Troubleshooting and diagnostics

Check network connectivity

sbgrid-cli check-connection

Provides network diagnostics for connectivity to SBGrid at Harvard Medical School.

$ sbgrid-cli check-connection
info: (1/1) Checking connection...
info: Checking services...
info: Checking sync2.sbgrid.org (port: 8080) ...
info: Checking sync2.sbgrid.org (port: 873) ...
info: Checking sync2.sbgrid.org (port: 27010) ...
info: Checking sbgrid.org (HTTPS) ...
info: Checking sbgrid.org (HTTP) ...
info: Connectivity test succeeded, all remote services are reachable

Diagnostics and tests

diag

Run troubleshooting and diagnostic tests for the software collection.

Verify configuration files

verify

Lists missing software versions and .rc files.

Install software for multiple platforms

On Linux, use the --darwin flag to install or remove software for macOS. On Linux, add the --darwin command to install / remove for macOS. Conversely, use the --linux flag to install or remove software for Linux while on macOS. These flags can be added to many of the subcommands to limit to Linux or macOS. Useful for servers that share a software stack over NFS.

sbgrid-cli list --darwin

This will list all software available for macOS. The platform flag (--linux or --darwin) is implied for the platform used to install the software, i.e. on Linux, --linux is redundant.

Logging

The platform flag (--linux or --darwin) is implied for the platform used to install the software. For example, on Linux, --linux is redundant.

Configuring a proxy

sbgrid-cli will use the HTTP_PROXY and/or HTTPS_PROXY environment variables if set. For example, adding

export HTTP_PROXY="http://my.example.proxy:3128"

will use the value above to make outbound http connections.

Software Version Management in the SBGrid environment

If you have a single version of an application installed, explicit version selection in your environment is not needed.

If multiple versions are installed, the SBGrid Default version will be available at the terminal unless configured otherwise in ~/.sbgrid.conf.

In the case of multiple non-default versions installed, the latest release will be version available in your shell. If you would like to have more than one version of a title installed, and prefer to use an older release or the non-default version when a default version is installed, you must set this explicitly in your ~/.sbgrid.conf file. This is the same as in the standard SBGrid environment.

Version priority in the shell

~/.sbgrid.conf
Installed single version
Installed Default version
Latest installed release

There is more info on how to manage versions here --> SBGrid version overrides

Running SBGrid software

To use the software at the terminal in bash, open a new terminal and run

source /programs/sbgrid.shrc

or in tcsh

source /programs/sbgrid.cshrc

For more info on system configuration for SBGrid software, please check here ---> Workstation setup.

Known Issues

rsync required on 873 or 8080. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available. You can check if you can access port 873 here and port 8080 here.

For help or to report issues, please email bugs@sbgrid.org.