#PBS -N Cherry-mpi-infernal-align #PBS -l nodes=20:ppn=4 #PBS -l mem=20gb #PBS -l walltime=20:00:00 #PBS -q biocluster-6 #PBS -j oe #PBS -o $HOME/job_output_files/mpi_infernal_aligner_111614_Cherry.$PBS_JOBID module load mvapich2/1.9 cd $TMPDIR OUTPUT=$HOME/data/qiime_files/all_gom_seqs/test_fastas/infernal_align_hpc_clust/pre_clustered_seqs_sized_sorted_aligned.$PBS_JOBID.pfam CM=$BACT_CM INPUT=$HOME/data/qiime_files/all_gom_seqs/test_fastas/test_600k_nochim.fasta PROCS=`wc -l < ${PBS_NODEFILE}` echo "started on `/bin/hostname`" echo echo "PATH is [$PATH]" echo echo "Nodes chosen are:" cat $PBS_NODEFILE echo COMMAND="mpirun -np $PROCS -hostfile $PBS_NODEFILE cmalign --mpi -o $OUTPUT --outformat Pfam --matchonly --mxsize 5000 --noprob $CM $INPUT" time $COMMAND echo $COMMAND