Difference between revisions of "GlueX Offline FAQ"

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(What is the Volatile disk?)
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See http://scicomp.jlab.org/disk/volatile.faces for details of who has what space and how the space is managed.
See http://scicomp.jlab.org/disk/volatile.faces for details of who has what space and how the space is managed.
===What is the difference between /work/halld and /work/halld2?===
See the [https://mailman.jlab.org/pipermail/halld-offline/2015-November/002162.html email] announcing /work/halld2.
===Why does sudo not work for me?===
===Why does sudo not work for me?===

Revision as of 08:24, 6 November 2015

This is the GlueX Offline Frequently-Asked Questions list. If you cannot find an answer to your question, please send it to the Offline Software Coordinator (currently Mark Ito).



Where do I find information about GlueX software?

The best place is this wiki. The highest-level page dealing with software is the Offline Software page. The offline page is linked from the front page of the wiki at http://wiki.gluex.org .


How do I get an account on the wiki?

All members of the halld group at JLab can log into the wiki. Use your JLab CUE username and password.

How do I get privilege to check stuff into the Subversion repository?

Become a member of the halld unix group.

How do I get emails when files are checked into the Subversion repository? Stop the emails from coming?

If you look in the directory /group/halld/Repositories/svnroot/hooks there is a file called post-commit, with several backups. That is the file you need to change. If you look at it it is pretty clear what to do. People in the halld group should have privilege to modify it.

Note that you can "subscribe" to only a subset of check-ins as well, selection by directory.


How do I install a certificate in my browser so that I can view secure web sites at JLab (without creating a security exception)?

Go to http://www.jlab.org/PKI , select the browser you are using, and follow the instructions.

I cannot log into the ifarm machines. How do I get access?

You have to be member of the "halld" Unix group (or an analogous Unix group associated with one of the other experimental halls).

How do I become a member of the "halld" Unix group?

Ask the Software Coordinator to add you.

How do I subscribe to a GlueX email list?

There is a wiki page listing email lists of interest to GlueX collaboarators. To subscribe to any of them, click on the appropriate "information page".

How do I get personal web space at JLab?

The standard /home/username/public_html has been deprecated at the Lab as of August 2011. Another system has been set up on the /userweb partition. There is a HOWTO that explains the procedure for getting space there.

What is the Volatile disk?

We now have access to up to 40 TB of disk space on the "volatile" file system.

  • storage is temporary; there are scripts which run to delete old files
  • a quota system is enforced by the operation of these cleaning scripts
  • the system has two disk usage level triggers, called "quota" and "reservation", the former is a global maximum per group, the latter is used when the disk as a whole runs out of space (the sum of all quotas exceeds the available space, by design)
  • the system is explained at the bottom of the page referenced in Sandy's message

The /volatile partition is only available from the farm nodes at the Lab. This space is independent of our "work" space (/work/halld). Work space is not subject to deletion by scripts.

Two possible use cases for this space are (1) for staging files into and out of farm nodes and (2) for storage of data that are permanently stored elsewhere (e. g., on tape) for repeated analysis at the Lab.

There is a directory, /volatile/halld/home, for users to put their personal directories.

See http://scicomp.jlab.org/disk/volatile.faces for details of who has what space and how the space is managed.

What is the difference between /work/halld and /work/halld2?

See the email announcing /work/halld2.

Why does sudo not work for me?

At JLab, /apps/bin/sudo is configured for use by Computer Center personnel. It does not reference your local sudoers file. To use sudo locally, make sure you are using /usr/bin/sudo (i. e., check your PATH variable).

How do I kill all of my farm jobs?

jkill 0 will kill all farm jobs submitted by the logged in user, independent of the state of the jobs.


How do I resolve problem jobs so I can start the workflow going again?

You can use 'modify-jobs' if you want to retry them with altered cores/time/ram/disk. If you simply want to try again, use 'retry-jobs'. To just fail them, use 'abandon-jobs'.

If you want to put off thinking about it, you can up the error threshold to, say, 1000 by using 'swif run -workflow <> -errorlimit 1000'.


I have a build of sim-recon that I want to use. How do I set up my environment?

Source either the setenv.csh or the the setenv.sh that was created when sim-recon was built. For the details, see the setenv section of the wiki page Setting Up the GlueX Environment.

How do I get debug symbols in my sim-recon binary?

Debug symbols are put in by default by the SBMS system. You don't have to do anything.

How do I create EVIO data from an HDDM file produced by HDGeant?

hd_ana -PPLUGINS=rawevent file.hddm

How do I analyze a raw data file in EVIO format with DANA?

G.Vasileiadis 04/09/15 Added comment on DAQ, TTab plugins

hd_root -PPLUGINS=DAQ,TTab file.evio

Note: The DAQ and TTab plugins have been converted into statically linked libraries in sim-recon. This means you will no longer need to add them to your plugin list when running things like hd_ana, hd_root, hdview2, etc.


Where can I get help with Git?

See Git Help Resources on this wiki.

What are the basic git commands that I need to know?

  • git help: get a help message (e. g., git help clone)
  • git clone: get a complete copy of a repository
  • git status: show the status of your files (changed, added to index, etc.)
  • git checkout: change to another branch
  • git add: add modified files to the index
  • git commit: commit files in the index to your repository
  • git branch: show, create, delete branches
  • git tag: show, create, delete tags
  • git fetch: get remote repository information, do not change files
  • git pull: get changed files from remote repository
  • git push: write changed files to remote repository

What happens when I do a git clone?

When you clone a repository to your local disk, you get not only get the main line of code (in SVN: the trunk, in Git: the master branch), but all branches and tags and the history of all of the above. The directory that is created contains the actual files being controlled consistent with the master branch. In the top level directory there is a hidden directory, .git, that contains all of the versioning information. There are no .git directories in the subdirectories. You are meant to work with the files you see. You do not checkout the code to a separate directory as you do with SVN or CVS. The repository and the working files co-exist in the same tree.

What is a remote repository?

A remote repository is any repository outside of your repository that your repository is aware of. A network of remote repositories will have a common ancestor. When you clone a repository, your new repository is automatically aware if one remote repository: the repository from which it was cloned. The remote repository is called "origin" on your local repository by default. Remote repositories can be added and removed. They can be pushed to or pulled from. To see your remote repositories do a "git remote".

What is a tracking branch?

If you're on a tracking branch and type git push, Git automatically knows which server and branch to push to. Also, running git pull while on one of these branches fetches all the remote references and then automatically merges in the corresponding remote branch.

From http://stackoverflow.com/questions/4693588/git-what-is-a-tracking-branch

How do I create a tracking branch?

When branches are created using the --track option, they will be set up linked to the remote branch. For example, if you wanted to create a new branch from the master branch from the origin remote, using this would set it up so it would pull from the remote and branch automatically:

$ git branch --track feature1 origin/master

Branch feature1 set up to track remote branch refs/remotes/origin/master.

From http://gitready.com/beginner/2009/03/09/remote-tracking-branches.html

How do I make an existing branch track a remote branch?

As of Git 1.8.0:

git branch -u upstream/foo

Or, if local branch foo is not the current branch:

git branch -u upstream/foo foo

Or, if you like to type longer commands, these are equivalent to the above two:

git branch --set-upstream-to=upstream/foo
git branch --set-upstream-to=upstream/foo foo

As of Git 1.7.0:

git branch --set-upstream foo upstream/foo

All of the above commands will cause local branch foo to track remote branch foo from remote upstream. The old (1.7.x) syntax is deprecated in favor of the new (1.8+) syntax. The new syntax is intended to be more intuitive and easier to remember.

From http://stackoverflow.com/questions/520650/make-an-existing-git-branch-track-a-remote-branch

What is a topic branch?

A topic branch is a branch that is created, and possibly shared, to work on some particular issue. The name of the branch should be descriptive of the issue, of course. The concept emphasizes separation of work on one issue from work on others. One may have several topic branches going at the same time. The word "topic" is descriptive and has no operational significance.

What is the difference between Git and GitHub?

Git is the underlying software package that performs the direct operations on Git repositories. It is open source. As a software project, it is completely independent of GitHub. One can profitably run a project under Git without ever using a web browser.

GitHub is a commercial site that is in the business of hosting Git repositories and providing web tools for working with them. Jefferson Lab has a contract with GitHub to host repositories for doing Lab-related work. Public repositories are free; private repositories can potentially incur charges.

How do I get privilege to create pull requests on GitHub?

Find the instructions here.

Why is there no "git pull-request" command?

Generically, a pull request is any communication from one developer to another asking that changes on the one's branch be incorporated on the others remote branch via a "git pull". As your question implies, there is no native Git command for doing this.

On GitHub, there is a site-specific set of tools (web pages and web forms) for issuing pull requests which includes a conversation between developers on the proposed change. These tools work only for the case when the source and the target branch are both hosted on GitHub. The repositories need not be owned by the same account.

How are we notified of pull requests?

Those interested in acting on pull requests should "watch" the appropriate repository on GitHub. Go to settings/notification to configure how you are notified (email, website, or both). Then go to the repository page to mark the repository as being watched/not-watched/ignored by you.

What is the difference between a clone and a fork?

A fork is a clone from a GitHub-hosted repository to another GitHub-hosted repository. It is a GitHub-specific term.

What happens to forks when a repository is deleted or changes visibility?

When you delete a public repository, one of the existing public forks is chosen to be the new parent repository. All other repositories are forked off of this new parent and subsequent pull requests go to this new parent.

From https://help.github.com/articles/what-happens-to-forks-when-a-repository-is-deleted-or-changes-visibility/

What happens when I checkout another branch when there are uncommitted changes on the current branch?

If the new branch contains edits that are different from the current branch for that particular changed file, then it will not allow you to switch branches until the change is committed or stashed. If the changed file is the same on both branches (that is, the committed version of that file), then you can switch freely.

From http://stackoverflow.com/questions/22053757/git-checkout-another-branch-when-there-are-uncommitted-changes-on-the-current

I cannot clone a GitHub repository on the Gluon Cluster. What is the trick?

setenv HTTPS_PROXY https://jprox:8082


export HTTPS_PROXY=https://jprox:8082

I am getting a "403 Forbidden" error when trying to push to a GitHub repository from JLab. What is wrong?

You might be using an old version of git. On the JLab CUE or on the Gluon Cluster, use the version of git from /apps/bin and not the one in /usr/bin. (Version 1.7.1 has given problems; version seems OK. See https://help.github.com/articles/https-cloning-errors/). In addition the version of /apps/bin/git on the CentOS 6.2 farm nodes (e. g., ifarm62) gives error messages. It is not known if commands are executing correctly or not.

After a branch is deleted on GitHub, I still see it when I do a git branch -r on my local repository, even after a git fetch. How do I get rid of it?

git remote prune origin will remove all such stale branches.

From http://stackoverflow.com/questions/5094293/git-remote-branch-deleted-but-still-appears-in-branch-a

How do I get to the compare view on GitHub?

To get to the compare view, append /compare to your repository's path.


I plan to buy a computer to work on data analysis and simulation for Hall D. What version of Linux I should install?

  • CentOS 7 would be a good choice if you want something free and modern. It is not used at the lab much, but will be more and more. It is basically a free version of Red Hat Enterprise Linux 7.
  • CentOS 6 is free and is compatible with most of the machines at the Lab now.
  • Red Hat Enterprise 6 or 7 comes with support from Red Hat, is exactly what we run at the Lab, but it costs $300 a year to have them help you.
  • Ubuntu is very popular. It is a bit different from Red Hat though.
  • Fedora changes all the time so you get the latest stuff, but the problem is that it changes all the time.

--Mark Ito 15:09, 3 February 2015 (EST)