Has anyone used PBS to run CD-HIT, I try to run it but it has error like this:
> my job id is 4967.admin1 run nodes is following: begin time is Fri Dec
> 28 16:07:39 CST 2018
> -------------------------------------------------------------------------- Open MPI tried to fork a new process via the "execve" system call but
> failed. Open MPI checks many things before attempting to launch a
> child process, but nothing is perfect. This error may be indicative of
> another problem on the target host, or even something as silly as
> having specified a directory for your application. Your job will now
> abort.
>
> Local host: smp1 Application name: hit Error:
> Exec format error
> -------------------------------------------------------------------------- end time is Fri Dec 28 16:07:39 CST 2018
And my command is:
cd-hit-est -i merge.fna -o unigene.fasta -c 0.95 -n 8
I try to run it on the command node but it shows:
./hit
================================================================
Program: CD-HIT, V4.7 (+OpenMP), Jul 13 2018, 17:17:44
Command: cd-hit-est -i merge.fna -o unigene.fasta -c 0.95 -n 8
Started: Fri Dec 28 16:18:11 2018
================================================================
Output
----------------------------------------------------------------
total seq: 180956
Warning:
Some seqs are too long, please rebuild the program with make parameter MAX_SEQ=new-maximum-length (e.g. make MAX_SEQ=10000000)
Not fatal, but may affect results !!
longest and shortest : 662596 and 500
Total letters: 433057744
Sequences have been sorted
Approximated minimal memory consumption:
Sequence : 457M
Buffer : 1 X 155M = 155M
Table : 1 X 3M = 3M
Miscellaneous : 2M
Total : 619M
Table limit with the given memory limit:
Max number of representatives: 40000
Max number of word counting entries: 22619494
comparing sequences from 0 to 82
./hit: line 1: 2160 Segmentation fault (core dumped) cd-hit-est -i
cd-hit-est -i merge.fna -o unigene.fasta -c 0.95 -n 8
I have no experience in PBS, so I wonder if it is because of my PBS script. Suggestions will be appreciated:
#!/bin/sh
#PBS -N hit
#PBS -l nodes=1:ppn=1
#PBS -j oe
#PBS -l walltime=480:00:00
#PBS -q smp
source /public/home/software/mpi/openmpi.sh
echo my job id is $PBS_JOBID | tee openmpi.log
echo run nodes is following: | tee -a openmpi.log
echo begin time is `date` | tee -a openmpi.log
mpirun /public/home/wuyue/data_P101SC18100564-01-B1-21/htest/hit | tee -a openmpi.log
echo end time is `date` | tee -a openmpi.log
for some more info on this have a look at this stackoverflow post : https://stackoverflow.com/questions/32464084 (thx to h.mon )