Using the lsst-dev Server

lsst-dev is the development cluster of servers run by NCSA for LSST DM development work. The cname lsst-dev.ncsa.illinois.edu directs to lsst-dev01.ncsa.illinois.edu and this system serves as the primary development server for the team. There are currently 3 identical development servers to choose from:

• lsst-dev01.ncsa.illinois.edu
• lsst-dev02.ncsa.illinois.edu
• lsst-dev03.ncsa.illinois.edu

To get an account, see the Onboarding Checklist.

This page is designed to assist developers in their work on the lsst-dev servers:

1. Overview of Cluster Resources
2. Account Password
3. Set up SSH Keys
4. Select Appropriate Developer Tools
5. Load the LSST Environment
6. Validation/Test Data Sets
7. Configure Git LFS
8. Configure Remote Display with xpra

Overview of Cluster Resources

• List of available development servers and their intended use.
• Service status including announcements of upcoming planned down-time.
• Real-time system status (requires login).
• All of the lsst-dev systems have access to the GPFS Directory Spaces, including:
  • Reference/test data from SDSS DR7 for Stripe82, which is located at /datasets/sdss/preprocessed/dr7.
  • Several other datasets available in /datasets. See README files in each dataset.
• To report system issues, file a JIRA ticket in the IT Helpdesk Support (IHS) project.

Account Password

You can log into LSST development servers at NCSA with your NCSA account and password. You can reset your NCSA password at the following URL:

• https://identity.lsst.org/reset

Set up SSH Keys

You can establish public/private keys to access NCSA development machines via SSH. Here’s how to set up your SSH client to use keys:

1. Generate a key pair

If you haven’t already, generate your key pair on your local machine (you should always use a strong password for your passphrase). On most machines, you can use OpenSSH:

mkdir ~/.ssh
chmod 700 ~/.ssh
ssh-keygen -t rsa

Enter your passphrase at the prompts:

Generating public/private rsa key pair.
Enter file in which to save the key (/home/username/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/username/.ssh/id_rsa.
Your public key has been saved in /home/username/.ssh/id_rsa.pub.
The key fingerprint is:
a1:b2:c3:45:67:89:d1:e2:f3:54:76:98:00:aa:bb:01 username@hostname.lsstcorp.org

Note

If you used a program other than OpenSSH for this step, make sure your public key is formatted as a single line (most SSH clients provide it as an option). Otherwise, the next step will not work.

2. Install the public key on lsst-dev01

Install the public key on the remote server, ~/.ssh/id_rsa.pub, to lsst-dev01.ncsa.illinois.edu:

scp .ssh/id_rsa.pub lsst-dev01.ncsa.illinois.edu:mymachine_rsa.pub
ssh lsst-dev01.ncsa.illinois.edu

On lsst-dev01.ncsa.illinois.edu:

touch ~/.ssh/authorized_keys
chmod 600 ~/.ssh/authorized_keys
cat mydevmachine_rsa.pub >> ~/.ssh/authorized_keys
exit

3. Login

Login without a password to lsst-dev01:

ssh lsst-dev01.ncsa.illinois.edu
Enter passphrase for key '/home/username/.ssh/id_rsa': # type your key passphrase

For more information on using SSH public/private keys:

• SSH Keygen Wikipedia Article
• OpenSSH Public and Private Keys (from Ubuntu)
• Using SSH Public Key Authentication
• SSH Public Key Based Authentication Howto

Select Appropriate Developer Tools

The lsst-dev systems are configured with the latest CentOS 7.x as its operating system. This release of CentOS provides an old set of development tools, centered around version 4.8.5 of the GNU Compiler Collection (GCC). Updated toolchains are made available through the “Software Collection” system. The following Software Collections are currently available:

Name	Description
devtoolset-3	Updated compiler toolchain providing GCC 4.9.2.
devtoolset-4	Updated compiler toolchain providing GCC 5.3.1.
devtoolset-6	Updated compiler toolchain providing GCC 6.3.1.
devtoolset-7	Updated compiler toolchain providing GCC 7.1.1.
git19	The Git version control system version 1.9.4.
rh-git29	The Git version control system version 2.9.3.

To enable a particular Software Collection use the scl command. For example:

scl enable devtoolset-6 bash
gcc --version
gcc (GCC) 6.3.1 20170216 (Red Hat 6.3.1-3)
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Warning

Code compiled by different versions of GCC may not be compatible: it is generally better to stick to a particular toolchain for a given project. In particular, if you are using a shared stack you must use the matching toolchain.

You may wish to automatically enable a particular software collection every time you log in to lsst-dev01 and other LSST systems. Take care if you do this: it’s easy to accidentally to either start recursively spawning shells and run out of resources or lock yourself out of machines which don’t have the particular collection you’re interested in installed. If you are using Bash — the default shell on lsst-dev servers — try placing the following at the end of ~/.bash_profile and customising the list of desired_scls.

# User-specified space-delimited list of SCLs to enable.
desired_scls="rh-git29 devtoolset-6"

# Only do anything if /usr/bin/scl is executable.
if [ -x /usr/bin/scl ]; then

    # Select the union of the user's desired SCLs with those which are both
    # available and not currently enabled.
    avail_scls=$(scl --list)
    for scl in $desired_scls; do
        if [[ $avail_scls =~ $scl && ! $X_SCLS =~ $scl ]]; then
            scls[${#scls[@]}]=$scl
        fi
    done

    # Use `tty -s` to output messages only if connected to a terminal;
    # avoids causing problems for non-interactive sessions.
    if [ ${#scls[@]} != 0 ]; then
        tty -s && echo "Enabling ${scls[@]}."
        exec scl enable ${scls[@]} bash
    else
        tty -s && echo "No software collections to enable."
    fi
fi

Load the LSST Environment

We provide a ready-to-use “shared” version of the LSST software stack to enable developers to get up and running quickly with no installation step. The shared stack includes a fully-fledged Miniconda-based Python environment, a selection of additional development tools, and a selection of builds of the lsst_distrib meta-package. It is located on GPFS-based network storage; as such, it is cross-mounted across a variety of LSST systems at the Data Facility including those configured as part of the HTCondor pool and Verification Cluster. The currently stack is regularly updated to include the latest weekly release, which is tagged as current.

The following stacks are currently being updated:

Path	Toolchain	Description
/software/lsstsw/stack_20190330	devtoolset-6	Provides weekly w_2019_12 and later. Based on the post-RFC-584 Conda environment.

The following stacks are not currently being updated, but remain available.

Note

When using a shared stack, you must use the corresponding developer toolchain. See above for details on how to Select Appropriate Developer Tools.

In addition, the following symbolic links point to particular versions of the stack:

Path	Description
/software/lsstsw/stack	The latest version of the stack.

Add a shared stack to your environment and set up the latest build of the LSST applications by running, for example:

source /software/lsstsw/stack/loadLSST.bash
setup lsst_apps

(substitute loadLSST.csh, loadLSST.ksh or loadLSST.zsh, depending on your preferred shell).

Tip

Initializing the stack will prepend the string (lsst-scipipe) to your prompt. If you wish, you can disable this by running

conda config --set changeps1 false

Although the latest weeklies of LSST software are regularly installed into the shared stacks, the rest of their contents is held fixed (to avoid API or ABI incompatibilities with old stack builds). We therefore periodically retire old stacks and replace them with new ones. The following retired stacks are currently available:

Path	Toolchain	Description
/software/lsstsw/stack_20171023	devtoolset-6	Provides a selection of weekly and release builds dating between October 2017 and October 2018.
/software/lsstsw/stack_20181012	devtoolset-6	Provides weeklies w_2018_41 through w_2019_12; release candidates v17_0_rc1, v17_0_rc2, and v17_0_1_rc1; and releases v_17_0 and v_17_0_1. Based on the pre-RFC-584 Conda environment.

Administrators may wish to note that the shared stack is automatically updated using the script ~lsstsw/shared-stack/shared_stack.py, which is executed nightly by Cron.

Validation/Test Data Sets

There are two cron jobs that will update a set of validation data repositories and test data repositories. These updates will trigger overnight on the lsst-dev system. In most cases, this will be a fairly straightforward git pull, but if corruption is detected, the repository will be cloned afresh. The verification data are currently being used primarily by validate_drp to measure various metrics on the reduced data. The test data serve a variety of purposes, but generally are included via a setupOptional in a package table file.

Test data location is: /project/shared/data/test_data

Included test data repositories are:

testdata_jointcal
testdata_cfht
testdata_subaru
testdata_decam
testdata_lsst
ap_verify_testdata
ap_pipe_testdata
ci_hsc
afwdata

Validation data location is: /project/shared/data/validation_data

Included validation data repositories are:

validation_data_hsc
validation_data_decam
validation_data_cfht

These are maintained by the lsstsw user (this is the same user that curates the shared stack on the lsst-dev system). Please ask in the #dm-infrastructure Slack channel in case of problems.

Configure Git LFS

After you have initialized a shared stack, you can enable Git LFS using EUPS:

setup git_lfs

The first time you use Git LFS you’ll need to configure it by following these steps from DM’s Git LFS guide:

1. Basic configuration
2. Configuring Git LFS

Configure Remote Display with xpra

xpra can be thought of as “screen for X” and offers advantages over VNC. It can be very handy and efficient for remote display to your machine from the LSST cluster (e.g., debugging with ds9) because it is much faster than a regular X connection when you don’t have a lot of bandwidth (e.g., working remotely), and it saves state between connections. Here’s how to use it:

On lsst-dev01:

xpra start :10
export DISPLAY=:10

You may have to choose a different display number (>10) if :10 is already in use.

On your local machine, do:

xpra attach ssh:lsst-dev01.ncsa.illinois.edu:10

You may leave that running, or put it in the background and later use:

xpra detach

Then you can open windows on lsst-dev01 (with DISPLAY=:10) and they will appear on your machine. If you now kill the xpra attach on your machine, you’ll lose those windows. When you reattach, they’ll reappear.

Note

xpra requires the use of Python 2.

If you are using a Python 3 LSST Stack, you’ll encounter a error like the following:

[...]
File "/ssd/lsstsw/stack3_20171021/stack/miniconda3-4.3.21-10a4fa6/Linux64/pyyaml/3.11.lsst2/lib/python/yaml/__init__.py", line 284
  class YAMLObject(metaclass=YAMLObjectMetaclass):
                            ^
SyntaxError: invalid syntax

The solution in this case is to start xpra in a separate shell where you haven’t yet setup the Python 3 LSST Stack.