HOWTO Execute a Launch using NERSC

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This page gives some instructions on executing a launch at NERSC. Note that some steps must be completed to make sure things are set up at Cori and Globus prior to submitting any jobs.

The following is based on steps used to do RunPeriod-2018-01 monitoring launch ver 18 using swif2.

NERSC Account

To run jobs at NERSC you need to get a user account there. This account will need to be associated with a repository which is what they call a project that has some resources allocated to it. At this time, the GlueX project is m3120. You can find instructions for applying for an account here:

Setting up SSH

Swif2 will access Cori at NERSC via passwordless login. To set this up, you’ll need a RSA key with empty passphrase and the public key installed on the NERSC account to be used. Chris’ instruction for this are:

(2-a) See
(2-b) As the user who owns the workflow, generate an ssh key as specified, supply no passphrase
(2-c) log in to, and under "My ssh keys" add the public key you generated in (2-b)
(2-d) verify that you can login to without a password after logging in to ifarm as the workflow user.

For this to actually work, you must make sure that the key created above is what is used when authenticating. I created a dedicated key pair with the names ~/.ssh/id_rsa_nersc and ~/.ssh/ . There are multiple ways to use this key (ssh-agent, using the ‘-i’ option with the ssh command,...). The best way to use it with swif2 though is to specify the key in the ~/.ssh/config file. There you can specify that the special key is used when logging into and furthermore which username to use when logging in. This last part is important since I needed it to log into my davidl account from the gxproj4 account at jlab.

Here are the lines that need to be in the ~/.ssh/config file:

# The following is to allow passwordless login to
# without having to run an agent or
# explicitly give the key on the ssh command.
# n.b. this will login as davidl and not in some
# group account at nersc (since none currently
# exists)
# 7/18/2018 DL
Host cori
    IdentityFile ~/.ssh/id_rsa_nersc
    User davidl

Files and directories on Cori at NERSC

When jobs are run at NERSC that will need access to a couple of files from the launch directory where we keep GlueX farm submission scripts and files. This is kept in our subversion repository at JLab. When a job is started at NERSC it will look for this directory in the project directory that swif2 is using for the workflow (see next section). The launch directory should already be checked out there but for completeness, here is how you would do it:

cd /global/project/projectdirs/m3120
svn co

If the directory is there, make sure it is up to date:

cd /global/project/projectdirs/m3120
svn update

The most important files are the script and the jana_offmon_nersc.config (jana_recon_nersc.config) files. This first is what is actually run inside of the container when the job wakes up. The second specifies the plugins and other settings. For the most part, the "nersc" versions of the jana config files should be kept in alignment with the JLab versions. One notable difference is that the NERSC jobs are always run on whole nodes so NTHREADS is always set to "Ncores" whereas at JLab they are usually set to 24.

Globus Endpoint Authentication

Submitting jobs to swif2

The offsite jobs at NERSC are managed from the gxproj4 account. This is a group account with access limited to certain users. Your ssh key must be added to the account by an existing member. Contact the software group to request access.

Generally, one would log into an appropriate computer with:

ssh gxproj4@ifarm

The following are some steps needed to create a workflow and submit jobs.

Create a new workflow

This step can actually be skipped since the script in the next step will automatically create the workflow with the correct name and parameters if it does not already exist. These are instructions in case you want/need to create the workflow yourself.

The workflow name follows a convention based on the type of launch, run period, version, and optional extra qualifiers. Here is the command used to create the workflow for offline monitoring launch ver18 for RunPeriod-2018-01:

swif2 create -workflow offmon_2018-01_ver18 -max-concurrent 2000 -site nersc/cori -site-storage nersc:m3120

The -max-concurrent 2000 option tells swif2 to limit the number of dispatched jobs to no more than 2000. The primary concern here is in scratch disk space at NERSC. If each input file is 20GB and produces 7GB of output then the we need 27GB * 2000 = 54 TB of free scratch disk space. If multiple launches are running at the same time and using the same account's scratch disk then it is up to you to make sure the sum of requirements does not exceed the quota. At this point in time we have a quota of 60TB of scratch space, though they have claimed that they will revisit that at the beginning of the year.

The -site nersc/cori is required at the moment and is the only allowed option for "site".

The -site-storage nersc:m3120 is used to specify which NERSC project assigned disk space to use. At this point, swif2 has been changed to use scratch disk space assigned to the personal account being used to run the jobs so I believe this is being ignored.

Prepare working directory at JLab

Create a working directory in the gxproj4 account and checkout the launch scripts. This is done so that the scripts can be modified for the specific launch in case some tweaks are needed. Changes should eventually be pushed back into the repository, but having a dedicated directory for the launch can help with managing things, especially when there are multiple launches.

mkdir ~gxproj4/NERSC/2018.10.05.offmon_ver18
cd ~gxproj4/NERSC/2018.10.05.offmon_ver18
svn co

Configure the parameters for the launch

At this time the parameters used for a NERSC launch are specified in the script. This is slightly different for jobs run at JLab which use the script that reads the configuration from a separate file. At some point the NERSC system should be brought more into alignment with that, but for now, this is how it is.

Edit the file launch/ to adjust all of the settings at the top to be consistent with the current launch. All of the parameters are at the top of the file in a well marked section. Here is an explanation of the parameters:

Parameter Description
TESTMODE Set this to "True" so the script can be tested without actually submitting any jobs. When finally ready to actually submit jobs to swif2, set it to "False"
VERBOSE Default is 1. Set to zero for minimal messages or 3 for all messages
RUNPERIOD e.g. "2018-01"
LAUNCHTYPE either "offmon" or "recon"
VER Version of this particular type of launch
WORKFLOW This will be set automatically based on other values. Only change this if there default name is not appropriate
NAME Similar to above, this is automatically set. It is used to set the job names.
RCDB_QUERY If specific runs are not set in RUNS (see below) then this is used to query the RCDB for runs in the specified range that should be processed.
RUNS Normally this is set to an empty array and the list of runs obtained from the RCDB. This can be set to a specific run list and only those will be processed.
MINRUN If RUNS is an empty set, this is used along with MAXRUN and RCDB_QUERY to extract the list of runs to process from the RCDB. Note that this should be in a range consistent with RUNPERIOD. No check is made in this script that ensures this otherwise.
MINFILENO Minimum file number to process for each run. Normally this is set to 0. See MAXFILENO below for more details.
MAXFILENO Maximum file number to process for each run. If doing a monitoring launch then this would normally be set to 4 so that files 000-004 are processed. Set this to a large number like 10000 to process all files in each run. The RCDB will be queried for each run to so that only files that actually exist in the specified range are submitted as jobs.
MAX_CONCURRENT_JOBS This is a limit set on the swif2 workflow for how many jobs can be in-flight at once. This can only be specified when the workflow is created. If the workflow was created outside of this script then this will do nothing.
PROJECT The NERSC project. Use 'm3120' for the GlueX allocation
TIMELIMIT Maximum time job may run. If a job runs longer than this it will be killed. Keep in mind that jobs run on KNL take about 2.4 times as long to run as on Haswell. (See NODETYPE below.)
QOS Should be 'debug', 'regular', or 'premium'. Usually you will just want 'regular'
NODETYPE 'haswell' or 'knl'. Jobs will take about 2.4 times longer to run on knl as haswell and the charge rate is 20% more per node hour. However, there are only 2k haswell nodes and 9k knl nodes and much more demand for haswell. Note that the setting of TIMELIMIT should be adjusted based on this.
IMAGE Shifter image. Actually, this is the same name as the Docker image used to create the Shifter image. Note that this image will need to already exist in Shifter since it will not be pulled in automatically. The image used up to now is 'docker:markito3/gluex_docker_devel'
RECONVERSION This the version of the reconstruction code that should be used. The executables will be read from CVMFS from a directory that mirrors the directory /group/halld/Software/builds/Linux_CentOS7-x86_64-gcc4.8.5-cntr. This value should be a directory relative to that such as: halld_recon/halld_recon-recon-ver03.2
SCRIPTFILE The script to run inside the container for the job. The container will mount the launch directory as /launch in the container so this should normally be set to '/launch/
CONFIG The jana config file to use. This is set automatically but can be overridden if really needed. As with the SCRIPTFILE, this should access the file via the launch directory mounted in the container as /launch
OUTPUTTOP Location on the JLab queue to copy files back to. Usually, this will start with mss:/mss/halld/ indicating a place on the tape system. This specifies the top-level directory and the script will specify the subdirectories where individual output files should be copied.
RCDB_HOST Were the script should access the RCDB to extract the run numbers to be used for this launch.
RCDB_USER User to connect to the RCDB as. (See RCDB_HOST above.)
RCDB This is used internally in the script and should always be set to None