Base repository for art-based code
Running art
Generating documentation
Developing EMPHATICSoft Code
Get a ticket for access EMPHATIC computer:
Log into emphaticgpvm01.fnal.gov via kerberized ssh. If you have never used kerberos before, it is easy to install on most platforms (and usually most Linux- and unix-based OSs have this pre-installed). Replace the standard /etc/krb5.conf file with an appropriate file obtained from https://authentication.fnal.gov/krb5conf/.
kinit username@FNAL.GOV
klist
ssh -Y username@emphaticgpvm0X.fnal.govWhere "X" should be replaced with "1", "2" or "3", to login to one of emmphatic's three virtual machines.
If you are using Linux you need to include another flag:
ssh -K -Y username@emphaticgpvm0X.fnal.govNote to Mac users: add the following lines to your $HOME/.ssh/config file:
Host *.fnal.gov
Protocol 2
GSSAPIAuthentication yes
GSSAPIDelegateCredentials yes
ForwardAgent yes
ForwardX11 yes
ForwardX11Trusted yes
ServerAliveInterval 60 #For some users these lines need to be commented outMac users may sometimes need additional environment variable:
export KRB5CCNAME=FILE:/tmp/krb5cc_`id -u` You should add that export command to your bash login so you don't have to do it or remember it every time.
mkdir /exp/emph/app/users/[username]git clone https://github.com/EmphaticSoft/emphaticsoftYou will prompted to enter your github username and a password. The password should be your personal access token, which you should obtain by following the instructions here: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token.
source /exp/emph/app/users/[username]/<directory-you-chose>/emphaticsoft/setup/setup_emphatic.sh
sl7-emph
cd /exp/emph/app/users/[username]/<directory-you-chose>/
mkdir buildcd /exp/emph/app/users/[username]/<directory-you-chose>/build
source /exp/emph/app/users/[username]/<directory-you-chose>/emphaticsoft/ups/setup_for_development -p
Note: You must run this "source" command within the build directorybuildtool --generator=ninjaNote, once you've done this step, you can simply call "ninja" to compile changes.
Docker is a commercial software (free for now) that allows EMPHATIC to release the software we use, including all the dependencies and for users to run it on a variety of operating systems. Docker images of EMPHATIC software are made available via a networked file system provided by CERN, namely CVMFS.
/etc/cvmfs/default.local and add the following lines (you will likely need to edit this as root or use sudo):
CVMFS_REPOSITORIES=emphatic.opensciencegrid.org
CVMFS_HTTP_PROXY=DIRECTsudo mkdir -p /cvmfs/emphatic.opensciencegrid.org
sudo mkdir -p /cvmfs/fermilab.opensciencegrid.orgResources->File Sharing and add /cvmfs to the list, then click Apply & Restart. (Note: Adding /cvmfs to File Sharing is only needed if we put the image on cvmfs rather than just pulling it from DockerHub.)git clone https://github.com/EmphaticSoft/emphaticsoftmkdir build). Mounting this in the container will speed up the build process (after the first build).
sudo mount -t cvmfs emphatic.opensciencegrid.org /cvmfs/emphatic.opensciencegrid.org/
sudo mount -t cvmfs fermilab.opensciencegrid.org /cvmfs/fermilab.opensciencegrid.org/docker run --rm -it -v <path-to-your-local-repo>:/emphaticsoft -v /cvmfs:/cvmfs:cached -v <path-to-your-build-directory>:/build lackey32/emphaticsoft-sl7source emphaticsoft/setup/setup_emphatic.sh
cd build
source ../emphaticsoft/ups/setup_for_development -pTo compile the code:
for the first time (must be in the build directory):
buildtool --generator=ninjaany subsequent builds (still have to be in the build directory):
ninjaNow that you have build shared objects that could run under art, the real work can start, i.e., running art and your EMPHATIC shared objects to get some histograms that can be seen using root, or simple ASCII .csv files, that can be studied with any analysis tools you like. These intructions are valid if you are on emphaticgpvm0X.fnal.gov or your own machine. First, go to the build directory, and if you have not done so, execute the two setups mentioned above.
For instance, for the username lebrun, one has:
-bash-4.2$ cd /exp/emph/app/users/lebrun/build
-bash-4.2$ source ../emphaticsoft/setup/setup_emphatic.sh
Setting up emphatic UPS area... /cvmfs/emphatic.opensciencegrid.org/products/
-bash-4.2$ source ../emphaticsoft/ups/setup_for_development -p
The working build directory is /exp/emph/app/users/lebrun/build
The source code directory is /exp/emph/app/users/lebrun/emphaticsoft
---------------------- check this block for errors ---------------------
------------------------------------------------------------------------
To inspect build variable settings, execute /exp/emph/app/users/lebrun/build/cetpkg_info.sh
Please use "buildtool" to configure and build emphaticsoft, e.g.:
buildtool -I <ups-topdir> -vTl [-jN]
See "buildtool --usage" (short usage help) or "buildtool -h|--help"
(full help) for more details.The FHICL_FILE_PATH is an environmental variable which holds multipath, the first one being the one /exp/emph/app/users/lebrun/build/fcl, where our fcl files do reside. Then, art will find the top level (the one in the Unix command you invoke), and all the subsequent ones. Such that the command:
-bash-4.2$ art -c onmonprod_job.fcl /exp/emph/app/users/lebrun/data/emphdata_r466_s1.rootwill work..
Refer to docs
In order to make changes to EMPHATIC software, you will need to create your own git Branch. After you have pulled the emphaticsoft repository, you can create a new branch and switch to it by executing:
git branch <your_branch_name>
git checkout <your_branch_name>where you should change
When you create a branch, it will be a static copy of emphaticsoft at the time you created a branch. But in general, it is good practice to merge in changes that others make to the main branch so your branch does not fall far behind the main branch. You can do that by e.g.:
git checkout main
git pull
git checkout <your_branch_name>
git merge main
git push origin <your_branch_name>Once your changes are thoroughly tested and your are ready for them to go into the main branch, you should execute a pull request. To do this, first make sure your branch is up to date with changes from the main branch (see above), then go to the https://github.com/EMPHATICSoft/emphaticsoft/branches, find your branch, click the "new pull request" button next to your branch, and follow the resulting instructions to create a new pull request. You should then ask another EMPHATICsoft developer to review your changes. Contact Laura Fields, Jon Paley, and Gavin Davies if you aren't sure who should review it. Once that person has signed off on your code, you should then merge the pull request and delete your branch. Instructions here: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/merging-a-pull-request.
This section explains how to:
/exp/emph/app/users/dhuerta/) git_practice)git clone https://github.com/EmphaticSoft/emphaticsoft
emphaticsoft directory git checkout -b <new_branch_name>
git branch to see what branch we are in (* on side) and the other branches in that directory listed below git checkout <branch_name> to change between branchesgit add <1st_file_name> <2nd_file_name> .... to add as many new files to the main branch as you want
git push -u origin <branch_name>
git push git status to see the differences between the branch you are in and main at any point mkdir buildsource /exp/emph/app/users/<your_username>/git_practice/emphaticsoft/setup/setup_emphatic.shcd /exp/emph/app/users/<your_username>/git_practice/build ) source /exp/emph/app/users/<your_username>/git_practice/emphaticsoft/ups/setup_for_development -p buildtool --generator=ninja the first time and just ninja any time after that)
/exp/emph/app/users/<your_username>/git_practice/emphaticsoft git push
To merge your branch into main:
git checkout main to switch into the main branch git merge <branch_name> git add <file_to_merge> git push to make changes to the main branchTo merge main into your branch:
git checkout main to switch into the main branchgit pullgit checkout <branch_name>git merge maingit add <file_to_merge> git push to make changes to your branchCopyright © 2023 FERMI NATIONAL ACCELERATOR LABORATORY for the benefit of the EMPHATIC Collaboration.
This repository, and all software contained within, except where noted within the individual source files, is licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Copyright is granted to FERMI NATIONAL ACCELERATOR LABORATORY on behalf of the Experiment to Measure the Production of Hadrons At a Test beam In Chicagoland (EMPHATIC) experiment. Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.