Questions tagged [pbs]

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torque/undelivered - collect finished jobs

I had the problem that due to an incorrectly configured ssh the pbs_mom couldn't send the finished data (.ER and .OU files) back to the server. After a look into the log, I could locate the data on ...
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2 votes
1 answer
209 views

How can I set up interactive-job-only or batch-job-only partition on a SLURM cluster?

I'm managing a PBS/torque HPC cluster, and now I'm setting up another cluster with SLURM. On the PBS cluster, I can set a queue to accept only interactive jobs by qmgr -c "set queue interactive_q ...
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  • 143
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User Statistics from PBS

Is there a way to check on the usage-statistics of the Portable Batch System (PBS), i.e. check how many real-time or CPU hours were consumed by one particular user or the users themselves? qstat --...
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1 answer
348 views

How to launch a PBS job with hybrid MPI/Openmp

I would like to understand how a GROMACS job launched on my SGI cluster with PBS/Torque using a hybrid parallelization MPI/OpenMPI, works. The cluster is hyper-threading enabled and each node has 16 ...
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-1 votes
1 answer
196 views

PBS/Torque priority vs MPI program priority

We have a Cluster performing different tasks. It is computing simulations using the Torque scheduler. We also have an interactive simulation, which also needs the full computation power. The ...
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1 answer
768 views

How to append PBS job output to log files instead of overwriting it?

I'm using Torque and I want my PBS log+error output to be appended to previous log/error file instead of overwriting it.
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1 answer
52 views

Library not found only when application is executed from PBS file.

I have a compiled file a.out that runs fine when executed directly from my terminal. However, trying to execute that file from my PBS file yields a missing library libmkl_intel_lp64.so. I have already ...
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2 votes
1 answer
1k views

Job submitted to Torque does not generate error/log file

As stated, I have just installed Torque on a Ubuntu 16.04 machine. The submitted jobs complete just fine but the -e and -o flags seem to not be working. No error and log files are created even though ...
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1 vote
0 answers
524 views

How to setup bash environment inside Torque PBS? Why source ~/.bashrc doesn't work?

I have successfully installed Torque PBS on my ubuntu server. Job submission is fine. However there is an annoying thing. I found bash environment is not right inside PBS for example echo 'echo $...
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1 vote
0 answers
351 views

PBS Torque Limit Resource by Time of Day

I am using Torque to manage software that I have a limited number of licenses of (4 to be exact). During the day I need to keep 2 licenses free for use of setting up cases and at night and over the ...
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  • 111
2 votes
0 answers
77 views

Torque pbs queue system runs queue in reverse

I have a small compute cluster set up on Redhat 7.1. It runs the PBS torque queue system with version 5.1.1. When I queue several jobs it starts to run the jobs in "backwards" priority. It starts ...
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1 vote
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109 views

Torque queue issue

I am having troubles with Torque + Maui. The problem is the following: I have 2 queues, each queue has 10 associated nodes. If i submit 10k jobs to the first queue and i submit 1 job to the second ...
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-1 votes
1 answer
1k views

How can we configure torque with multiple nodes for a workstation? [closed]

I've got a GPU workstation with 48 core CPU + 4 NVIDIA GPU. I am going to make this machine to be a small cluster which contains: 4 nodes 12 core +1 CPU/node I've installed Torque in this machine ...
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1 answer
59 views

PBS, adding job - job added, seems that it didnt run at all

First of all, Im very new to clusters and PBS systems. I was told to prepare a simple script (which I did): #PBS -S /bin/bash #PBS -o host_out #PBS -e host_err #PBS -q batch hostname date exit 0 ...
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  • 159
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1 answer
731 views

prevent normal users from running code on a cluster outside of pbs system

In our cluster with PBS batch system (torque) installed, we wish all the users execute their jobs by qsub so that the CPU resources can be well managed. However, it is found that users in our cluster ...
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1 answer
2k views

Torque reports error when posting job to client nodes

The system has two machines, one (called macondo02) runs pbs_server and pbs_schedule, another (called macondo01) runs pbs_mom. I have ensured that the host can clearly identify the existance of the ...
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3 votes
2 answers
5k views

How to find out the PBS version installed in a cluster?

Whenever I submit a job array, I get one job ID in this form: 463880-1.hostname with 463880 being the job ID and 1 the array ID, one job for each "array position". Today I'm using a different ...
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  • 163
1 vote
1 answer
3k views

pbs check how much cpu a job is using / job % cpu usage

On a cluster a job is submitted to run on N CPUs. qstat -f doesn't show how much CPU resources the job is using other than the time. How does one check whether 100% of each CPU power is used? It is ...
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0 votes
2 answers
4k views

Numerous pbs_server errors in /var/log/messages

On supercomputer's management node we receive numerous errors such as: pbs_server: LOG_ERROR::is_request, bad attempt to connect from 10.10.0.254:1023 (address not trusted - check entry in ...
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3 votes
0 answers
264 views

Email notifications per JOB ARRAY not per job in PBS torque

Is there a way to configure torque to send email notifications on start and end of job array, and not per job, Im managing job arrays of thousands of jobs, and I dont want to get flooded by mails. But ...
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1 vote
1 answer
2k views

Why does qdel comman return 'Unknown Job Id'

OS Version: CentOS release 4.6 (Final) Kernel \r on an \m 2.6.9-100.ELsmp Problem When I run qdel i get the following error: qdel: Unknown Job Id 20432.scyld.localdomain Information Output of ...
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1 vote
5 answers
16k views

I get the error qsub: Bad UID for job execution when trying to submit a job via PBS

OS Version: CentOS release 4.6 (Final) Kernel \r on an \m 2.6.9-100.ELsmp When I attempt to run a job it gives me the error as follows. qsub: Bad UID for job execution I have created a fresh user ...
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-1 votes
1 answer
123 views

Torque: How lock node cores to one application [closed]

I am having an issue that I do not know how to solve. Say I have 2 nodes (node1 and node2) each with 24 cores, I have software where I have a license for 32 cores. I want to be able to configure ...
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5 votes
0 answers
6k views

torque pbs 4.0.1 job stays queued ('Q') state; the scheduler seems not receiving any notification

I am using torque 4.0.1 on openSUSE 12.1 in a cluster environment. When I qsub a job (simple as "echo hello"), it remains in 'Q' state, and never gets scheduled. I can force the job to run with qrun, ...
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3 votes
2 answers
264 views

Can read/write jobs be put in a queue?

I share a server with HAL. The server has 32 GB of memory. I rarely use more than 1 GB of memory, and when I do, it is for a few minutes at a time, and I don't mind sending such jobs to the back of ...
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2 votes
1 answer
843 views

PBS Jobs - serial vs parallel job which one is better for my scenario

I have access to a cluster that uses 'torque' (I think) and we use PBS scripts to submit jobs. I need to run more then 200 instances of an app that I've developed in java. The app acts as a peer ...
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  • 133
2 votes
1 answer
1k views

pbs/Torque interactive jobs: bash trick to run command after launch

I'm using pbs interactive jobs in bash, launched using qsub -I, and I'd like to run some command after launch. After this command is run, I'd like to continue to use the interactive reservation as ...
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  • 398
1 vote
1 answer
895 views

Non-exclusive job scheduling in PBS/Torque

The cluster resource manager Torque typically allocates compute nodes on an exclusive basis. However, when you have a lot of small jobs (like we do) running against multi-core compute nodes, this can ...
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  • 1,281
3 votes
2 answers
5k views

Torque jobs does not enter "E" state (unless "qrun")

Jobs I add to the queue stays there in "Queued" state without attempts to be executed (unless I manually qrun them) /var/spool/torque/server_logs say just 04/11/2011 12:43:27;0100;PBS_Server;Job;16....
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  • 821
0 votes
1 answer
437 views

Only half of my pbs/Torque jobs are being scheduled

My supercomputing center recently moved from SGE to pbs/Torque. Now, when I schedule my array jobs, only half of the jobs in the array get scheduled. When they finish, the other half get scheduled. ...
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