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HPC - JGU - Life Sciences
seq-analysis
Commits
1c4fe802
Commit
1c4fe802
authored
Jan 15, 2019
by
Christian Meesters
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Plain Diff
added ramdisk size inference to hot fix
parent
879e5f51
Changes
1
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1 changed file
with
4 additions
and
18 deletions
+4
-18
blast/parallel_BLAST/parallel_BLAST
blast/parallel_BLAST/parallel_BLAST
+4
-18
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blast/parallel_BLAST/parallel_BLAST
View file @
1c4fe802
...
...
@@ -293,23 +293,6 @@ do
fi
_arg_blastparams
=
"
$_val
"
;;
-r
*
|
--ramdisk
|
--ramdisk
=
*
)
_val_from_long
=
"
${
_key
##--ramdisk=
}
"
_val_from_short
=
"
${
_key
##-r
}
"
if
test
"
$_val_from_long
"
!=
"
$_key
"
then
_val
=
"
$_val_from_long
"
elif
test
"
$_val_from_short
"
!=
"
$_key
"
-a
-n
"
$_val_from_short
"
then
_val
=
"
$_val_from_short
"
else
test
$#
-lt
2
&&
die
"Missing value for the optional argument '
$_key
'."
1
_val
=
"
$2
"
shift
fi
_arg_ramdisk
=
"
$_val
"
[[
$_arg_ramdisk
!=
*
"G"
*
]]
&&
_arg_ramdisk
=
$_arg_ramdisk
"G"
;;
-t
*
|
--threads
|
--threads
=
*
)
_val_from_long
=
"
${
_key
##--threads=
}
"
_val_from_short
=
"
${
_key
##-t
}
"
...
...
@@ -503,6 +486,9 @@ if [ -z $BLASTEXE ] && [[ $_arg_test == "off" ]]; then
exit
fi
### which is the reference directory size?
_arg_ramdisk
=
$(
du
-shL
--block-size
=
1M "
;
$_arg_reference
"
;
|
cut
-f1
)
M</pre>
### setup variable for THIS script; giving absolute path if necessary
SCRIPT
=
"
$0
"
...
...
@@ -555,7 +541,7 @@ EOF
### check if this script is on node by checking env-variable $SLURM_JOB_ID, else send it to SLURM with given parameters and exit
if
[
-z
"
$SLURM_JOB_ID
"
]
;
then
submit_call
=
"sbatch --no-requeue -o
${
JOBTAG
}
_%j.out -J
$JOBTAG
-p
$_arg_queue
-A
$_arg_assoc
-t
$_arg_runlimit
-N
$_arg_nodes
-n
$((
64
*
$_arg_nodes
/
$_arg_blast_threads
))
--mem=
$_arg_mem
--
gres=ramdisk:
$_arg_ramdisk
-c
$_arg_blast_threads
--reservation=
$_arg_reservation
$SCRIPT
--partition
$_arg_queue
--account
$_arg_assoc
--nodes
$_arg_nodes
--time
$_arg_runlimit
--reservation=
$_arg_reservation
--ramdisk
$_arg_ramdisk
--threads
$_arg_blast_threads
--splitup
$_arg_splitup_per_queryfile
--blastparams=
\"
$BLASTPARAMS
\"
--executable=
$_arg_executable
$FASTA
$DATABASE
"
submit_call
=
"sbatch --no-requeue -o
${
JOBTAG
}
_%j.out -J
$JOBTAG
-p
$_arg_queue
-A
$_arg_assoc
-t
$_arg_runlimit
-N
$_arg_nodes
-n
$((
64
*
$_arg_nodes
/
$_arg_blast_threads
))
--mem=
$_arg_mem
--
ramdisk=
${
_arg_ramdisk
}
-c
$_arg_blast_threads
--reservation=
$_arg_reservation
$SCRIPT
--partition
$_arg_queue
--account
$_arg_assoc
--nodes
$_arg_nodes
--time
$_arg_runlimit
--reservation=
$_arg_reservation
--ramdisk
$_arg_ramdisk
--threads
$_arg_blast_threads
--splitup
$_arg_splitup_per_queryfile
--blastparams=
\"
$BLASTPARAMS
\"
--executable=
$_arg_executable
$FASTA
$DATABASE
"
if
[[
$_arg_test
==
"on"
]]
;
then
echo
"Just testing - this command would be submitted:"
echo
$submit_call
...
...
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