The command activate python with RADICAL Cybertools, otherwise python does not recognize RCT e.g. EnTK.
source $HOME/simple_mdff/bin/activate
Conda works fine, if preferred. e.g. conda activate simple_mdff
The special script for Summit loads configuration files and start a workflow described by:
python simple_mdff.summit.py
The example output message on the screen is like:
EnTK session: re.session.login4.hrlee.018391.0000
Creating AppManagerSetting up RabbitMQ system ok
ok
Validating and assigning resource manager ok
Setting up RabbitMQ system n/a
new session: [re.session.login4.hrlee.018391.0000] \
database : [mongodb://rct:[email protected]/rct_test] ok
create pilot manager ok
submit 1 pilot(s)
[ornl.summit:336]
ok
All components created
create unit managerUpdate: simple-mdff state: SCHEDULING
Update: simple-mdff.Generating a simulated density map state: SCHEDULING
Update: simple-mdff.Generating a simulated density map.Starting to load the target PDB state: SCHEDULING
Update: simple-mdff.Generating a simulated density map.Starting to load the target PDB state: SCHEDULED
Update: simple-mdff.Generating a simulated density map state: SCHEDULED
...
It shows that one pilot job (here it is a EnTK workflow) is submitted to ornl.summit resource with 336 cpu cores (== 2 nodes, where 1 node has 168 cores by 42 physical cores * 4 hw threads), and the first stage is scheduled to start. The messages of the sebsequent stages are supressed but states are reported like SCHEDULED, EXECUTED, and DONE. If there was a problem executing the task, you may find FAILED with the stage/task name on your screen. Also note that this runs on foreground so the terminal needs to be active until a job finishes. tmux, screen, or nohup are recommended to avoid any interruption if a workflow runs very long time.
We also have tested XSEDE Bridges with the following script. Run it like:
python simple_mdff.py --resource xsede_bridges
If you remember your session id of your last run e.g. re.session.login4.hrlee.018391.0000, you will find raw output/results here on Summit:
$MEMBERWORK/[PROJECT ID]/radical.pilot.sandbox/[SESSION ID]/pilot.0000
for example with the session id above and project id csc393:
cd $MEMBERWORK/csc393/radical.pilot.sandbox/re.session.login4.hrlee.018391.0000/pilot.0000
$ ls -d uni*/
unit.000000/ unit.000001/ unit.000002/ unit.000003/ unit.000004/ unit.000005/ unit.000006/ unit.000007/ unit.000008/ unit.000009/
- VMD
- NAMD
- fftw (Summit)
- radical.entk
- pyaml
Necessary modules are loaded first before to use python and pip for installation.
module load python/3.7.0-anaconda3-5.3.0
module load py-virtualenv/16.0.0
module load python3
virtualenv $HOME/simple_mdff
source $HOME/simple_mdff/bin/activate
pip install radical.entk pyaml
Conda env also works fine.
A job submission with a number of CPUs/GPUs, computing expected duration, and project ID to consume allocation is defined in the yaml file, and multiple HPC platforms are supported, e.g. ORNL Summit, XSEDE Bridges.
ornl_summit: # key name to recognize resource, this is also used in the parameter of `simple_mdff.py`. This has to be identical to the key name used in the workflow yaml file.
label: 'ornl.summit' # Unique name to identify HPC platform, find a full list here: https://github.com/radical-cybertools/radical.pilot/blob/devel/examples/config.json
walltime: 30 # walltime in minute
cpus: 168 # the number of CPUs, and the number of nodes is calculated based on the cpu counts. For example, Summit provides 168 usable processes per node, and then 168 requires 1 node. 169+ requires 2+ nodes as well.
gpus: 0 # the number of GPUs, and the number of nodes is calculated based on the gpu counts. Upper bounds of CPUs/GPUs are used to calculate the number of nodes.
queue: 'batch' # system queue name which the job will be dispatched, Summit has `batch` and `killable` queues with different policies.
access_schema: 'local' # remote access method, there are `ssh`, `gsissh`, and `local`
project: 'CSC393' # project id to gain allocation
Simulation/analysis tasks have individual resource requirements such as cpu counts and a list of pre-executables.
ornl_summit:
simulation:
pre_exec: # list of commands prior to execute
- 'module load fftw/3.3.8' # new command can be added in a new line
cpus: 160
Workflow state and session data are exchanged by RabbitMQ and stored by MongoDB in RADICAL-Cybertools. The default values are provided but a local system can be used instead.
- cfg/resource_cfg.yml:
rabbitmq:
hostname: '129.114.17.233'
port: 33239
mongodb:
url: 'mongodb://rct:[email protected]:27017/rct_test'
129.114.17.233 is a temporal host IP address, radical-project.org will be back online soon.
The raw results of the experiments are stored on the following directory, experiments per HPC system.
Find the README for the details of :
- Q. Does an argument exist to specify the number of nodes in the resource file resource_cfg.yml?
- A. It does not have an argument for node counts but cpu counts. For example, you place 56 cpus on Bridges (56cpus = 2nodes; 28 each according to the document). For summit, 168 cpus indicate 1 node (2 sockets * 21 cpus * 4 hw threads) according to the document. For more number of nodes e.g. 4,8,16, … you can multiply cpu counts in the file.
If there are any issues/questions, please create a ticket in the EnTK repository
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