I found that, if this is "bash", "foreach" does not work.
I use "for" instead.
Hence, I have modified the code as follows:
Nonetheless, I have received an error:
I have an ftp user, which has been setup to run ftp jobs to a specific machine (different jobs). for the first job i created .netrc in the ftp users home directory and added the appropriate commands
machine FTPBOX01 login user1 password xxx
macdef init
etc
etc
get file
bye
I use the... (3 Replies)
Is there any way I can submit a job to a remote machine and return immediately without withing for the job to finish?
What I mean is this...using rsh I can submit a job to a remote machine like this:
rsh remotemac1 job.sh
But this doesn't return untill the job has finished and as a... (3 Replies)
I have a list of jobs. their expected start time and their expected duration.
my needs are
monitor multiple jobs (starting at different time and their execution time also differs)
Need to mail if any of the job running longer than its expected duration.
Whats the efficient way to scripting... (1 Reply)
Hello,
I would like to write a perl script which executes several jobs. The key thing is I only want 4 jobs to be executed at one time (that's because my machine as 4 cpu, and I want one job per cpu). Is there any way that I can get perl to co-operate with me in this?
Thanks! (1 Reply)
Hello,
I have a perl script that takes in one file of input and outputs to a file. I would like to run this script on several input files, and I would like to run it with qsub, something like this:
Input files:
FileListDssp.txt.numaa
FileListDssp.txt.numab
FileListDssp.txt.numac
etc..
... (1 Reply)
I have a sequence of tasks that I routinely run and I'm trying to parallelize certain portions of the sequence. Specifically, there are 3 tasks which all read from the same file, each performing different operations and writing to their own seperate file. I was wondering if I could execute these... (3 Replies)
Hi,
I ran two crontab commands
using:
crontab program1
crontab program2
However when I type crontab -l only the second cron job shows up, how do I see all cron jobs running and how do I edit all at the same time
Thanks in Advance
S:D (10 Replies)
Hi
I am new to submitting jobs. I am trying to submit my perl file to the cluster.
This is what my shell file looks like (shell1.sh):
#!/bin/sh
#$ -S /bin/sh
cd data/projects/mydir/abbc
perl autocorro.pl
followed by qsub shell1.sh
It takes the qsub, but does nothing. I check... (1 Reply)
I have multiple jobs and each job dependent on other job.
Each Job generates a log and If job completed successfully log file end's with JOB ENDED SUCCESSFULLY message and if it failed then it will end with JOB ENDED with FAILURE.
I need an help how to start.
Attaching the JOB dependency... (3 Replies)
I have two scripts which I'm tying to run one after the other- this is what I've tried:
00 14 * * * /path/one.sh && /path/two.sh
I've also tried putting each script on a different line:
00 14 * * * /path/one.sh
00 14 * * * /path/two.sh
Can this be done? (1 Reply)
Discussion started by: $shell_Learner
1 Replies
LEARN ABOUT DEBIAN
cd-hit-para
CD-HIT-PARA.PL(1) User Commands CD-HIT-PARA.PL(1)NAME
cd-hit-para.pl - divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs
SYNOPSIS
cd-hit-para.pl options
DESCRIPTION
This script divide a big clustering job into pieces and submit jobs to remote computers over a network to make it parallel. After
all the jobs finished, the script merge the clustering results as if you just run a single cd-hit or cd-hit-est.
You can also use it to divide big jobs on a single computer if your computer does not have enough RAM (with -L option).
Requirements:
1 When run this script over a network, the directory where you
run the scripts and the input files must be available on all the remote hosts with identical path.
2 If you choose "ssh" to submit jobs, you have to have
passwordless ssh to any remote host, see ssh manual to know how to set up passwordless ssh.
3 I suggest to use queuing system instead of ssh,
I currently support PBS and SGE
4 cd-hit cd-hit-2d cd-hit-est cd-hit-est-2d
cd-hit-div cd-hit-div.pl must be in same directory where this script is in.
Options
-i input filename in fasta format, required
-o output filename, required
--P program, "cd-hit" or "cd-hit-est", default "cd-hit"
--B filename of list of hosts,
requred unless -Q or -L option is supplied
--L number of cpus on local computer, default 0
when you are not running it over a cluster, you can use this option to divide a big clustering jobs into small pieces, I suggest you
just use "--L 1" unless you have enough RAM for each cpu
--S Number of segments to split input DB into, default 64
--Q number of jobs to submit to queue queuing system, default 0
by default, the program use ssh mode to submit remote jobs
--T type of queuing system, "PBS", "SGE" are supported, default PBS
--R restart file, used after a crash of run
-h print this help
More cd-hit/cd-hit-est options can be speicified in command line
Questions, bugs, contact Weizhong Li at liwz@sdsc.edu
cd-hit-para.pl 4.6-2012-04-25 April 2012 CD-HIT-PARA.PL(1)