I'm trying to run some computations on a cluster and have found that a bsub array is what I need.. So I tried running a simple example I found
This should create 10 jobs that output "Job 1" "Job 2" .. etc. But when I run this from afs space I get the message
"LSB_JOBINDEX: Undefined variable."
LSB_JOBINDEX should be the index of the current array job.. Any ideas what's going on?
Dear Experts,
please help me out once again my array concepts is not very clear i have one text file like.
1|usa|hh
2|usa|ll
3|usa|vg
4|uk|nn
5|uk|bb
6|kuwait|mm
6|kuwait|jkj
7|dubai|hh
i want to store the third fied of a text file in he array and after that it should give me some... (6 Replies)
I am using /bin/ksh for this problem.
I have created some arrays with variable names as the array names:
cnt=1
{ while read myline; do
tempmeas="${meas%%;*}"
cto="${meas#*;}"
tempstream=$stream
# wholemeas holds the name of the array
# each array name... (0 Replies)
Hi,
I am REALLY a newbie of Unix: hope this question is not too odd.
Here is my problem:
I have to submit jobs to a remote platform (an IBM BCX/5120).
To submit I have tobsub < filename.jcf
and the .jcf file has usually the following content:
#!/bin/bash
#BSUB <commands of the bsub>... (1 Reply)
Hi!
I am currently using the bsub command to submit jobs to a cluster and I need to specify the name of the node to which i want the job sent. What do I add to my .pbs script to specify this?
Cheers (0 Replies)
Hi There!
I'm writing this LSF script to make it easier to send jobs to a cluster when varying certain parameters. At one point I'd like to do something like:
set NPROC = 10
and later on call BSUB using something like:
#BSUB -n $NPROC
unfortunately for me, this throws an error:
... (4 Replies)
"bsub -o /dev/null -P something -q normal -a optimize -n 1 -R \"rusage\ span\\" -J GUISETUP_${PID} \"dc_shell-t -f .dc_script_$job_index.tcl -output_log_file .dc_shell_$job_index.log \""
Can anybody please tell me the qsub equivalent for this command?
---------- Post updated at 06:48 AM... (0 Replies)
Hi everyone,
I must write a Linux script for a biological analysis. I have an example for that which involves the "bsub" and "bsub-o" command, respectively. I cannot find a description for this command. Can you please help me? (2 Replies)
The red text at the bottom represents the three lines I want to address.
I'm dynamically creating a bsub with a perl script and would like to create the fasta_16S variable in a single line....not three. I'm having difficulty in getting the syntax correct. Obviously, there is some confusion... (3 Replies)
Hello,
When I'm trying to send bsub job using script that executes fine in command line, I get nothing.
I do this for testing purposes, and the script scr_test is just one line:
pwd > outfile
So when I'm executing it in command line:
$ ./scr_test
it works fine producing the outfile with... (2 Replies)
Discussion started by: Sergey Aliev
2 Replies
LEARN ABOUT X11R4
qstat
QSTAT(1) User Contributed Perl Documentation QSTAT(1)NAME
qstat - display job/partition information in a familiar pbs format
SYNOPSIS
qstat [-f] [-a|-i|-r] [-n [-1]] [-G|-M] [-u user_list] [-? | --help] [--man] [job_id...]
qstat -Q [-f]
qstat -q
DESCRIPTION
The qstat command displays information about jobs.
OPTIONS -a Displays all jobs in a single-line format. See the STANDARD OUTPUT section for format details.
-i Displays information about idle jobs. This includes jobs which are queued or held.
-f Displays the full information for each selected job in a multi-line format. See the STANDARD OUTPUT section for format details.
-G Display size information in gigabytes.
-M Show size information, disk or memory in mega-words. A word is considered to be 8 bytes.
-n Displays nodes allocated to a job in addition to the basic information.
-1 In combination with -n, the -1 option puts all of the nodes on the same line as the job id.
-r Displays information about running jobs. This includes jobs which are running or suspended.
-u user_list
Display job information for all jobs owned by the specified user(s). The format of user_list is: user_name[,user_name...].
-? | --help
brief help message
--man
full documentation
STANDARD OUTPUT
Displaying Job Status
If the -a, -i, -f, -r, -u, -n, -G, and -M options are not specified, the brief single-line display format is used. The following items are
displayed on a single line, in the specified order, separated by white space:
the job id
the job name
the job owner
the cpu time used
the job state
C - Job is completed after having run E - Job is exiting after having run. H - Job is held. Q - job is queued, eligible to run or
routed. R - job is running. T - job is being moved to new location. W - job is waiting for its execution time (-a option) to be
reached. S - job is suspended.
the queue that the job is in
If the -f option is specified, the multi-line display format is used. The output for each job consists of the header line: Job Id: job
identifier followed by one line per job attribute of the form: attribute_name = value
If any of the options -a, -i, -r, -u, -n, -G or -M are specified, the normal single-line display format is used. The following items are
displayed on a single line, in the specified order, separated by white space:
the job id
the job owner
the queue the job is in
the job name
the session id (if the job is running)
the number of nodes requested by the job
the number of cpus or tasks requested by the job
the amount of memory requested by the job
either the cpu time, if specified, or wall time requested by the job, (in hh:mm)
the job state
The amount of cpu time or wall time used by the job (in hh:mm)
EXIT STATUS
On success, qstat will exit with a value of zero. On failure, qstat will exit with a value greater than zero.
perl v5.14.2 2012-04-10 QSTAT(1)