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HPC - JGU - Life Sciences
seq-analysis
Commits
879e5f51
Commit
879e5f51
authored
Jan 15, 2019
by
Christian Meesters
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hot fix - untested
parent
47938455
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blast/parallel_BLAST/parallel_BLAST
blast/parallel_BLAST/parallel_BLAST
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blast/parallel_BLAST/parallel_BLAST
View file @
879e5f51
...
...
@@ -690,13 +690,21 @@ chmod +x $cmd
trap
"rm -f
$cmd
"
EXIT
# define our srun-dropin for the subsequent call to be distributed amoung the reserved nodes
srun
=
"srun -n 1 -N1 --exclusive -c
$SLURM_CPUS_PER_TASK
--jobid
$SLURM_JOBID
--mem-per-cpu=
$((
SLURM_MEM_PER_NODE
/
SLURM_NTASKS
))
"
#
srun="srun -n 1 -N1 --exclusive -c $SLURM_CPUS_PER_TASK --jobid $SLURM_JOBID --mem-per-cpu=$((SLURM_MEM_PER_NODE / SLURM_NTASKS))"
# likewise the correct number of semaphores
parallel
=
"parallel --no-notice -j
$((
$SLURM_CPUS_ON_NODE
/
$SLURM_CPUS_PER_TASK
*
$SLURM_JOB_NUM_NODES
))
"
#
parallel="parallel --no-notice -j $(($SLURM_CPUS_ON_NODE / $SLURM_CPUS_PER_TASK * $SLURM_JOB_NUM_NODES)) "
HOSTLIST
=
$(
scontrol show
hostname
$SLURM_JOB_NODELIST
|
paste
-d
,
-s
)
#
HOSTLIST=$(scontrol show hostname $SLURM_JOB_NODELIST | paste -d, -s )
#parallel --controlmaster --workdir --sshdelay 0.2 $PWD -S $HOSTLIST -j $(($SLURM_JOB_NUM_NODES*$SLURM_CPUS_ON_NODE/$SLURM_CPUS_PER_TASK)) --env run_blast run_blast ::: $(find -type f -name 'group*.fasta')
parallel
--workdir
$PWD
--sshdelay
0.1
-S
$HOSTLIST
-j
$((
$SLURM_CPUS_ON_NODE
/
$SLURM_CPUS_PER_TASK
))
$cmd
:::
$(
find
$(
pwd
)
-type
f
-name
'group*.fasta'
)
task_cpus
=
$((
SLURM_NTASKS_PER_NODE
*
SLURM_CPUS_PER_TASK
))
mem_per_process
=
$((
SLURM_MEM_PER_NODE
/
task_cpus
))
srun
=
"srun --cpu-bind=q --mem-bind=q -n 1 -N1 --exclusive -c
$SLURM_CPUS_PER_TASK
--jobid
$SLURM_JOBID
--mem-per-cpu=
$((
SLURM_MEM_PER_NODE
/
task_cpus
))
"
parallel
=
"parallel --no-notice -j
$SLURM_NTASKS
-P
$SLURM_NTASKS
"
$parallel
$cmd
:::
$(
find
$(
pwd
)
-type
f
-name
'group*.fasta'
)
wait
...
...
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