I have a master and two nodes. They are install with SGN. And I have a shell script ready on all the nodes as well. Now I want to use a qsub to submit the job on all my nodes.
I used:
qsub -V -b n -cwd /root/remotescript.sh
but it seems that only one node is doing the job. I am wondering how do I submit jobs for all nodes. What would the command be.
My reference is this enter link description here
SGE is meant to dispatch jobs to worker nodes. In your example, you create one job so one node will run it. If you want to run a job on each of your node, you need to submit more than one job. If you want to target nodes you probably should use something closer to
qsub -V -b n -cwd -l hostname=node001 /root/remotescript.sh
qsub -V -b n -cwd -l hostname=node002 /root/remotescript.sh
The "-l hostname=*" parameter will require a specific host to run the job.
What are you trying to do? The general use case of using a grid engine is to let the scheduler dispatch the jobs so you don't have to use the "-l hostname=*" parameter. So technically you should just submit a bunch of jobs to SGE and let it dispatch it with the nodes availability.
Finch_Powers answer is good for describing how SGE allocates resources. So, I'll elaborate below on specifics of you question, which may be why you are not getting the desired outcome.
You mention launching remote script via:
qsub -V -b n -cwd /root/remotescript.sh
Also, you mention again that these scripts are located on the nodes:
"And I have a shell script ready on all the nodes as well"
This is not how SGE is designed to work, although it can do this. Typical usage is to have same single (or multiple) scripts accessible to all nodes via network mounted storage on the execution nodes and let SGE decide which nodes to run the script on.
To run remote code, you may be better served using plain SSH.
Related
I need to run many (hundreds) commands in shell, but I only want to have a maximum of 4 processes running (from the queue) at once. Each process will last several hours.
When a process finishes I want the next command to be "popped" from the queue and executed.
I also want to be able to add more process after the beginning, and it will be great if I could remove some jobs from the queue, or at least empty the queue.
I have seen solutions using makefile, but this only work if I have all my list of commands before the beginning. Also tried using mkfifo sjobq, and others, but I never could reach my needs...
Does anyone have code to solve this problem?
Edit: In response to Mark Setchell
The solution with tail -f and parallel is almost perfect, but when I do it, it always keep not launching the last 4 commands until I add more, and so on, I don't know why, and it is quite troublesome...
As for Redis, good solution also, but it takes more time to master all of it.
Thanks !
Use GNU Parallel to make a job queue like this:
# Clear out file containing job queue
> jobqueue
# Start GNU Parallel processing jobs from queue
# -k means "keep" output in order
# -j 4 means run 4 jobs at a time
tail -f jobqueue | parallel -k -j 4
# From another terminal, submit 40 jobs to the queue
for i in {1..40}; do echo "sleep 5;date +'%H:%M:%S Job $i'"; done >> jobqueue
Another option is to use REDIS - see my answer here Run several jobs parallelly and Efficiently
I have a matlab script that processes a large amount of data using torque job arrays.
The server that I SSH into lacks the memory to load the data in the first place, so I need to request the compute node resources as a torque job, as follows:
qsub -I -V -l nodes=1:ppn=1,walltime=12:00:00,vmem=80G
However, when I now run the matlab script I am unable to submit torque job array requests. The error I am getting is as follows:
qsub: submit error (Job rejected by all possible destinations (check syntax, queue resources, ...))
The job array request given was:
qsub -t 1-$1 -l vmem=16G -l nodes=1:ppn=1,walltime=48:00:00 -v batchID=$2,batchDir=$3,funcName=$4 -e $5 -o $6 $HOME/scripts/job.sh
This command works fine outside of a qsub session, and the above error is not transient, so it appears that I cannot submit a request for a torque job array from within a qsub session.
How do I obtain the necessary memory resources from the compute nodes while also being able to submit requests for torque job arrays?
The cluster may not allow you to submit jobs from nodes in the cluster. You may be able to ask the admin to change this behavior or you can ssh to the head from within your first job and run the qsub there.
ssh head "qsub -t .........."
I want to run a job on all the active nodes of a 64 node Sun Grid Engine Cluster, scheduled using qsub. I am currently using array-job variable for the same, but sometimes the program is scheduled multiple times on the same node.
qsub -t 1-64:1 -S /home/user/.local/bin/bash program.sh
Is it possible to schedule only one job per node, on all nodes parallely?
You could use a parallel environment. Create a parallel environment with :
qconf -ap "parallel_environment_name"
and set "allocation_rule" to 1, which means that all processes will have to reside on different hosts. Then when submitting your array job, specify your the number of nodes you want to use with your parallel environment. In your case :
qsub -t 1-64:1 -pe "parallel_environment_name" 64 -S /home/user/.local/bin/bash program.sh
For more information, check these links: http://linux.die.net/man/5/sge_pe and Configuring a new parallel environment at DanT's Grid Blog (link no longer working; there are copies on the wayback machine and softpanorama).
I you have a bash terminal, you can run
for host in $(qhost | tail -n +4 | cut -d " " -f 1); do qsub -l hostname=$host program.sh; done
"-l hostname=" specifies on which host to run the job.
The for loop iterates over the result returned by qstat to take each node and call the command specifying the host to use.
I am trying to run some code across multiple CPUs using MPI.
I run using:
$ mpirun -np 24 python mycode.py
I'm running on a cluster with 8 nodes, each with 12 CPUs. My 24 processes get scattered across all nodes.
Let's call the nodes node1, node2, ..., node8 and assume that the master process is on node1 and my job is the only one running. So node1 has the master process and a few slave processes, the rest of the nodes have only slave processes.
Only the node with the master process (ie node1) is being used. I can tell because nodes2-8 have load ~0 and node1 has load ~24 (whereas I would expect the load on each node to be approximately equal to the number of CPUs allocated to my job from that node). Also, each time a function is evaluated, I get it to print out the name of the host on which its running, and it prints out "node1" every time. I don't know whether the master process is the only one doing anything or if the slave processes on the same node as the master are also being used.
The cluster I'm running on was recently upgraded. Before the upgrade, I was using the same code and it behaved entirely as expected (i.e. when I asked for 24 CPUs, it gave me 24 CPUs and then used all 24 CPUs). This problem has only arisen since the upgrade, so I assume a setting somewhere got changed or reset. Has anyone seen this problem before and know how I might fix it?
Edit: This is submitted as a job to a scheduler using:
#!/bin/bash
#
#$ -cwd
#$ -pe * 24
#$ -o $JOB_ID.out
#$ -e $JOB_ID.err
#$ -r no
#$ -m n
#$ -l h_rt=24:00:00
echo job_id $JOB_ID
echo hostname $HOSTNAME
mpirun -np $NSLOTS python mycode.py
The cluster is running SGE and I submit this job using:
qsub myjob
It's also possible to specify where you want your jobs to run by using a hostfile. How the hostfile is formatted and used varies by MPI implementation so you'll need to consult the documentation for the one you have installed (man mpiexec) to find out how to use it.
The basic idea is that inside that file, you can define the nodes that you want to use and how many ranks you want on those nodes. This may require using other flags to specify how the processes are mapped to your nodes, but it the end, you can usually control how everything is laid out yourself.
All of this is different if you're using a scheduler like PBS, TORQUE, LoadLeveler, etc. as those can sometimes do some of this for you or have different ways of mapping jobs themselves. You'll have to consult the documentation for those separately or ask another question about them with the appropriate tags here.
Clusters usually have a batch scheduler like PBS, TORQUE, LoadLeveler, etc. These are generally given a shell script that contains your mpirun command along with environment variables that the scheduler needs. You should ask the administrator of your cluster what the process is for submitting batch MPI jobs.
Currently, I have a driver program that runs several thousand instances of a "payload" program and does some post-processing of the output. The driver currently calls the payload program directly, using a shell() function, from multiple threads. The shell() function executes a command in the current working directory, blocks until the command is finished running, and returns the data that was sent to stdout by the command. This works well on a single multicore machine. I want to modify the driver to submit qsub jobs to a large compute cluster instead, for more parallelism.
Is there a way to make the qsub command output its results to stdout instead of a file and block until the job is finished? Basically, I want it to act as much like "normal" execution of a command as possible, so that I can parallelize to the cluster with as little modification of my driver program as possible.
Edit: I thought all the grid engines were pretty much standardized. If they're not and it matters, I'm using Torque.
You don't mention what queuing system you're using, but SGE supports the '-sync y' option to qsub which will cause it to block until the job completes or exits.
In TORQUE this is done using the -x and -I options. qsub -I specifies that it should be interactive and -x says run only the command specified. For example:
qsub -I -x myscript.sh
will not return until myscript.sh finishes execution.
In PBS you can use qsub -Wblock=true <command>