
'
header_str
=
[
'
Data Set
'
,
'
Steps
'
,
'
Q Tol
'
,
'
Pre T
'
,
'
Pre Comp
'
,
'
Pre App
'
,
'
Iters
'
,
'
SpMV
'
,
'
QEq
'
,
'
Threads
'
,
'
Time (s)
'
]
body_fmt_str
=
'
{:20} {:5} {:5} {:5} {:10.6f} {:10.6f} {:10.6f} {:10.6f} {:10.6f} {:10} {:10.6f}
\n
'
params
=
{
'
ensemble_type
'
:
[
'
0
'
],
'
nsteps
'
:
[
'
20
'
,
'
100
'
,
'
500
'
,
'
1000
'
],
'
qeq_solver_type
'
:
[
'
0
'
],
'
qeq_solver_q_err
'
:
[
'
1e-6
'
,
'
1e-10
'
],
# 'qeq_solver_q_err': ['1e-6', '1e-8', '1e-10', '1e-14'],
'
pre_comp_type
'
:
[
'
0
'
],
# 'pre_comp_type': ['0', '1', '2'],
'
pre_comp_refactor
'
:
[
'
1
'
],
# 'pre_comp_sweeps': ['3'],
# 'pre_app_type': ['0'],
# 'pre_app_jacobi_iters': ['50'],
'
threads
'
:
[
'
12
'
],
# 'threads': ['1', '2', '4', '12', '24'],
'
geo_format
'
:
[
'
1
'
],
}
test_cases
=
[
TestCase
(
path
.
join
(
data_dir
,
'
water/water_6540.pdb
'
),
path
.
join
(
data_dir
,
'
water/ffield.water
'
),
path
.
join
(
control_dir
,
'
param.gpu.water
'
),
params
=
params
,
result_header_fmt
=
header_fmt_str
,
result_header
=
header_str
,
result_body_fmt
=
body_fmt_str
),
# TestCase(path.join(data_dir, 'water/water_78480.pdb'),
# path.join(data_dir, 'water/ffield.water'),
# path.join(control_dir, 'param.gpu.water'),
# params=params, result_header_fmt=header_fmt_str, result_header = header_str, result_body_fmt=body_fmt_str),
# TestCase(path.join(data_dir, 'water/water_327000.geo'),
# path.join(data_dir, 'water/ffield.water'),
# path.join(control_dir, 'param.gpu.water'),
# params=params, result_header_fmt=header_fmt_str, result_header = header_str, result_body_fmt=body_fmt_str),
TestCase
(
path
.
join
(
data_dir
,
'
bilayer/bilayer_56800.pdb
'
),
path
.
join
(
data_dir
,
'
bilayer/ffield-bio
'
),
path
.
join
(
control_dir
,
'
param.gpu.water
'
),
params
=
params
,
result_header_fmt
=
header_fmt_str
,
result_header
=
header_str
,
result_body_fmt
=
body_fmt_str
),
TestCase
(
path
.
join
(
data_dir
,
'
dna/dna_19733.pdb
'
),
path
.
join
(
data_dir
,
'
dna/ffield-dna
'
),
path
.
join
(
control_dir
,
'
param.gpu.water
'
),
params
=
params
,
result_header_fmt
=
header_fmt_str
,
result_header
=
header_str
,
result_body_fmt
=
body_fmt_str
),
TestCase
(
path
.
join
(
data_dir
,
'
silica/silica_6000.pdb
'
),
path
.
join
(
data_dir
,
'
silica/ffield-bio
'
),
path
.
join
(
control_dir
,
'
param.gpu.water
'
),
params
=
params
,
result_header_fmt
=
header_fmt_str
,
result_header
=
header_str
,
result_body_fmt
=
body_fmt_str
),
# TestCase(path.join(data_dir, 'silica/silica_72000.geo'),
# path.join(data_dir, 'silica/ffield-bio'),
# path.join(control_dir, 'param.gpu.water'),
# params=params, result_header_fmt=header_fmt_str, result_header = header_str, result_body_fmt=body_fmt_str),
# TestCase(path.join(data_dir, 'silica/silica_300000.geo'),
# path.join(data_dir, 'silica/ffield-bio'),
# path.join(control_dir, 'param.gpu.water'),
# params=params, result_header_fmt=header_fmt_str, result_header = header_str, result_body_fmt=body_fmt_str),
TestCase
(
path
.
join
(
data_dir
,
'
petn/petn_48256.pdb
'
),
path
.
join
(
data_dir
,
'
petn/ffield.petn
'
),
path
.
join
(
control_dir
,
'
param.gpu.water
'
),
params
=
params
,
result_header_fmt
=
header_fmt_str
,
result_header
=
header_str
,
result_body_fmt
=
body_fmt_str
),
]
for
test
in
test_cases
:
test
.
run
(
bin_file
=
'
sPuReMD/bin/spuremd
'
)
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