Besides post-processing tools and a programmatic interface to generate input files, AbiPy also provides a pythonic API to execute small Abinit tasks directly or submit calculations on supercomputing clusters. This section discusses how to create the configuration files required to interface AbiPy with Abinit.

We assume that Abinit is already available on your machine and that you know how to configure your environment so that the operating system can load and execute Abinit. In other words, we assume that you know how to set the $PATH and $LD_LIBRARY_PATH ($DYLD_LIBRARY_PATH on Mac) environment variables, load modules with module load, run MPI applications with mpirun, etc. Important Please make sure that you can execute Abinit interactively with simple input files and that it works as expected before proceeding with the rest of the tutorial. It’s also a very good idea to run the Abinit test suite with the runtest.py script before running production calculations. Tip A pre-compiled sequential version of Abinit for Linux and OSx can be installed directly from the abinit-channel on the anaconda cloud with: conda install abinit --channel abinit  ## How to configure the TaskManager¶ The TaskManager takes care of task submission. This includes the creation of the submission script, the initialization of the environment as well as the optimization of the parallel algorithms (number of MPI processes, number of OpenMP threads, automatic parallelization with Abinit autoparal feature). AbiPy obtains the information needed to create the correct TaskManager for a specific cluster (personal computer) from the manager.yml configuration file. The file is written in YAML a human-readable data serialization language commonly used for configuration files (a good introduction to the YAML syntax can be found here. See also this reference card) By default, AbiPy looks for a manager.yml file in the current working directory i.e. the directory in which you execute your script in first and then inside $HOME/.abinit/abipy. If no file is found, the code aborts immediately.

An important piece of information for the TaskManager is the type of queueing system available on the cluster, the list of queues and their specifications. In AbiPy queueing systems or resource managers are supported via quadapters. At the time of writing (Feb 22, 2020), AbiPy provides qadapters for the following resource managers:

Manager configuration files for typical cases are available inside ~abipy/data/managers.

We first discuss how to configure AbiPy on a personal computer and then we look at the more complicated case in which the calculation must be submitted to a queue.

## TaskManager for a personal computer¶

Let’s start from the simplest case i.e. a personal computer in which we can execute applications directly from the shell (qtype: shell). In this case, the configuration file is relatively easy because we can run Abinit directly without having to generate and submit a script to the resource manager. In its simplest form, the manager.yml file consists of a list of qadapters:

qadapters:


Each item in the qadapters list is essentially a YAML dictionary with the following sub-dictionaries:

queue

Dictionary with the name of the queue and optional parameters used to build and customize the header of the submission script.

job

Dictionary with the options used to prepare the environment before submitting the job.

limits

Dictionary with the constraints that must be fulfilled in order to run with this qadapter.

hardware

Dictionary with information on the hardware available on this particular queue. Used by Abinit autoparal to optimize parallel execution.

The qadapter is therefore responsible for all interactions with a specific queue management system (shell, Slurm, PBS, etc), including handling all details of queue script format as well as queue submission and management.

Note

Multiple qadapters are useful if you are running on a cluster with different queues but we post-pone the discussion of this rather technical point. For the time being, we use a manager.yml with a single adapter.

A typical configuration file used on a laptop to run jobs via the shell is:

qadapters: # List of qadapters objects  (just one in this simplified example)

-  priority: 1
queue:
qtype: shell        # "Submit" jobs via the shell.
qname: localhost    # "Submit" to the localhost queue
# (it's a fake queue in this case)

job:
pre_run: "export PATH=$HOME/git_repos/abinit/build_gcc/src/98_main:$PATH"
mpi_runner: "mpirun"

limits:
timelimit: 1:00:00   #  Time-limit for each task.
max_cores: 2         #  Max number of cores that can be used by a single task.

hardware:
num_nodes: 1
sockets_per_node: 1
cores_per_socket: 2
mem_per_node: 4 Gb


The job section is the most critical one, in particular the pre_run option that will be executed by the shell script before invoking Abinit. In this case Abinit is not installed by default (the executable is not already in the path). The directory where the Abinit executables are located hence have to be prepended to the original $PATH variable. Change pre_run according to your Abinit installation and make sure that mpirun is also in $PATH. If you don’t use a parallel version of Abinit, just set mpi_runner: null (null is the YAML version of the Python None). Note this approach also allows you to safely use multiple versions.

Copy this example and change the entries in the hardware and the limits section according to your machine, in particular make sure that max_cores is not greater than the number of physical cores available on your personal computer. Save the file in the current working directory and run the abicheck.py script provided by AbiPy. If everything is configured properly, you should see something like this in the terminal.

$abicheck.py --no-colors AbiPy Manager: [Qadapter 0] ShellAdapter:gmac Hardware: num_nodes: 1, sockets_per_node: 1, cores_per_socket: 2, mem_per_node 4096, Qadapter selected: 0 Abinitbuild: Abinit Build Information: Abinit version: 9.0.0 MPI: True, MPI-IO: True, OpenMP: False Netcdf: True Abipy Scheduler: PyFlowScheduler, Pid: 54070 Scheduler options: {'weeks': 0, 'days': 0, 'hours': 0, 'minutes': 0, 'seconds': 2} Installed packages: Package Version -------------- --------- system Darwin python_version 3.7.0 numpy 1.18.1 scipy 1.3.1 netCDF4 1.5.1.2 apscheduler 2.1.0 pydispatch 2.0.5 yaml 5.3 pymatgen 2020.1.28 Abipy requirements are properly configured  This message tells us that everything is in place and we can finally run our first calculation. The directory ~abipy/data/runs contains python scripts to generate workflows for typical ab-initio calculations. Here we focus on the configuration of the manager and the execution of the flow so we don’t discuss how to generate input files and create Flow objects in python. This topic is covered in more detail in our collection of jupyter notebooks Let’s start from the simplest example i.e. the run_si_ebands.py script that generates a flow to compute the band structure of silicon at the Kohn-Sham level (GS calculation to get the density followed by a NSCF run along a k-path in the first Brillouin zone). Cd to ~abipy/data/runs and execute run_si_ebands.py to generate the flow: cd ~abipy/data/runs ./run_si_ebands.py  At this point, you should have a directory flow_si_ebands with the following structure: tree flow_si_ebands/ flow_si_ebands/ ├── __AbinitFlow__.pickle ├── indata ├── outdata ├── tmpdata └── w0 ├── indata ├── outdata ├── t0 │ ├── indata │ ├── job.sh │ ├── outdata │ ├── run.abi │ ├── run.files │ └── tmpdata ├── t1 │ ├── indata │ ├── job.sh │ ├── outdata │ ├── run.abi │ ├── run.files │ └── tmpdata └── tmpdata 15 directories, 7 files  w0/ is the directory containing the input files of the first workflow (well, we have only one workflow in our example). w0/t0/ and w0/t1/ contain the input files need to run the SCF and the NSC run, respectively. You might have noticed that each task directory (w0/t0, w0/t1) presents the same structure: • run.abi: Abinit input file. • run.files: Abinit files file. • job.sh: Submission/shell script. • outdata: Directory with output data files. • indata: Directory with input data files. • tmpdata: Directory with temporary files. Danger __AbinitFlow__.pickle is the pickle file used to save the status of the Flow. Don’t touch it! The job.sh script has been generated by the TaskManager using the information provided by manager.yml. In this case it is a simple shell script that executes the code directly as we are using qtype: shell. The script will get more complicated when we start to submit jobs on a cluster with a resource manager. We usually interact with the AbiPy flow via the abirun.py script whose syntax is: abirun.py FLOWDIR command [options]  where FLOWDIR is the directory containing the flow and command defines the action to perform (use abirun.py --help to get the list of possible commands). abirun.py reconstructs the python Flow from the pickle file __AbinitFlow__.pickle located in FLOWDIR and invokes the methods of the object depending on the options passed via the command line. Use: abirun.py flow_si_ebands status  to get a summary with the status of the different tasks and: abirun.py flow_si_ebands deps  to print the dependencies of the tasks in textual format. <ScfTask, node_id=75244, workdir=flow_si_ebands/w0/t0> <NscfTask, node_id=75245, workdir=flow_si_ebands/w0/t1> +--<ScfTask, node_id=75244, workdir=flow_si_ebands/w0/t0>  Tip Alternatively one can use abirun.py flow_si_ebands networkx to visualize the connections with the networkx package. In this case, we have a flow with one work (w0) that contains two tasks. The second task (w0/t1) depends on first one that is a ScfTask, more specifically w0/t1 depends on the density file produced by w0/t0. This means that w0/t1 cannot be executed/submitted until we have completed the first task. AbiPy is aware of this dependency and will use this information to manage the submission/execution of our flow. There are two commands that can be used to launch tasks: single and rapid. The single command executes the first task in the flow that is in the READY state that is a task whose dependencies have been fulfilled. rapid, on the other hand, submits all tasks of the flow that are in the READY state. Let’s try to run the flow with the rapid command… abirun.py flow_si_ebands rapid Running on gmac2 -- system Darwin -- Python 2.7.12 -- abirun-0.1.0 Number of tasks launched: 1 Work #0: <BandStructureWork, node_id=75239, workdir=flow_si_ebands/w0>, Finalized=False +--------+-------------+-----------------+--------------+------------+----------+-----------------+----------+-----------+ | Task | Status | Queue | MPI|Omp|Gb | Warn|Com | Class | Sub|Rest|Corr | Time | Node_ID | +========+=============+=================+==============+============+==========+=================+==========+===========+ | w0_t0 | Submitted | 71573@localhost | 2| 1|2.0 | 1| 0 | ScfTask | (1, 0, 0) | 0:00:00Q | 75240 | +--------+-------------+-----------------+--------------+------------+----------+-----------------+----------+-----------+ | w0_t1 | Initialized | None | 1| 1|2.0 | NA|NA | NscfTask | (0, 0, 0) | None | 75241 | +--------+-------------+-----------------+--------------+------------+----------+-----------------+----------+-----------+  What’s happening here? The rapid command tried to execute all tasks that are READY but since the second task depends on the first one only the first task gets submitted. Note that the SCF task (w0_t0) has been submitted with 2 MPI processes. Before submitting the task, indeed, AbiPy invokes Abinit to get all the possible parallel configurations compatible within the limits specified by the user (e.g. max_cores), select an “optimal” configuration according to some policy and then submit the task with the optimized parameters. At this point, there’s no other task that can be executed, the script exits and we have to wait for the SCF task before running the second part of the flow. At each iteration, abirun.py prints a table with the status of the different tasks. The meaning of the columns is as follows: Queue String in the form JobID @ QueueName where JobID is the process identifier if we are in the shell or the job ID assigned by the resource manager (e.g. slurm) if we are submitting to a queue. MPI Number of MPI processes used. This value is obtained automatically by calling Abinit in autoparal mode, cannot exceed max_ncpus. OMP Number of OpenMP threads. Gb Memory requested in Gb. Meaningless when qtype: shell. Warn Number of warning messages found in the log file. Com Number of comments found in the log file. Sub Number of submissions. It can be > 1 if AbiPy encounters a problem and resubmit the task with different parameters without performing any operation that can change the physics of the system). Rest Number of restarts. AbiPy can restart the job if convergence has not been reached. Corr Number of corrections performed by AbiPy to fix runtime errors. These operations can change the physics of the system. Time Time spent in the queue (if string ends with Q) or running time (if string ends with R). Node_ID Node identifier used by AbiPy to identify each node of the flow. Note When the submission is done through the shell there’s almost no difference between job submission and job execution. The scenario is completely different if you are submitting jobs to a resource manager because the task will get a priority value and will enter the queue. If you execute status again, you should see that the first task is completed. We can thus run rapid again to launch the abipy.flowtk.tasks.NscfTask. The second task won’t take long and if you issue status again, you should see that the entire flow completed successfully. To understand what happened in more detail, use the history command to get the list of operations performed by AbiPy on each task. abirun.py flow_si_ebands history ============================================================================================================================== =================================== <ScfTask, node_id=75244, workdir=flow_si_ebands/w0/t0> =================================== ============================================================================================================================== [Mon Mar 6 21:46:00 2017] Status changed to Ready. msg: Status set to Ready [Mon Mar 6 21:46:00 2017] Setting input variables: {'max_ncpus': 2, 'autoparal': 1} [Mon Mar 6 21:46:00 2017] Old values: {'max_ncpus': None, 'autoparal': None} [Mon Mar 6 21:46:00 2017] Setting input variables: {'npband': 1, 'bandpp': 1, 'npimage': 1, 'npspinor': 1, 'npfft': 1, 'npkpt': 2} [Mon Mar 6 21:46:00 2017] Old values: {'npband': None, 'npfft': None, 'npkpt': None, 'npimage': None, 'npspinor': None, 'bandpp': None} [Mon Mar 6 21:46:00 2017] Status changed to Initialized. msg: finished autoparallel run [Mon Mar 6 21:46:00 2017] Submitted with MPI=2, Omp=1, Memproc=2.0 [Gb] submitted to queue [Mon Mar 6 21:46:15 2017] Task completed status set to ok based on abiout [Mon Mar 6 21:46:15 2017] Finalized set to True ============================================================================================================================= ================================== <NscfTask, node_id=75245, workdir=flow_si_ebands/w0/t1> ================================== ============================================================================================================================= [Mon Mar 6 21:46:15 2017] Status changed to Ready. msg: Status set to Ready [Mon Mar 6 21:46:15 2017] Adding connecting vars {u'irdden': 1} [Mon Mar 6 21:46:15 2017] Setting input variables: {u'irdden': 1} [Mon Mar 6 21:46:15 2017] Old values: {u'irdden': None} [Mon Mar 6 21:46:15 2017] Setting input variables: {'max_ncpus': 2, 'autoparal': 1} [Mon Mar 6 21:46:15 2017] Old values: {'max_ncpus': None, 'autoparal': None} [Mon Mar 6 21:46:15 2017] Setting input variables: {'npband': 1, 'bandpp': 1, 'npimage': 1, 'npspinor': 1, 'npfft': 1, 'npkpt': 2} [Mon Mar 6 21:46:15 2017] Old values: {'npband': None, 'npfft': None, 'npkpt': None, 'npimage': None, 'npspinor': None, 'bandpp': None} [Mon Mar 6 21:46:15 2017] Status changed to Initialized. msg: finished autoparallel run [Mon Mar 6 21:46:15 2017] Submitted with MPI=2, Omp=1, Memproc=2.0 [Gb] submitted to queue [Mon Mar 6 21:49:48 2017] Task completed status set to ok based on abiout [Mon Mar 6 21:49:48 2017] Finalized set to True  A closer inspection of the logs reveal that before submitting the first task, python has executed Abinit in autoparal mode to get the list of possible parallel configuration and the calculation is then submitted. At this point, AbiPy starts to look at the output files produced by the task to understand what’s happening. When the first task completes, the status of the second task is automatically changed to READY, the irdden input variable is added to the input file of the second task and a symbolic link to the DEN file produced by w0/t0 is created in the indata directory of w0/t1. Another auto-parallel run is executed for the NSCF calculation and the second task is finally submitted. The command line interface is very flexible and sometimes it’s the only tool available. However, there are cases in which we would like to have a global view of what’s happening. The command: $ abirun.py flow_si_ebands notebook


generates a jupyter notebook with pre-defined python code that can be executed to get a graphical representation of the status of our flow inside a web browser (requires jupyter, nbformat and, obviously, a web browser).

Expert users may want to use:

$abirun.py flow_si_ebands ipython  to open the flow in the ipython shell to have direct access to the API provided by the flow. Once manager.yml is properly configured, it is possible to use the AbiPy objects to invoke Abinit and perform useful operations. For example, one can use the abipy.abio.inputs.AbinitInput object to get the list of k-points in the IBZ, the list of independent DFPT perturbations, the possible parallel configurations reported by autoparal etc. This programmatic interface can be used in scripts to facilitate the creation of input files and workflows. For example, one can call Abinit to get the list of perturbations for each q-point in the IBZ and then generate automatically all the input files for DFPT calculations (actually this is the approach used to generated DFPT workflows in the AbiPy factory functions). Note that manager.yml is also used to invoke other executables (anaddb, optic, mrgddb, etcetera) thus creating some sort of interface between the python language and the Fortran executables. Thanks to this interface, one can perform relatively simple ab-initio calculations directly in AbiPy. For instance one can open a DDB file in a jupyter notebook, call anaddb to compute the phonon frequencies and plot the DOS and the phonon band structure with matplotlib. Tip abirun.py . doc_manager gives the full documentation for the different entries of manager.yml. $ abirun.py . doc_manager

# TaskManager configuration file (YAML Format)

policy:
# Dictionary with options used to control the execution of the tasks.

# List of qadapters objects (mandatory)

db_connector:
# Connection to MongoDB database (optional)

# Adapter used to submit flows with batch script. (optional)

##########################################
# Individual entries are documented below:
##########################################

policy:
autoparal:                # (integer). 0 to disable the autoparal feature (DEFAULT: 1 i.e. autoparal is on)
condition:                # condition used to filter the autoparal configurations (Mongodb-like syntax).
# DEFAULT: empty i.e. ignored.
vars_condition:           # Condition used to filter the list of ABINIT variables reported by autoparal
# (Mongodb-like syntax). DEFAULT: empty i.e. ignored.
frozen_timeout:           # A job is considered frozen and its status is set to ERROR if no change to
# the output file has been done for frozen_timeout seconds. Accepts int with seconds or
# string in slurm form i.e. days-hours:minutes:seconds. DEFAULT: 1 hour.
precedence:               # Under development.
autoparal_priorities:     # Under development.

# Dictionary with info on the hardware available on this queue.
hardware:
num_nodes:           # Number of nodes available on this queue (integer, MANDATORY).
sockets_per_node:    # Number of sockets per node (integer, MANDATORY).
cores_per_socket:    # Number of cores per socket (integer, MANDATORY).
# The total number of cores available on this queue is
# num_nodes * sockets_per_node * cores_per_socket.

# Dictionary with the options used to prepare the enviroment before submitting the job
job:
setup:                # List of commands (strings) executed before running (DEFAULT: empty)
omp_env:              # Dictionary with OpenMP environment variables (DEFAULT: empty i.e. no OpenMP)
modules:              # List of modules to be imported before running the code (DEFAULT: empty).
# NB: Error messages produced by module load are redirected to mods.err
shell_env:            # Dictionary with shell environment variables.
mpi_runner:           # MPI runner. Possible values in ["mpirun", "mpiexec", "srun", None]
# DEFAULT: None i.e. no mpirunner is used.
mpi_runner_options    # String with optional options passed to the mpi_runner e.g. "--bind-to None"
shell_runner:         # Used for running small sequential jobs on the front-end. Set it to None
# if mpirun or mpiexec are not available on the fron-end. If not
# given, small sequential jobs are executed with mpi_runner.
shell_runner_options  # Similar to mpi_runner_options but for the runner used on the front-end.
pre_run:              # List of commands (strings) executed before the run (DEFAULT: empty)
post_run:             # List of commands (strings) executed after the run (DEFAULT: empty)

# dictionary with the name of the queue and optional parameters
# used to build/customize the header of the submission script.
queue:
qtype:                # String defining the qapapter type e.g. slurm, shell ...
qname:                # Name of the submission queue (string, MANDATORY)
qparams:              # Dictionary with values used to generate the header of the job script
# We use the *normalized* version of the options i.e dashes in the official name
# are replaced by underscores e.g. --mail-type becomes mail_type
# See pymatgen.io.abinit.qadapters.py for the list of supported values.
# Use qverbatim to pass additional options that are not included in the template.

# dictionary with the constraints that must be fulfilled in order to run on this queue.
limits:
min_cores:             # Minimum number of cores (integer, DEFAULT: 1)
max_cores:             # Maximum number of cores (integer, MANDATORY). Hard limit to hint_cores:
# it's the limit beyond which the scheduler will not accept the job (MANDATORY).
hint_cores:            # The limit used in the initial setup of jobs.
# Fix_Critical method may increase this number until max_cores is reached
min_mem_per_proc:      # Minimum memory per MPI process in Mb, units can be specified e.g. 1.4 Gb
# (DEFAULT: hardware.mem_per_core)
max_mem_per_proc:      # Maximum memory per MPI process in Mb, units can be specified e.g. 1.4Gb
# (DEFAULT: hardware.mem_per_node)
timelimit:             # Initial time-limit. Accepts time according to slurm-syntax i.e:
# "days-hours" or "days-hours:minutes" or "days-hours:minutes:seconds" or
# "minutes" or "minutes:seconds" or "hours:minutes:seconds",
timelimit_hard:        # The hard time-limit for this queue. Same format as timelimit.
# Error handlers could try to submit jobs with increased timelimit
# up to timelimit_hard. If not specified, timelimit_hard == timelimit
condition:             # MongoDB-like condition (DEFAULT: empty, i.e. not used)
allocation:            # String defining the policy used to select the optimal number of CPUs.
# possible values are in ["nodes", "force_nodes", "shared"]
# "nodes" means that we should try to allocate entire nodes if possible.
# This is a soft limit, in the sense that the qadapter may use a configuration
# that does not fulfill this requirement. In case of failure, it will try to use the
# smallest number of nodes compatible with the optimal configuration.
# Use force_nodes to enfore entire nodes allocation.
# shared mode does not enforce any constraint (DEFAULT: shared).
max_num_launches:      # Limit to the number of times a specific task can be restarted (integer, DEFAULT: 5)

qtype supported: ['bluegene', 'moab', 'pbspro', 'sge', 'shell', 'slurm', 'torque']
Use abirun.py . manager slurm to have the list of qparams for slurm.


## How to configure the scheduler¶

In the previous example, we ran a simple band structure calculation for silicon in a few seconds on a laptop but one might have more complicated flows requiring hours or even days to complete. For such cases, the single and rapid commands are not handy because we are supposed to monitor the evolution of the flow and re-run abirun.py when a new task is READY. In these cases, it is much easier to delegate all the repetitive work to a python scheduler, a process that runs in the background, submits tasks automatically and performs the actions required to complete the flow.

The parameters for the scheduler are declared in the YAML file scheduler.yml. Also in this case, AbiPy will look first in the working directory and then inside $HOME/.abinit/abipy. Create a scheduler.yml in the working directory by copying the example below: seconds: 5 # number of seconds to wait. #minutes: 0 # number of minutes to wait. #hours: 0 # number of hours to wait.  This file tells the scheduler to wake up every 5 seconds, inspect the status of the tasks in the flow and perform the actions required for reach completion Important Remember to set the time interval to a reasonable value. A small value leads to an increase of the submission rate but it also increases the CPU load and the pressure on the hardware and on the resource manager. A too large time interval can have a detrimental effect on the throughput, especially if you are submitting many small jobs. At this point, we are ready to run our first calculation with the scheduler. To make things more interesting, we execute a slightly more complicated flow that computes the G0W0 corrections to the direct band gap of silicon at the Gamma point. The flow consists of the following six tasks: • 0: Ground state calculation to get the density. • 1: NSCF calculation with several empty states. • 2: Calculation of the screening using the WFK produced by task 2. • 3-4-5: Evaluation of the Self-Energy matrix elements with different values of nband using the WFK produced by task 2 and the SCR file produced by task 3 Generate the flow with: ./run_si_g0w0.py  and let the scheduler manage the submission with: abirun.py flow_si_g0w0 scheduler  You should see the following output on the terminal abirun.py flow_si_ebands scheduler Abipy Scheduler: PyFlowScheduler, Pid: 72038 Scheduler options: {'seconds': 10, 'hours': 0, 'weeks': 0, 'minutes': 0, 'days': 0}  Pid is the process identifier associated the scheduler (also saved in in the _PyFlowScheduler.pid file). Important A _PyFlowScheduler.pid file in FLOWDIR means that there’s a scheduler running the flow. Note that there must be only one scheduler associated to a given flow. As you can easily understand the scheduler brings additional power to the AbiPy flow because it is possible to automate complicated ab-initio workflows with little effort: write a script that implements the flow in python and save it to disk, run it with abirun.py FLOWDIR scheduler and finally use the AbiPy/Pymatgen tools to analyze the final results. Even complicated convergence studies for G0W0 calculations can be implemented along these lines as shown by this video. The only problem is that at a certain point our flow will become too big or too computational expensive that cannot be executed on a personal computer anymore and we have to move to a supercomputing center. The next section discusses how to configure AbiPy to run on a cluster with a queue management system. Tip Use abirun.py . doc_scheduler to get the full list of options supported by the scheduler. $ abirun.py doc_scheduler
Options that can be specified in scheduler.yml:

weeks: number of weeks to wait (DEFAULT: 0).
days: number of days to wait (DEFAULT: 0).
hours: number of hours to wait (DEFAULT: 0).
minutes: number of minutes to wait (DEFAULT: 0).
seconds: number of seconds to wait (DEFAULT: 0).
mailto: The scheduler will send an email to mailto every remindme_s seconds.
(DEFAULT: None i.e. not used).
verbose: (int) verbosity level. (DEFAULT: 0)
use_dynamic_manager: "yes" if the |TaskManager| must be re-initialized from
file before launching the jobs. (DEFAULT: "no")
max_njobs_inqueue: Limit on the number of jobs that can be present in the queue. (DEFAULT: 200)
max_ncores_used: Maximum number of cores that can be used by the scheduler.
remindme_s: The scheduler will send an email to the user specified
by mailto every remindme_s seconds. (int, DEFAULT: 1 day).
max_num_pyexcs: The scheduler will exit if the number of python exceptions is > max_num_pyexcs
(int, DEFAULT: 0)
max_num_abierrs: The scheduler will exit if the number of errored tasks is > max_num_abierrs
(int, DEFAULT: 0)
safety_ratio: The scheduler will exits if the number of jobs launched becomes greater than
safety_ratio * total_number_of_tasks_in_flow. (int, DEFAULT: 5)
max_nlaunches: Maximum number of tasks launched in a single iteration of the scheduler.
(DEFAULT: -1 i.e. no limit)
debug: Debug level. Use 0 for production (int, DEFAULT: 0)
fix_qcritical: "yes" if the launcher should try to fix QCritical Errors (DEFAULT: "no")
rmflow: If "yes", the scheduler will remove the flow directory if the calculation
completed successfully. (DEFAULT: "no")
killjobs_if_errors: "yes" if the scheduler should try to kill all the runnnig jobs
before exiting due to an error. (DEFAULT: "yes")


## Configuring AbiPy on a cluster¶

In this section we discuss how to configure the manager to run flows on a cluster. The configuration depends on specific queue management system (Slurm, PBS, etc) hence we assume that you are already familiar with job submissions and you know the options that mush be specified in the submission script in order to have your job accepted and executed by the management system (username, name of the queue, memory …)

Let’s assume that our computing center uses slurm and our jobs must be submitted to the default_queue partition. In the best case, the system administrator of our cluster (or you create one yourself) already provides an Abinit module that can be loaded directly with module load before invoking the code. To make things a little bit more difficult, however, we assume the we had to compile our own version of Abinit inside the build directory ${HOME}/git_repos/abinit/build_impi using the following two modules already installed by the system administrator: compiler/intel/composerxe/2013_sp1.1.106 intelmpi  In this case, we have to be careful with the configuration of our environment because the Slurm submission script should load the modules and modify our $PATH so that our version of Abinit can be found. A manager.yml with a single qadapter looks like:

qadapters:
- priority: 1

queue:
qtype: slurm
qname: default_queue
qparams: # Slurm options added to job.sh
mail_type: FAIL
mail_user: john@doe

job:
modules:
- compiler/intel/composerxe/2013_sp1.1.106
- intelmpi
shell_env:
PATH: ${HOME}/git_repos/abinit/build_impi/src/98_main:$PATH
pre_run:
- ulimit -s unlimited
mpi_runner: mpirun

limits:
timelimit: 0:20:0
max_cores: 16
min_mem_per_proc: 1Gb

hardware:
num_nodes: 120
sockets_per_node: 2
cores_per_socket: 8
mem_per_node: 64Gb


Tip

abirun.py FLOWDIR doc_manager script

prints to screen the submission script that will be generated by AbiPy at runtime.

Let’s discuss the different options in more detail. Let’s start from the queue section:

qtype

String specifying the resource manager. This option tells AbiPy which qadapter to use to generate the submission script, submit them, kill jobs in the queue and how to interpret the other options passed by the user.

qname

Name of the submission queue (string, MANDATORY)

qparams

Dictionary with the parameters passed to the resource manager. We use the normalized version of the options i.e. dashes in the official name of the parameter are replaced by underscores e.g. --mail-type becomes mail_type. For the list of supported options use the doc_manager command. Use qverbatim to pass additional options that are not included in the template.

Note that we are not specifying the number of cores in qparams because AbiPy will find an appropriate value at run-time.

The job section is the most critical one because it defines how to configure the environment before executing the application and how to run the code. The modules entry specifies the list of modules to load, shell_env allows us to modify the $PATH environment variables so that the OS can find our Abinit executable. Important Various resource managers will first execute your .bashrc before starting to load the new modules. We also increase the size of the stack with ulimit before running the code and we run Abinit with the mpirun provided by the modules. The limits section defines the constraints that must be fulfilled in order to run on this queue while hardware is a dictionary with info on the hardware available on this queue. Every job will have a timelimit of 20 minutes, cannot use more that max_cores cores, and the first job submission will request 1 Gb of memory. Note that the actual number of cores will be determined at runtime by calling Abinit in autoparal mode to get all parallel configurations up to max_cores. If the job is killed due to insufficient memory, AbiPy will resubmit the task with increased resources and it will stop when it reaches the maximum amount given by mem_per_node. Note that there are more advances options supported by limits and other options will be added as time goes by. The get the complete list of options supported by the Slurm qadapter use: $ abirun.py . doc_manager slurm

# TaskManager configuration file (YAML Format)

policy:
# Dictionary with options used to control the execution of the tasks.

# List of qadapters objects (mandatory)

db_connector:
# Connection to MongoDB database (optional)

# Adapter used to submit flows with batch script. (optional)

##########################################
# Individual entries are documented below:
##########################################

policy:
autoparal:                # (integer). 0 to disable the autoparal feature (DEFAULT: 1 i.e. autoparal is on)
condition:                # condition used to filter the autoparal configurations (Mongodb-like syntax).
# DEFAULT: empty i.e. ignored.
vars_condition:           # Condition used to filter the list of ABINIT variables reported by autoparal
# (Mongodb-like syntax). DEFAULT: empty i.e. ignored.
frozen_timeout:           # A job is considered frozen and its status is set to ERROR if no change to
# the output file has been done for frozen_timeout seconds. Accepts int with seconds or
# string in slurm form i.e. days-hours:minutes:seconds. DEFAULT: 1 hour.
precedence:               # Under development.
autoparal_priorities:     # Under development.

# Dictionary with info on the hardware available on this queue.
hardware:
num_nodes:           # Number of nodes available on this queue (integer, MANDATORY).
sockets_per_node:    # Number of sockets per node (integer, MANDATORY).
cores_per_socket:    # Number of cores per socket (integer, MANDATORY).
# The total number of cores available on this queue is
# num_nodes * sockets_per_node * cores_per_socket.

# Dictionary with the options used to prepare the enviroment before submitting the job
job:
setup:                # List of commands (strings) executed before running (DEFAULT: empty)
omp_env:              # Dictionary with OpenMP environment variables (DEFAULT: empty i.e. no OpenMP)
modules:              # List of modules to be imported before running the code (DEFAULT: empty).
# NB: Error messages produced by module load are redirected to mods.err
shell_env:            # Dictionary with shell environment variables.
mpi_runner:           # MPI runner. Possible values in ["mpirun", "mpiexec", "srun", None]
# DEFAULT: None i.e. no mpirunner is used.
mpi_runner_options    # String with optional options passed to the mpi_runner e.g. "--bind-to None"
shell_runner:         # Used for running small sequential jobs on the front-end. Set it to None
# if mpirun or mpiexec are not available on the fron-end. If not
# given, small sequential jobs are executed with mpi_runner.
shell_runner_options  # Similar to mpi_runner_options but for the runner used on the front-end.
pre_run:              # List of commands (strings) executed before the run (DEFAULT: empty)
post_run:             # List of commands (strings) executed after the run (DEFAULT: empty)

# dictionary with the name of the queue and optional parameters
# used to build/customize the header of the submission script.
queue:
qtype:                # String defining the qapapter type e.g. slurm, shell ...
qname:                # Name of the submission queue (string, MANDATORY)
qparams:              # Dictionary with values used to generate the header of the job script
# We use the *normalized* version of the options i.e dashes in the official name
# are replaced by underscores e.g. --mail-type becomes mail_type
# See pymatgen.io.abinit.qadapters.py for the list of supported values.
# Use qverbatim to pass additional options that are not included in the template.

# dictionary with the constraints that must be fulfilled in order to run on this queue.
limits:
min_cores:             # Minimum number of cores (integer, DEFAULT: 1)
max_cores:             # Maximum number of cores (integer, MANDATORY). Hard limit to hint_cores:
# it's the limit beyond which the scheduler will not accept the job (MANDATORY).
hint_cores:            # The limit used in the initial setup of jobs.
# Fix_Critical method may increase this number until max_cores is reached
min_mem_per_proc:      # Minimum memory per MPI process in Mb, units can be specified e.g. 1.4 Gb
# (DEFAULT: hardware.mem_per_core)
max_mem_per_proc:      # Maximum memory per MPI process in Mb, units can be specified e.g. 1.4Gb
# (DEFAULT: hardware.mem_per_node)
timelimit:             # Initial time-limit. Accepts time according to slurm-syntax i.e:
# "days-hours" or "days-hours:minutes" or "days-hours:minutes:seconds" or
# "minutes" or "minutes:seconds" or "hours:minutes:seconds",
timelimit_hard:        # The hard time-limit for this queue. Same format as timelimit.
# Error handlers could try to submit jobs with increased timelimit
# up to timelimit_hard. If not specified, timelimit_hard == timelimit
condition:             # MongoDB-like condition (DEFAULT: empty, i.e. not used)
allocation:            # String defining the policy used to select the optimal number of CPUs.
# possible values are in ["nodes", "force_nodes", "shared"]
# "nodes" means that we should try to allocate entire nodes if possible.
# This is a soft limit, in the sense that the qadapter may use a configuration
# that does not fulfill this requirement. In case of failure, it will try to use the
# smallest number of nodes compatible with the optimal configuration.
# Use force_nodes to enfore entire nodes allocation.
# shared mode does not enforce any constraint (DEFAULT: shared).
max_num_launches:      # Limit to the number of times a specific task can be restarted (integer, DEFAULT: 5)

qtype supported: ['bluegene', 'moab', 'pbspro', 'sge', 'shell', 'slurm', 'torque']
Use abirun.py . manager slurm to have the list of qparams for slurm.

QPARAMS for slurm
#!/bin/bash

#SBATCH --partition=$${partition} #SBATCH --job-name=$${job_name}
#SBATCH --nodes=$${nodes} #SBATCH --total_tasks=$${total_tasks}
#SBATCH --ntasks=$${ntasks} #SBATCH --ntasks-per-node=$${ntasks_per_node}
#SBATCH --cpus-per-task=$${cpus_per_task} #####SBATCH --mem=$${mem}
#SBATCH --mem-per-cpu=$${mem_per_cpu} #SBATCH --hint=$${hint}
#SBATCH --time=$${time} #SBATCH --exclude=$${exclude_nodes}
#SBATCH --account=$${account} #SBATCH --mail-user=$${mail_user}
#SBATCH --mail-type=$${mail_type} #SBATCH --constraint=$${constraint}
#SBATCH --gres=$${gres} #SBATCH --requeue=$${requeue}
#SBATCH --nodelist=$${nodelist} #SBATCH --propagate=$${propagate}
#SBATCH --licenses=$${licenses} #SBATCH --output=$${_qout_path}
#SBATCH --error=$${_qerr_path} #SBATCH --qos=$${qos}
{qverbatim}


Important

If you need to cancel all tasks that have been submitted to the resource manager, use:

abirun.py FLOWDIR cancel


Note that the script will ask for confirmation before killing all the jobs belonging to the flow.

Once you have a manager.yml properly configured for your cluster, you can start to use the scheduler to automate job submission. Very likely your flows will require hours or even days to complete and, in principle, you should maintain an active connection to the machine in order to keep your scheduler alive (if your session expires, all subprocesses launched within your terminal, including the python scheduler, will be automatically killed). Fortunately there is a standard Unix tool called nohup that comes to our rescue.

For long-running jobs, we strongly suggest to start the scheduler with:

nohup abirun.py FLOWDIR scheduler > sched.stdout 2> sched.stderr &


This command executes the scheduler in background and redirects the stdout and stderr to sched.log and sched.err, respectively. The process identifier of the scheduler is saved in the _PyFlowScheduler.pid file inside FLOWDIR and this file is removed automatically when the scheduler completes its execution. Thanks to the nohup command, we can close our session, let the scheduler work overnight and reconnect the day after to collect our data.

Important

Use abirun.py FLOWDIR cancel to cancel the jobs of a flow that is being executed by a scheduler. AbiPy will detect that there is a scheduler already attached to the flow and will cancel the jobs of the flow and kill the scheduler as well.

## Inspecting the Flow¶

abirun.py also provides tools to analyze the results of the flow at runtime. The simplest command is:

abirun.py FLOWDIR tail


that is the analogous of Unix tail but a little bit more smarter in the sense that abirun.py will only print to screen the final part of the output files of the tasks that are RUNNING.

If you have matplotlib installed, you may want to use:

$abirun.py FLOWDIR inspect  Several AbiPy tasks, indeed, provide an inspect method producing matplotlib figures with data extracted from the output files. For example, a GsTask prints the evolution of the ground-state SCF cycle. The inspect command of abirun.py just loops over the tasks of the flow and calls the inspect method on each of them. The command: abirun.py FLOWDIR inputs  prints the input files of the different tasks (can use --nids to select a subset of tasks or, alternatively, replace FLOWDIR with the FLOWDIR/w0/t0 syntax) The command: abirun.py FLOWDIR listext EXTENSION  prints a table with the nodes of the flow who have produced an Abinit output file with the given extension. Use e.g.: abirun.py FLOWDIR listext GSR.nc  to show the nodes of the flow who have produced a GSR.nc file. The command: abirun.py FLOWDIR notebook  generates a jupyter notebook with pre-defined python code that can be executed to get a graphical representation of the status of the flow inside a web browser (requires jupyter, nbformat and, obviously, a web browser). Expert users may want to use: abirun.py FLOWDIR ipython  to open the flow in the ipython shell to have direct access to the API provided by the flow. ## Event handlers¶ An event handler is an action that is executed in response of a particular event. The AbiPy tasks are equipped with built-in events handlers that are be executed to fix typical Abinit runtime errors. To list the event handlers installed in a given flow use: abirun.py FLOWDIR handlers  The --verbose option produces a more detailed description of the action performed by the event handlers. abirun.py FLOWDIR handlers --verbose List of event handlers installed: event name = !DilatmxError event documentation: This Error occurs in variable cell calculations when the increase in the unit cell volume is too large. handler documentation: Handle DilatmxError. Abinit produces a netcdf file with the last structure before aborting The handler changes the structure in the input with the last configuration and modify the value of dilatmx. event name = !TolSymError event documentation: Class of errors raised by Abinit when it cannot detect the symmetries of the system. The handler assumes the structure makes sense and the error is just due to numerical inaccuracies. We increase the value of tolsym in the input file (default 1-8) so that Abinit can find the space group and re-symmetrize the input structure. handler documentation: Increase the value of tolsym in the input file. event name = !MemanaError event documentation: Class of errors raised by the memory analyzer. (the section that estimates the memory requirements from the input parameters). handler documentation: Set mem_test to 0 to bypass the memory check. event name = !MemoryError event documentation: This error occurs when a checked allocation fails in Abinit The only way to go is to increase memory handler documentation: Handle MemoryError. Increase the resources requirements  Note New error handlers will be added in the new versions of Abipy/Abinit. Please, let us know if you need handlers for errors commonly occuring in your calculations. ## Troubleshooting¶ There are two abirun.py commands that are very useful especially if something goes wrong: events and debug. To print the Abinit events (Warnings, Errors, Comments) found in the log files of the different tasks use: abirun.py FLOWDIR events  To analyze error files and log files for possible error messages, use: abirun.py FLOWDIR debug  By default, these commands will analyze the entire flow so the output on the terminal can be very verbose. If you are interested in a particular task e.g. w0/t1 use the syntax: abirun.py FLOWDIR/w0/t1 events  to select all the tasks in a work directory e.g. w0 use: abirun.py FLOWDIR/w0 events  to select an arbitrary subset of nodes of the flow use the syntax: abirun.py FLOWDIR events -nids=12,13,16  where nids is a list of AbiPy node identifiers. Tip abirun.py events --help is your best friend $ abirun.py events --help
usage: abirun.py [flowdir] events [-h] [-v] [--no-colors] [--no-logo]
[--loglevel LOGLEVEL] [--remove-lock]

optional arguments:
-h, --help            show this help message and exit
-v, --verbose         verbose, can be supplied multiple times to increase
verbosity.
--no-colors           Disable ASCII colors.
--no-logo             Disable AbiPy logo.
--loglevel LOGLEVEL   Set the loglevel. Possible values: CRITICAL, ERROR
(default), WARNING, INFO, DEBUG.
--remove-lock         Remove the lock on the pickle file used to save the
status of the flow.
-n NIDS, --nids NIDS  Node identifier(s) used to select the task. Accept
single integer, comma-separated list of integers or
python slice. Use status command to get the node
ids. Examples: --nids=12 --nids=12,13,16 --nids=10:12
to select 10 and 11 (slice syntax), --nids=2:5:2 to
select 2,4.
-w WSLICE, --wslice WSLICE
Select the list of works to analyze (python syntax for
slices): Examples: --wslice=1 to select the second
workflow, --wslice=:3 for 0,1,2, --wslice=-1 for the
last workflow, --wslice::2 for even indices.
Select only the tasks with the given status. Default:
None i.e. ignored. Possible values: ['Initialized',
'AbiCritical', 'QCritical', 'Unconverged', 'Error',
'Completed'].
Select only tasks with the given class e.g. -t
NscfTask.


To get information on the Abinit executable called by AbiPy, use:

abirun.py abibuild


or the verbose variant:

abirun.py abibuild --verbose


At this point, you may wonder why we need to specify all these parameters in the configuration file. The reason is that, before submitting a job to a resource manager, AbiPy will use the autoparal feature of ABINIT to get all the possible parallel configurations with ncpus <= max_cores. On the basis of these results, AbiPy selects the “optimal” one, and changes the ABINIT input file and the submission script accordingly . (this is a very useful feature, especially for calculations done with paral_kgb=1 that require the specification of npkpt, npfft, npband, etc). If more than one QueueAdapter is specified, AbiPy will first compute all the possible configuration and then select the “optimal” QueueAdapter according to some kind of policy
In some cases, you may want to enforce some constraint on the “optimal” configuration. For example, you may want to select only those configurations whose parallel efficiency is greater than 0.7 and whose number of MPI nodes is divisible by 4. One can easily enforce this constraint via the condition dictionary whose syntax is similar to the one used in mongodb.
policy:
condition: {$and: [ {"efficiency": {$gt: 0.7}}, {"tot_ncpus": {$divisible: 4}} ]}  The parallel efficiency is defined as$epsilon = dfrac{T_1}{T_N * N}$where$N$is the number of MPI processes and$T_j$is the wall time needed to complete the calculation with$j$MPI processes. For a perfect scaling implementation$epsilon$is equal to one. The parallel speedup with N processors is given by$S = T_N / T_1\$. Note that autoparal = 1 will automatically change your job.sh script as well as the input file so that we can run the job in parallel with the optimal configuration required by the user. For example, you can use paral_kgb = 1 in GS calculations and AbiPy will automatically set the values of npband, npfft, npkpt … for you! Note that if no configuration fulfills the given condition, AbiPy will use the optimal configuration that leads to the highest parallel speedup (not necessarily the most efficient one).
policy
This section governs the automatic parallelization of the run: in this case AbiPy will use the autoparal capabilities of Abinit to determine an optimal configuration with maximum max_ncpus MPI nodes. Setting autoparal to 0 disable the automatic parallelization. Other values of autoparal are not supported.