PSNC DRMAA for SLURM

Please note: this is only one slurm-drmaa user's import/clone and fork of the canonical PSNC slurm-drmaa.

Introduction

PSNC DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource Management Application API) specification for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems.

This software also enables the integration of QCG-Computing with the underlying Slurm system for remote multi-user job submission and control over Web Services.

Although this fork is not the canonical source of slurm-drmaa, it has become mildly popular among the Galaxy community, especially as development on PSNC slurm-drmaa has slowed folliwing the death of the previous mantainer, Mariusz Mamonski. I will do my best to incorporate both upstream and contributed changes, but credit belongs to the original authors (found below). In this repository, I've imported the SVN history and attempted to attribute contributions correctly.

Download

DRMAA for Slurm is distributed as a source package which can be downloaded via the Releases section.

Installation

To compile and install the library just go to main source directory and type:

$ ./configure [options] && make
$ sudo make install

The library was tested with Slurm versions 14.03, 14.11, and 15.08. If you encountered any problems using the library on the different systems, please see the contact section.

Notable ./configure script options:

--with-slurm-inc SLURM_INCLUDE_PATH

Path to Slurm header files (i.e. directory containing slurm/slurm.h ). By default the library tries to guess the SLURM_INCLUDE_PATH and SLURM_LIBRARY_PATH based on location of the srun executable.

--with-slurm-lib SLURM_LIBRARY_PATH

Path to Slurm libraries (i.e. directory containing libslurm.a ).

--prefix INSTALLATION_DIRECTORY

Root directory where PSNC DRMAA for Slurm shall be installed. When not given library is installed in /usr/local.

--enable-debug

Compiles library with debugging enabled (with debugging symbols not stripped, without optimizations, and with many log messages enabled). Useful when you are to debug DRMAA enabled application or investigate problems with DRMAA library itself.

There are no unusual requirements for basic usage of library: ANSI C compiler and standard make program should suffice. If you have taken sources directly from this repository or wish to run test-suite you would need additional developer tools.

Configuration

During DRMAA session initialization (drmaa_init) library tries to read its configuration parameters from locations: /etc/slurm_drmaa.conf, ~/.slurm_drmaa.conf and from file given in SLURM_DRMAA_CONF environment variable (if set to non-empty string). If multiple configuration sources are present then all configurations are merged with values from user-defined files taking precedence (in following order: $SLURM_DRMAA_CONF, ~/.slurm_drmaa.conf, /etc/slurm_drmaa.conf).

Currently recognized configuration parameters are:

cache_job_state
According to DRMAA specification every drmaa_job_ps() call should query DRM system for job state. With this option one may optimize communication with DRM. If set to positive integer drmaa_job_ps() returns remembered job state without communicating with DRM for cache_job_state seconds since last update. By default library conforms to the specification (no caching will be performed).

Type: integer, default: 0

job_categories
Dictionary of job categories. Its keys are job categories names mapped to native specification strings. Attributes set by job category can be overridden by corresponding DRMAA attributes or native specification. Special category name default is used when drmaa_job_category job attribute was not set.

Type: dictionary with string values, default: empty dictionary

Configuration file syntax

Configuration file is in a form of a dictionary. Dictionary is set of zero or more key-value pairs. Key is a string while value could be a string, an integer or another dictionary.

  configuration: dictionary | dictionary_body
  dictionary: '{' dictionary_body '}'
  dictionary_body: (string ':' value ',')*
  value: integer | string | dictionary
  string: unquoted-string | single-quoted-string | double-quoted-string
  unquoted-string: [^ \t\n\r:,0-9][^ \t\n\r:,]*
  single-quoted-string: '[^']*'
  double-quoted-string: "[^"]*"
  integer: [0-9]+

Native specification

DRMAA interface allows to pass DRM dependent job submission options. Those options may be specified directly by setting drmaa_native_specification job template attribute or indirectly by the drmaa_job_category job template attribute. The legal format of the native options looks like:

  -A My_job_name -s -N 1-10

List of parameters that can be passed in the drmaa_native_specification attribute:

Native specification	Description
-A, --account=name	Charge job to specified accounts
--acctg-freq=list	Define the job accounting sampling interval
--comment=string	An arbitrary comment
-C, --constraint=list	Specify a list of constraints
--contiguous	If set, then the allocated nodes must form a contiguous set
--exclusive	Allocate nodenumber of tasks to invoke on each nodes in exclusive mode when cpu consumable resource is enabled
--mem=MB	Minimum amount of real memory
--mem-per-cpu=MB	Maximum amount of real memory per allocated cpu required by a job
--mincpus=n	Minimum number of logical processors (threads) per node
-N, --nodes=minnodes[-maxnodes]	Number of nodes on which to run
--ntasks-per-node=n	Number of tasks to invoke on each node
-p, --partition=partition	Partition requested
--qos=qos	Quality of Serice
--requeue	If set, permit the job to be requeued
--reservation=name	Allocate resources from named reservation
-s, --share	Job allocation can share nodes with other running jobs
-w, --nodelist=hosts	Request a specific list of hosts
-t, --time=hours:minutes	Set a maximum job wallclock time
-n, --ntasks=n	Number of tasks
--gres=list	Specifies a comma delimited list of generic consumable resources
--no-kill	Do not automatically terminate a job of one of the nodes it has been allocated fails
--licenses=license	Specification of licenses
--mail-type=type	Notify user by email when certain event types occur. Valid type values are BEGIN, END, FAIL, REQUEUE, and ALL (any state change)
--no-requeue	Specifies that the batch job should not be requeued after node failure
-x, --exclude=nodelist	Explicitly exclude certain nodes from the resources granted to the job
--tmp=size[units]	Specify a minimum amount of temporary disk space
-M, --clusters=list	Comma delimited list of clusters to issue commands to

Description of each parameter can be found in man sbatch.

Changelog

1.0.7 - user supplied (via DRMAA attribute) native specification now takes precedence over the native specification provided in configuration file.
1.0.6 - added support for --gres, --no-kill, --licenses, --mail-type=, --no-requeue, --exclude, --tmp in native specification attribute. Implemented handling of missing jobs.
1.0.5 - better handling of --time (-t) (thanks to Roman Valls Guimera) and added support for --ntasks (-n) in native specification attribute. Fixed DRMAA_V_EMAIL attribute handling
1.0.4 - support for SLURM 2.3
1.0.3 - the --time native option support
1.0.2 - environment variables are now propagated from submission host to the worker nodes
1.0.1 - added support for SLURM 2.2
1.0.0 - first public release

Known bugs and limitations

Library covers all DRMAA 1.0 specification with exceptions listed below. It was successfully tested with Slurm 14.03, 14.11, and 15.08. Known limitations:

drmaa_control options DRMAA_CONTROL_HOLD, DRMAA_CONTROL_RELEASE are only available for users being Slurm administrators (in version prior 2.2)
drmaa_control options DRMAA_CONTROL_SUSPEND, DRMAA_CONTROL_RESUME are only available for users being Slurm administrators
drmaa_wct_slimit not implemented
optional attributes drmaa_deadline_time, drmaa_duration_hlimit, drmaa_duration_slimit, drmaa_transfer_files not implemented
The SPANK client side (i.e. not remote) plugins chain is not invoked in DRMAA run job call. For this reason we advice you to use TASK BLOCKS in the UseEnv SPANK plugin.

Development and Pre-releases

Please note the ./autogen.sh and ./autoclean.sh scripts which calls the autotools command chain in appropriate order.

note: This repository depends on DRMAA Utils, which is configured as a submodule. When cloning this repository, you should clone recursively, e.g.:

$ git clone --recursive https://github.com/natefoo/slurm-drmaa.git

note: You need some developer tools to compile the source from git, rather than from a tarball release. Also, the development version may not always compile.

Developer tools

Although not needed for library user the following tools may be required if you intend to develop PSNC DRMAA for Slurm:

GNU autotools
- autoconf (tested with version 2.67)
- automake (tested with version 1.11)
- libtool (tested with version 2.2.8)
- m4 (tested with version 1.4.14)
Bison parser generator,
RAGEL State Machine Compiler,
gperf gperf - a perfect hash function generator.

Authors

The library was developed by:

Michal Matloka - first implementation
Mariusz Mamonski - maintainer since version 1.0.3
Piotr Kopta - maintainer since version 1.0.7

This library relies heavily on the Fedstage DRMAA utils code developed by:

Lukasz Ciesnik.

Contact

In case of any problems or questions regarding PSNC DRMAA for Slurm do not hesitate to contact us:

QosCosGrid Development Team - qcg(at)plgrid.pl

You can submit issues and pull requests for this fork of DRMAA for Slurm in GitHub.

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

scholtalbers / slurm-drmaa