#
# Run under bourne shell:
#PBS -S /bin/sh
#
# Give the job a name (optional)
#PBS -N "mpiblast"
#
# Specify the project the job should be accounted on (obligatory). 
# Check which accounts are available with the 'cost' command.
#PBS -A parallab
#
# The job needs at most 60 hours wall-clock time on 6 CPUs. Change this
# to more/less cpus by changing the nodes setting. Keep ppn=2 (2 processors per node).
#PBS -l walltime=60:00:00,nodes=3:ppn=2
#
# The job needs 400MB memory per cpu
#PBS -l pmem=400mb
#
# Write the standard output of the job to file 'mpiBLAST.out' (optional)
#PBS -o mpiBLAST.out
#
# Write the standard error of the job to file 'mpiBLAST.err' (optional)
#PBS -e mpiBLAST.err
#
mkdir -p /work/janfrode/blastdb
cd /work/janfrode/blastdb

# Need to use a unique local directory for each job:
LOCAL=/scratch/${LOGNAME}/${PBS_JOBID}
echo /work/janfrode/blastdb > /work/janfrode/blastdb/mpiblast.conf
echo $LOCAL >> /work/janfrode/blastdb/mpiblast.conf

for node in `cat $PBS_NODEFILE | sort | uniq` ; do
	mkdir -p /net/${node}/${LOCAL}
done

# How many cpus are we running on?:
NCPUS=`cat $PBS_NODEFILE | wc -l`

P4_GLOBMEMSIZE=171966464
export P4_GLOBMEMSIZE

# Check the date before and after splitting the database, to see
# how much time is wasted in non-parallel mode.
date
mpiformatdb -N $NCPUS -i /work/speil/flatdb/algae/uniprot_sp_trembl_no_algae_virus.fasta
date

mpiexec mpiblast --config-file=/work/janfrode/blastdb/mpiblast.conf \
	-d uniprot_sp_trembl_no_algae_virus.fasta -i \
	~janfrode/PBCV-1.fasta -p blastx -o ~/mpiblast.tab \
	--concurrent=10 --removedb

# Clean up:
cd /work/janfrode
rm -rf /work/janfrode/blastdb
for node in `cat $PBS_NODEFILE | sort | uniq` ; do
	rm -rf /net/${node}/${LOCAL}
done