As of this writing, access to S3DF is still by invitation. You can self-register following instructions here.
This page gives a very brief introduction to SLAC's new S3DF (SLAC Shared Scientific Data Facility) cluster to help you get started. We assume you already have a Unix account and your main intent is to run the Fermitools/Fermipy. During the transition, issues are discussed in the #s3df-migration slack channel. You can also join the #help-sdf channel if you wish to see SLAC-wide discussion of S3DF issues.
See the main S3DF documentation for detailed information about how to log in, use the SLURM batch system, and so on. Specify --account fermi:users.
Basically, ssh to s3dflogin.slac.stanford.edu and from there ssh to fermi-devl (no .slac.stanford.edu; it is a load balancer, but there is only one node so far) to do actual interactive work. The login nodes are not meant for doing analysis or accessing data. Of course, real computational intensive tasks are meant for the batch system and not the interactive nodes either. Send email to s3df-help at slac.stanford.edu for issues.
passwordless ssh to fermi-devl
You can modify your .ssh config to allow direct passwordless access from your device to fermi-devl, by adding this to your .ssh/config file on your end:
Host slac* User <you> Host slacl Hostname s3dflogin.slac.stanford.edu Host slacd Hostname fermi-devl ProxyJump slacl
and then add your e.g. ~/.ssh/id_rsa.pub
from from your device to ~/.ssh/authorized_keys
at SLAC, using:
ssh-copy-id <you>@s3dflogin.slac.stanford.edu
.bash_profile
.bashrc:
- a directory gets added to your home dir, called profile_d. It points back to the group equivalent in /sdf/group/fermi/sw/ and includes the contents of those conf files into your session's bashrc. Group-level settings go there, eg $LATCalibRoot.
- don't overwrite your .bash_profile or you'll lose the code that does this:
# SLAC S3DF - source all files under ~/.profile.d
if [[ -e ~/.profile.d && -n "$(ls -A ~/.profile.d/)" ]]; then
source <(cat $(find -L ~/.profile.d -name '*.conf'))
fi
Disk space
- Your home directory is in weka (/sdf/home/<first letter of your userid>/<your userid>) with 30 GB of space. This space is backed up and is where code, etc., should go.
- We have group space at /sdf/group/fermi/:
- some directories are under /sdf/data/fermi/, but we provide links into the group directory tree for easier access
- includes shared software, including conda envs for Fermitools and containers for running rhel6 executables
- Fermi-supplied user (i.e., on top of your home directory) space.
- You can find it in /sdf/group/fermi/u/<you>. There is a symlink to it, called "fermi-user", in your home directory for convenience.
- after gpfs is retired in late 2023, this is where your larger user space will be.
- group space in /sdf/group/fermi/g/ - a one-time copy has been done of all the gpfs g/ directories, under /nfs/farm/g/glast/g/.
- all of glast afs has been copied to /sdf/group/fermi/a/
- the nfs u<xx> partitions were copied to /sdf/group/fermi/n/ (including u52 which contains the GlastRelease rhel6 builds)
- your user/group space on the old clusters is not directly accessible from s3df - it currently needs to be copied over. (this access policy may get reversed soon)
- We're still providing additional user space from the old cluster, available on request via the slac-helplist mailing list. It is not backed up. This space is natively gpfs. User directories are available under: /gpfs/slac/fermi/fs2/u/<your_dir>.
- During the transition, read-only mounts of afs and gpfs are available on the interactive nodes (not batch!).
- afs is just the normal afs path, eg to your home directory (/afs/slac/u/ ...) - you may need to issue "aklog" to get an afs token.
- gpfs is /fs/gpfs/slac/fermi/fs2/u/ ...
- Scratch space:
- /sdf/scratch/<username_initial>/<username>: quota 100GB/per user. The space is visible on all interactive and batch nodes. Old data will be purged when overall space is needed, even if your usages is under the quota
- /lscratch: On each batch node, this is a local space. It is shared by all users. You are encourage to create your own sub-dir when running your job, and clean up your space (to zero) at the end of your job. Debris left behind by jobs will be purged periodically. The size of the /lscratch are subject to change and please refer to the table in Slurm partition for info about their size.
Handy urls
- Fermi s3df accounts status
- fermi-user and groups usage/quotas
- fermi-devl server metrics
- slurm
- weka filesystem
Access to SDF files
If you were working on SDF, note that S3DF is completely separate (aside from the account name). Even though path names might look similar, they are on different file systems. You can still access all your SDF files by prepending "/fs/ddn/" to the paths you were used to.
Software and Containers
Fermitools and other analysis software (e.g., 3ML) are available via shared Conda installation, so you don't need to install Conda yourself. See Fermitools/Conda Shared Installation at SLAC. If you do want your own Conda, you shouldn't install it in your home directory due to quota limits; put it in your Fermi-supplied user space. Follow the S3DF documentation instructions to install Conda and set a prefix path for the Conda installation that will put it and any environments you create in your group-provided space. However, you should use a prefix to your personal space, e.g., /sdf/group/fermi/u/$USER/miniconda3, instead of the path in their example.
You can also run a RHEL6 Singularity container (for apps that are not portable to RHEL/Centos7). See Using RHEL6 Singularity Container.
Slurm Batch Usage
For generic advice on running in batch, see Running on SLAC Central Linux. Note that the actual batch system has changed and we have not updated the doc to reflect that. This is advice on copying data to local scratch, etc.
- LSB_JOBID -> SLURM_JOB_ID
- scratch space during job execution:
- at job start, a directory is automatically created on the scratch of the worker: ${LSCRATCH} = /lscratch/${USER}/slurm_job_id_${SLURM_JOB_ID}
- once all of a user's jobs on a node are completed/exited, their corresponding LSCRATCH directory on that host is deleted.
You need to specify an account and "repo" on your slurm submissions. The repos allow subdivision of our allocation to different uses. There are 4 repos available under the fermi account. The format is "–-account fermi:<repo>" where repo is one of:
- default (jobs are pre-emptible - if "paying jobs" need slots, pre-emptible jobs will be killed)
- L1
- other-pipelines
- users
L1 and other-pipelines are restricted to known pipelines. Non-default repos have quality of service (qos) defaulting to normal (non-pre-emptible).
At time of writing, there is no accounting yet. When that is enabled, we'll have to decide how to split up our allocation into the various repos.
S3DF Slurm organizes the different hardware resource type under Slurm partitions. Slurm doesn't have the concept of batch queue. Users can specify the resource their job needs (because, for example a 12-core CPU request can be satisfied by different types of CPUs). The following is an example script that submits a job to Slurm:
#!/bin/bash
#SBATCH --account=fermi:users
##SBATCH --partition=ampere
#SBATCH --job-name=my_first_job
#SBATCH --output=output-%j.txt
#SBATCH --error=output-%j.txt
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=4g
#SBATCH --time=0-00:10:00
#SBATCH --gpus a100:1
hostname
Note that the specifying "--gpus a100:1" option is preferred over the specifying "–partition=ampere" (the latter is not needed). If GPU is not requested, you job will not have access to a GPU even if it is landed on an ampere node.
Using cron
You can run cronjobs in S3DF. Users don't have to worry about token expiration like on AFS. Select one of the iana interactive nodes (and remember which one!) to run on.
Note: crontab does NOT inherit your environment. You'll need to set that up yourself.
Since crontab is per host (no trscrontab), if the node is reinstalled or removed, the crontab will be lost. It's probably best to save your crontab as a file in your home directory so that you can re-add your cronjobs if this happens:
crontab -l > ~/crontab.backup
Then to re-add the jobs back in:
crontab ~/crontab.backup
command line xrootd access
xrootd CLI commands are available via cvmfs:
module load osg/client-latest
which xrdcp
module unload osg/client-latest #when done with xrootd
Oracle access
Oracle drivers etc have been installed in /sdf/group/fermi/sw/oracle/. The setup.sh file in the driver-version directory sets up everything needed to issue sqlplus commands from the command line.
Using Datacat & Pipeline-II
/sdf/home/g/glast/a/datacat/prod/datacat
/sdf/home/g/glast/a/pipeline-II/prod/pipeline
cvs access
For now, we are leaving the live cvs repo on nfs. The cvs client has been installed on the iana nodes.
Set:
CVSROOT=:ext:$<USER>@centaurusa.slac.stanford.edu:/nfs/slac/g/glast/ground/cvs