Table of Contents
- 1 The Odyssey cluster uses SLURM to manage jobs
- 2 General SLURM documentation is widely available.
- 3 Odyssey jobs are generally run from the command line
- 4 Odyssey applications should not be run from login nodes
- 5 An enhanced module system called Helmod is used for enabling applications
- 6 Summary of SLURM commands
- 7 General SLURM resources
- 8 Submitting batch jobs using the sbatch command
- 9 Monitoring job progress with squeue and sacct
- 10 Killing jobs with scancel
- 11 Interactive jobs and srun
- 12 Remote desktop access
- 13 SLURM partitions
- 14 Storage on Odyssey
- 15 A number of factors, including fair-share are used for job scheduling
- 16 Troubleshooting and common problems
- 17 Using MPI
- 18 Job arrays
- 19 Checkpointing
- 20 Job dependencies
The Odyssey cluster uses SLURM to manage jobs
SLURM is a queue management system and stands for Simple Linux Utility for Resource Management. SLURM was developed at the Lawrence Livermore National Lab and currently runs some of the largest compute clusters in the world.
SLURM is similar in many ways to most other queue systems. You write a batch script then submit it to the queue manager. The queue manager then schedules your job to run on the queue (or partition in SLURM parlance) that you designate. Below we will provide an outline of how to submit jobs to SLURM, how SLURM decides when to schedule your job and how to monitor progress.
SLURM has a number of valuable features compared to other job management systems:
- Kill and Requeue SLURM’s ability to kill and requeue is superior to that of other systems. It waits for jobs to be cleared before scheduling the high priority job. It also does kill and requeue on memory rather than just on core count.
- Memory Memory requests are sacrosanct in SLURM. Thus the amount of memory you request at run time is guaranteed to be there. No one can infringe on that memory space and you cannot exceed the amount of memory that you request.
- Accounting Tools SLURM has a back end database which stores historical information about the cluster. This information can be queried by the users who are curious about how much resources they have used.
General SLURM documentation is widely available.
The primary source for documentation on SLURM usage and commands can be found at the SLURM site. If you Google for SLURM questions, you'll often see the Lawrence Livermore pages as the top hits, but these tend to be outdated. A great way to get details on the SLURM commands is the man pages available from the Odyssey cluster. For example, if you type the following command:
you'll get the manual page for the sbatch command.
Odyssey jobs are generally run from the command line
Once you've gone through the account setup procedure and obtained a suitable terminal application, you can login to the Odyssey system via ssh
where <USERNAME> is the RC login you received from the account request tool. This is generally not the same as your HUIT machine login and is not your Harvard ID.
Odyssey computers run the CentOS 6.5 version of the Linux operating system and commands are run under the "bash" shell. There are a number of Linux and bash references, cheat sheets and tutorials available on the web. RC's own training are also available.
Odyssey applications should not be run from login nodes
Once you have logged in to the Odyssey system, you will be on one of a handful of access nodes (e.g. rclogin04). These nodes are shared entry points for all users and so cannot be used to run computationally intensive software.
Simple file copies, light text processing or editing, etc. are fine, but you should not run large graphical applications like Matlab, or computationally intensive command line tools.c
A culling program runs on these nodes that will kill any application that exceeds memory and computational limits.
Entry nodes for NoMachine remote desktops (see below) like
holynx01 are also to be treated like login nodes.
An enhanced module system called Helmod is used for enabling applications
Because of the diversity of investigations currently supported by FAS, thousands of applications and libraries are supported on the Odyssey cluster. Technically, it is impossible to include all of these tools in every user's environment.
The Research Computing and Informatics departments have developed an enhanced Linux module system, Helmod, based on the hierarchical Lmod module system from TACC. Helmod prevents enables applications much the same way as Linux modules, but also prevents multiple versions of the same tool from being loaded at the same time and separates tools that use particular compilers or MPI libraries entirely.
Please note that we are deprecating the older module system, which is based on categories (e.g.
hpc). We strongly advise you to switch over to the Helmod system ASAP and contact us via the RC portal if any software needs porting.
To start using the Helmod system, issue the command:
You can also add this statement to your
.bashrc login file so that you'll use the new system by default.
module load command enables a particular application in the environment, mainly by adding the application to your PATH variable. For example, to enable the currently supported R package:
Loading more complex modules can affect a number of environment variables including
PERL5LIB, etc. Modules may also load dependencies.
To determine what has been loaded in your environment, the
module list command will print all loaded modules.
module purge command will remove all currently loaded modules. This is particularly useful if you have to run incompatible software (e.g. python 2.x or python 3.x). The
module unload command will remove a specific module.
Finding the modules that are appropriate for your needs can be done in a couple of different ways. The module search page allows you to browse and search the list of modules that have been deployed to Odyssey.
There are a number of command line options for module searching, including the
module avail command for browsing the entire list of applications and the
module-query command for keyword searching.
Though there are many modules available by default, the hierarchical Helmod system enables additional modules after loading certain key libraries such as compilers and MPI packages. The
module avail command output reflects this.
module-query command supports more sophisticated queries and returns additional information for modules. If you query by the name of an application or library (e.g. hdf5), you'll retrieve a consolidated report showing all of the modules grouped together for a particular application.
A query for a single module, however, will return details about that build including module load statements and build comments (if any exist).
Summary of SLURM commands
The table below shows a summary of SLURM commands. These commands are described in more detail below along with links to the SLURM doc site.
|Submit a batch serial job||sbatch||
|Run a script interatively||srun||
|Kill a job||scancel||
|View status of queues||squeue||
|Check current job by id||sacct||
General SLURM resources
Though SLURM is not as common as SGE or LSF, documentation is readily available.
- Common SLURM commands
- Official SLURM web site
- Official SLURM documentation
- SLURM tutorial videos
- LLNL quick start user guide
Submitting batch jobs using the
The main way to run jobs on Odyssey is by submitting a script with the
sbatch command. The command to submit a job is as simple as:
The commands specified in the
runscript.sh file will then be run on the first available compute node that fits the resources requested in the script.
sbatch returns immediately after submission; commands are not run as foreground processes and won't stop if you disconnect from Odyssey.
A typical submission script, in this case using the
hostname command to get the computer name, will look like this:
#SBATCH -n 1 # Number of cores
#SBATCH -N 1 # Ensure that all cores are on one machine
#SBATCH -t 0-00:05 # Runtime in D-HH:MM
#SBATCH -p serial_requeue # Partition to submit to
#SBATCH --mem=100 # Memory pool for all cores (see also --mem-per-cpu)
#SBATCH -o hostname_%j.out # File to which STDOUT will be written
#SBATCH -e hostname_%j.err # File to which STDERR will be written
#SBATCH --mail-type=END # Type of email notification- BEGIN,END,FAIL,ALL
#SBATCH --firstname.lastname@example.org # Email to which notifications will be sent
In general, the script is composed of 3 parts.
#!/bin/bashline allows the script to be run as a bash script
#SBATCHlines are technically bash comments, but they set various parameters for the SLURM scheduler
- the command line itself.
#SBATCH lines shown above set key parameters. N.B. It is important to keep all
#SBATCH lines together and at the top of the script; no bash code or variables settings should be done until after the
#SBATCH lines. The SLURM system copies many environment variables from your current session to the compute host where the script is run including
PATH and your current working directory. As a result, you can specify files relative to your current location (e.g.
#SBATCH -n 1
This line sets the number of cores that you're requesting. Make sure that your tool can use multiple cores before requesting more than one. If this parameter is omitted, SLURM assumes
#SBATCH -N 1
This line requests that the cores are all on node. Only change this to >1 if you know your code uses a message passing protocol like MPI. SLURM makes no assumptions on this parameter -- if you request more than one core (-n > 1) and your forget this parameter, your job may be scheduled across nodes; and unless your job is MPI (multinode) aware, your job will run slowly, as it is oversubscribed on the master node and wasting resources on the other(s).
#SBATCH -t 5
This line specifies the running time for the job in minutes. You can also use the convenient format D-HH:MM. If your job runs longer than the value you specify here, it will be cancelled. Jobs have a maximum run time of 7 days on Odyssey, though extensions can be done. There is no penalty for over-requesting time. NOTE! If this parameter is omitted on any partition, the your job will be given the default of 10 minutes.
#SBATCH -p serial_requeue
This line specifies the SLURM partition (AKA queue) under which the script will be run. The serial_requeue partition is good for routine jobs that can handle being occasionally stopped and restarted. PENDING times are typically short for this queue. See the partitions description below for more information
The Odyssey cluster requires that you specify the amount of memory (in MB) that you will be using for your job. Accurate specifications allow jobs to be run with maximum efficiency on the system. There are two main options,
--mem option specifies the total memory pool for one or more cores, and is the recommended option to use. If you must do work across multiple compute nodes (e.g. MPI code), then you must use the
--mem-per-cpu option, as this will allocate the amount specified for each of the cores you're requested, whether it is on one node or multiple nodes. If this parameter is omitted, the smallest amount is allocated, usually 100 MB. And chances are good that your job will be killed as it will likely go over this amount.
#SBATCH -o hostname_%j.out
This line specifies the file to which standard out will be appended. If a relative file name is used, it will be relative to your current working directory. The
%j in the filename will be substituted by the jobID at runtime. If this parameter is omitted, any output will be directed to a file named SLURM-JOBID.out in the current directory.
#SBATCH -e hostname_%j.err
This line specifies the file to which standard error will be appended. SLURM submission and processing errors will also appear in the file. The
%j in the filename will be substituted by the jobID at runtime. If this parameter is omitted, any output will be directed to a file named SLURM-JOBID.out in the current directory.
Because jobs are processed in the "background" and can take some time to run, it is useful send an email message when the job has finished (--mail-type=END). Email can also be sent for other processing stages (START, FAIL) or at all of the times (ALL)
The email address to which the --mail-type messages will be sent.
It is important to accurately request resources, especially memory
Odyssey is a large, shared system that must have an accurate idea of the resources your program(s) will use so that it can effectively schedule jobs. If insufficient memory is allocated, your program may crash (often in an unintelligible way); if too much memory is allocated, resources that could be used for other jobs will be wasted. Additionally, your "fairshare", a number used in calculating the priority of your job for scheduling purposes, can be adversely affected by over-requesting. Therefore it is important to be as accurate as possible when requesting cores (
-n) and memory (
Many scientific computing tools can take advantage of multiple processing cores, but many cannot. A typical R script, for example will not use multiple cores. On the other hand, RStudio, a graphical console for R is a Java program that is improved substantially by using multiple cores. Or, you can use the Rmpi package and spawn "slaves" that correspond to the number of cores you've selected.
The distinction between
--mem-per-cpu is important when running multi-core jobs (for single core jobs, the two are equivalent).
--mem sets total memory across all cores, while
--mem-per-cpu sets the value for each requested core. If you request two cores (
-n 2) and 4 Gb with
--mem, each core will receive 2 Gb RAM. If you specify 4 Gb with
--mem-per-cpu, each core will receive 4 Gb for a total of 8 Gb.
Monitoring job progress with squeue and sacct
sacct are two different commands that allow you to monitor job activity in SLURM.
squeue is the primary and most accurate monitoring tool.
sacct gives you similar information for running jobs, and can also report on previously finished jobs, but because it accesses the SLURM database, there are some circumstances when the information is not in sync with
squeue without arguments will list all your currently running, pending, and completing jobs:
or for a particular job
If you include the
-l option (for "long" output) you can get useful data, including the running state of the job.
squeue tool in your PATH (
/usr/local/bin/squeue) is a modified version developed by FAS Informatics. To reduce the load on the SLURM scheduler (RC processes 2.5 million jobs each month), this tool actually queries a centrally collected result from the 'real'
squeue tool, which can be found at
/usr/bin/squeue. This data is collected approximately every 30 seconds. Many, but not all, of the options from the original tool are supported. Check this using the
squeue --help command.
If you need to use all of the options from the real
squeue tool, simply call it directly (
The current state of jobs can also be monitored via the FAS RC/Informatics portal jobs page. You will need to login with your RC credentials. This draws from the same shared data as the
squeue command line tool.
sacct command also provides details on the state of a particular job. An
squeue-like report on a single job is a simple command.
sacct can provide much more detail as it has access to many of the resource accounting fields that SLURM uses. For example, to get a detailed report on the memory and CPU usage for an array job (see below for details about job arrays):
Both tools provide information about the job State. This value will typically be one of PENDING, RUNNING, COMPLETED, CANCELLED, and FAILED.
|PENDING||Job is awaiting a slot suitable for the requested resources. Jobs with high resource demands may spend significant time PENDING.|
|RUNNING||Job is running.|
|COMPLETED||Job has finished and the command(s) have returned successfully (i.e. exit code 0).|
|CANCELLED||Job has been terminated by the user or administrator using scancel.|
|FAILED||Job finished with an exit code other than 0.|
Killing jobs with scancel
If for any reason, you need to kill a job that you've submitted, just use the
scancel command with the job ID.
If you don't keep track of the job ID returned from
sbatch, you should be able to find it with the
squeue command described above.
Interactive jobs and srun
Though batch submission is the best way to take full advantage of the compute power in Odyssey, foreground, interactive jobs can also be run. These can be useful for things like:
- Iterative data exploration at the command line
- RAM intensive graphical applications like MATLAB or SAS.
- Interactive "console tools" like R and iPython
- Significant software development and compiling efforts
An interactive job differs from a batch job in two important aspects: 1) the partition to be used is the
interact partition and, 2) jobs should be initiated with the
srun command instead of
sbatch. This command:
will start a command line shell (
/bin/bash) on the interactive queue with 500 MB of RAM for 6 hours; 1 core on 1 node is assumed as these parameters (
-n 1 -N 1) were left out. When the interactive session starts, you will notice that you are no longer on a login node, but rather one of the compute nodes dedicated to this queue. The
--pty option allows the session to act like a standard terminal. In a pinch, you can also run an application directly though this is discouraged due to problems setting up bash environment variables. After loading a module for MATLAB, you can start the application with the following command:
In this case, we've asked for more memory because of the larger MATLAB footprint. The
--x11-first option allows XWindows to operate between the login and compute nodes.
interact partition requires that you actually interact with the session. If you go more than an hour without any kind of input, it will assume that you have left the session and will terminate it. If you have interactive tasks that must stretch over days, you may be able to use the GNU Screen or tmux utility to prevent the termination of a session.
Remote desktop access
As described in the Access & Login page, you can connect to the Odyssey system through NX-based remote desktops. Remote desktop access is particularly useful for heavy client applications like MATLAB, SAS, and Spyder where the performance of X11 forwarding is poor. Once you have connected via NX, though, you should start an interactive session or run batch jobs. The
holynx servers are just like Odyssey login nodes and cannot support direct computation.
Partition is the term that SLURM uses for queues. Partitions can be thought of as a set of resources and parameters around their use (See also: Convenient SLURM Commands)
general partition has a maximum run time of 7 days. Serial, parallel, and interactive jobs are permitted on this queue, and this is the most appropriate location for MPI jobs. This queue is governed by backfill and FairShare (explained below).
general partition is populated with hardware that RC runs at the MGHPCC data center in Holyoke, MA. This queue has 214 nodes connected by a FDR InfiniBand (IB) fabric, where each node configured with 4 AMD Opteron Abu Dhabi CPUs, 256 GB of RAM, and 250 GB of local scratch space. Each AMD CPU has 8 Floating Point Units (FPU), 16 Integer Cores (IC), and 16 MB of cache. Thus, the entire system allocated to this partition has 13686 integer cores and 54 TB of RAM available for use.
When submitting MPI jobs on the
general partition, it is advisable to use the
--contiguous option for best communication performance. Though all of the nodes are connected by Infiniband fabric, there are multiple switches routing the MPI traffic. The
--contiguous option will ensure that the jobs are run on nodes connected by the same switch.
Serial and parallel (including MPI) jobs are permitted on this partition and no restriction on run time. Given this, there is no guarantee of 100% uptime. Running on this partition is done at the users own risk. Users should understand that if the queue is full it could take weeks or up to months for your job to be scheduled to run.
unrestricted is made up of 8 nodes (512 integer cores) of the same configuration as above for the
This partition is dedicated for interactive (foreground / live) work and for testing (interactively) code before submitting in batch and scaling. Small numbers (1 to 5) of serial and parallel jobs with small resource requirements (RAM/cores) are permitted on this partition; large numbers of interactive jobs or those requiring large resource requirements should really be done on another partition.
This partition is made up of 8 nodes of the same configuration as above for the general partition. This smaller, 512 integer core queue has a 3-day maximum run time.
This partition is appropriate for single core (serial) jobs or jobs that require up to 8 cores for small periods of time (less than 1 day). The maximum runtime for this queue is 7 days. MPI jobs are not appropriate for this partition. As this partition is made up of an assortment of nodes owned by other groups in addition to the general nodes, jobs in this partition may be killed but automatically requeued if a higher priority job (e.g. the job of a node owner) comes in. Because
serial_requeue takes advantage of slack time in owned partitions, times in the PENDING state can potentially be much shorter than the
Since jobs may be killed, requeued, and run a 2nd time, ensure that the jobs are a good match for this partition. For example, jobs that append output would not be good for
serial_requeue unless the data files were zeroed out at the start to ensure output from a previous (killed) run was removed. Also, to ensure your job need not redo all its compute again, it would be advisable to have breakpoints or branching instructions to bypass parts of work that have already been completed.
We do advise that you use the
--open-mode=append to see the requeue status/error messages in your log files. Without this option, your log files will be reset at the start of each (requeued) run, with no obvious indication of requeue events.
This partition should be used for large memory work requiring greater than 250 GB RAM per job, like genome / transcript assemblies. Jobs requesting less than 250 GB RAM are automatically rejected by the scheduler. There is no time limit for work here. MPI or low memory work is not appropriate for the this partition, and inappropriate jobs may be terminated without warning.
This partition has an allocation of 7 nodes with 512 GB of RAM
This 1 node partition is for individuals wishing to test GPGPU resources. One will need to include
#SBATCH --gres=gpu:n where n=1-8 in your SLURM submission scripts. This 1 node has 24 cores and is equipped with 8 x NVidia Tesla K20Xm. There are also private partitions that may have more GPU resources, but to which access may be controlled by the owners.
See our GPU Computing doc for more info.
Storage on Odyssey
Odyssey partitions have many owned and general purpose file systems attached for use. However, for best performance please use the
regal storage found at
/n/regal. This is a Lustre file system with 1.2 PB of storage and connected via Infiniband fabric. This space is available from all compute nodes. There are no quotas on this space, but there is a 90 day retention policy on the space. If you have not moved your data after 90 days it will be deleted to make space for other users. Please use
regal only for reading and writing data from the cluster. Please create a subdirectory in your lab group's folder here under
/n/regal/; please contact RCHelp if one does not yet exist.
We use a multifactor method of job scheduling on Odyssey. Job priority is assigned by a combination of fair-share, partition priority, and length of time a job has been sitting in the queue. The priority of the queue is the highest factor in the job priority calculation. For certain queues this will cause jobs on lower priority queues which overlap with that queue to be requeued.
The second most important factor is fair-share score. You can find a description of how SLURM calculates Fair-share here.
The third most important is how long you have been sitting in the queue. The longer your job sits in the queue the higher its priority grows. If everyone’s priority is equal then FIFO is the scheduling method. If you want to see what your current priority is just do
sprio -j JOBID which will show you the calculation it does to figure out your job priority. If you do
sshare -u USERNAME you can see your current fair-share and usage.
We also have backfill turned on. This allows for jobs which are smaller to sneak in while a larger higher priority job is waiting for nodes to free up. If your job can run in the amount of time it takes for the other job to get all the nodes it needs, SLURM will schedule you to run during that period. This means knowing how long your code will run for is very important and must be declared if you wish to leverage this feature. Otherwise the scheduler will just assume you will use the maximum allowed time for the partition when you run.
Troubleshooting and common problems
A variety of problems can arise when running jobs on Odyssey. Many are related to resource mis-allocation, but there are other common problems as well
||You did not specify enough time in your batch submission script. The
||Your job is attempting to use more memory than you've requested for it. Either increase the amount of memory requested by
||This message indicates a failure of the SLURM controller. Though there are many possible explanations, it is generally due to an overwhelming number of jobs being submitted, or, occasionally, finishing simultaneously. If you want to figure out if SLURM is working use the
||This message may arise for a variety of reasons, but it indicates that the host on which your job was running can no longer be contacted by SLURM.|
MPI (Message Passing Interface) is a standard that supports communication between separate processes, allowing parallel programs to simulate a large common memory space. OpenMPI and MVAPICH2 are available as modules on Odyssey as well as an Intel specific library.
As described in the Helmod documentation, MPI libraries are a special class of module, called "Comp", that is compiler dependent. To load an MPI library, load the compiler first.
Once an MPI module is loaded, applications built against that library are made available. This dynamic loading mechanism prevents conflicts that can arise between compiler versions and MPI library flavors.
An example MPI script with comments is shown below:
#SBATCH -n 128 # Number of cores
#SBATCH -t 5 # Runtime in minutes
#SBATCH -p general # Partition to submit to
#SBATCH --contiguous # Ensure that all of the cores are on the same Infiniband network
#SBATCH --mem-per-cpu=100 # Memory per cpu in MB (see also --mem)
module load intel/15.0.0-fasrc01 openmpi/1.10.0-fasrc01
module load MYPROGRAM
srun -n $SLURM_NTASKS --mpi=pmi2 MYPROGRAM > output.txt 2> errors.txt
There are a number of important aspects to an MPI SLURM job.
- MPI jobs must be run on a partition that supports MPI interconnects.
unrestrictedare MPI-enabled, but
serial_requeueincludes non-MPI resources and should be avoided.
--contiguousoption should be used to ensure that all cores are on the same Infiniband switch
- Memory should be allocated with the
--mem-per-cpuoption instead of
--memso that memory matches core utilization.
-npoption for mpirun or mpiexec (when these runners are used) should use the bash variable
$SLURM_NTASKSso that the correct number of cores is passed to the MPI engine at runtime.
- The application must be MPI-enabled. Applications cannot take advantage of MPI parallelization unless the source code is specifically built for it. All such applications in the Helmod module system can only be loaded if an MPI library is loaded first.
SLURM allows you to submit a number of "near identical" jobs simultaneously in the form of a job array. To take advantage of this, you will need a set of jobs that differ only by an "index" of some kind.
For example, say that you would like to run
tophat, a splice-aware transcript-to-genome mapping tool, on 30 separate transcript files named
trans3.fq, etc. First, construct a SLURM batch script, called
tophat.sh, using special SLURM job array variables:
#SBATCH -J tophat # A single job name for the array
#SBATCH -n 1 # Number of cores
#SBATCH -N 1 # All cores on one machine
#SBATCH -p serial_requeue # Partition
#SBATCH --mem 4000 # Memory request (4Gb)
#SBATCH -t 0-2:00 # Maximum execution time (D-HH:MM)
#SBATCH -o tophat_%A_%a.out # Standard output
#SBATCH -e tophat_%A_%a.err # Standard error
module load tophat/2.0.13-fasrc02
Then launch the batch process using the
--array option to specify the indexes.
In the script, two types of substitution variables are available when running job arrays. The first,
%a, represent the job ID and the job array index, respectively. These can be used in the sbatch parameters to generate unique names. The second,
SLURM_ARRAY_TASK_ID, is a bash environment variable that contains the current array index and can be used in the script itself. In this example, 30 jobs will be submitted each with a different input file and different standard error and standard out files.
More detail can be found on the SLURM job array documentation page.
SLURM supports checkpointing a job – stopping a job in the middle of processing and restarting from where it left off – using the BLCR framework. This subsystem only works if your application has been built to support it, though this may be as simple as linking in the appropriate libraries.
Many scientific computing tasks consist of serial processing steps. A genome assembly pipeline, for example, may require sequence quality trimming, assembly, and annotation steps that must occur in series. Launching each of these jobs without manual intervention can be done by repeatedly polling the controller with
sacct until the State is COMPLETED. However, it's much more efficient to let the SLURM controller handle this using the
When submitting a job, specify a combination of "dependency type" and job ID in the
afterok is an example of a dependency type that will run the dependent job if the parent job completes successfully (state goes to COMPLETED). The full list of dependency types can be found on the SLURM doc site in the man page for sbatch.
Last updated: March 22, 2017 at 13:28 pm
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