Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
Rogers, David
launchad
Commits
1ca85933
Commit
1ca85933
authored
Jun 17, 2020
by
David M. Rogers
Browse files
Changed to 6WQF structure.
parent
0084bae8
Changes
4
Hide whitespace changes
Inline
Side-by-side
loadem.py
View file @
1ca85933
...
...
@@ -6,12 +6,12 @@ from datetime import datetime
test
=
False
testone
=
False
hopper
=
Fals
e
hopper
=
Tru
e
conn_retries
=
0
def
stamp
():
return
datetime
.
now
().
strftime
(
"%Y-%m-%d %H:%M:%S.%f"
)
+
" v1.
0
"
return
datetime
.
now
().
strftime
(
"%Y-%m-%d %H:%M:%S.%f"
)
+
" v1.
1
"
def
run_redis
(
host
,
fn
):
global
conn_retries
...
...
@@ -49,7 +49,7 @@ def get_shard(host):
return
shard
return
shard
.
decode
(
'utf8'
)
out_pre
=
'/gpfs/alpine/world-shared/bif128/docked'
out_pre
=
'/gpfs/alpine/world-shared/bif128/
6WQF_
docked'
def
main
(
argv
):
global
conn_retries
...
...
@@ -60,6 +60,7 @@ def main(argv):
username
=
os
.
environ
[
'USER'
]
jobid
=
os
.
environ
[
'LSB_JOBID'
]
ret
=
subprocess
.
call
(
"mkdir -p %s/logs/%s"
%
(
out_pre
,
jobid
),
shell
=
True
)
ret
=
subprocess
.
call
(
"rm -fr /mnt/bb/%s/%d"
%
(
username
,
rank
),
shell
=
True
)
ofile
=
open
(
'%s/logs/%s/rank%04x.log'
%
(
out_pre
,
jobid
,
rank
),
"w"
)
time
.
sleep
(
rank
*
0.0001
)
# 10k connections per second at startup
...
...
run_ad.sh
View file @
1ca85933
...
...
@@ -9,7 +9,7 @@
export
OMP_NUM_THREADS
=
7
set
-e
version
=
"run_ad.sh v1.
0
"
version
=
"run_ad.sh v1.
1
"
if
[
$#
-ne
2
]
;
then
echo
"Usage:
$0
shard_name shard_segment"
...
...
@@ -23,14 +23,14 @@ if [ ! -s "$sfile" ]; then
exit
1
fi
pfile
=
/gpfs/alpine/world-shared/bif128/
final_Mpro_pdbqt_maps_for_1B
.tgz
pfile
=
/gpfs/alpine/world-shared/bif128/
6WQF_maps_Josh
.tgz
if
[
!
-s
$pfile
]
;
then
echo
"Missing
$pfile
"
exit
1
fi
HOST
=
`
hostname
`
OUT_DIR
=
/gpfs/alpine/world-shared/bif128/docked/
$LSB_JOBID
/
$HOST
OUT_DIR
=
/gpfs/alpine/world-shared/bif128/
6WQF_
docked/
$LSB_JOBID
/
$HOST
mkdir
-p
$OUT_DIR
log
()
{
...
...
@@ -55,7 +55,7 @@ if [ ! -s `basename $sfile` ]; then
# final_Mpro_pdbqt_maps_for_1B.tgz
# final_MPro_pdbqt_maps_for_1B
# ligands
mv
final_MPro_pdbqt_maps_for_1B/
*
.
[
-d
final_MPro_pdbqt_maps_for_1B
]
&&
mv
final_MPro_pdbqt_maps_for_1B/
*
.
ls
ligands/
*
>
liglist
ls
-1
ligands |
cut
-f
1
-d
'.'
>
lignames
log completed copyin
...
...
run_docking.lsf
View file @
1ca85933
#BSUB -nnodes
9
0
#BSUB -W
5:0
0
#BSUB -nnodes
1
0
#BSUB -W
1:2
0
#BSUB -q batch
#BSUB -P BIF128
#BSUB -J ADv1.
0
#BSUB -J ADv1.
1
#BSUB -o %J.out
#BSUB -alloc_flags "NVME"
...
...
@@ -10,7 +10,7 @@ source /ccs/proj/bif128/venvs/env.sh
PROJ=/gpfs/alpine/bif128/proj-shared/redis
gpus=$(( (LSB_MAX_NUM_PROCESSORS-1)/7 ))
echo "Starting $((gpus/6)) node run of ADv1.
0
at " `date`
echo "Starting $((gpus/6)) node run of ADv1.
1
at " `date`
[ -s $PROJ/shards.rdb ]
REMAKE=$?
...
...
@@ -27,6 +27,7 @@ for((i=0;i<120;i++)); do
[ $? -eq 0 ] && break
sleep 1
done
query set hopper $((gpus*2))
echo "$memb initial members at " `date`
...
...
shards.conf
View file @
1ca85933
...
...
@@ -320,7 +320,7 @@ rdbcompression yes
rdbchecksum
yes
# The filename where to dump the DB
dbfilename
shards
.
rdb
dbfilename
shards
_6WQF
.
rdb
# Remove RDB files used by replication in instances without persistence
# enabled. By default this option is disabled, however there are environments
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment