SJM is a program for managing a group of related jobs running on a compute cluster. It provides a convenient method for specifying dependencies between jobs and the resource requirements for each job (e.g. memory, CPU cores). It monitors the status of the jobs so you can tell when the whole group is done. If any of the jobs fails (e.g. due to a compute node crashing) SJM allows you to resume without rerunning the jobs that completed successfully. Finally, SJM provides a portable way to submit jobs to different job schedulers such as Sun Grid Engine or Platform LSF.
Installing SJM requires the following prerequisites:
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GCC to compile the program.
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The Boost regex library (http://www.boost.org). If you don't already have it on your system you must install boost before installing SJM. The easiest way is to install a prebuilt package, but you can download the source release from the boost web site and build it yourself. See the instructions here: http://www.boost.org/doc/libs/1_49_0/more/getting_started/index.html Be sure to follow the build instructions in the section called "Prepare to Use a Boost Library Binary".
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The TCLAP library (http://tclap.sourceforge.net/). Download and install it before installing SJM.
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A job scheduler: either Sun Grid Engine or Platform LSF. SJM doesn't currently support other schedulers but it is relatively easy to add a new one (see Other Job Schedulers below).
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For Sun Grid Engine: a parallel environment for running multi-core (threaded) jobs on a single node of the cluster. Common names for this PE are "smp" or "shm". Here is a sample SGE configuration:
$ qconf -sp smp pe_name smp slots 999 user_lists NONE xuser_lists NONE start_proc_args NONE stop_proc_args NONE allocation_rule $pe_slots control_slaves FALSE job_is_first_task TRUE urgency_slots min accounting_summary FALSE
- Environment modules (optional). SJM has optional features to integrate with environment modules, a system for managing the user environment (see http://modules.sourceforge.net/). It is a convenient way for users to switch between different versions of a software package and to use software packages installed in non-standard directories.
First download the release. Then unpack it:
$ tar xvzf scg-1.2.0.tgz
Finally, to compile and install sjm into /usr/local/bin run:
$ cd scg-1.2.0 $ ./configure $ make $ sudo make install
That's it unless you need to customize the installation. The rest of this section describes various additional options you can use.
To install in a different location use the --prefix option:
$ ./configure --prefix=/destination/directory
The configure script will try to identify the job scheduler on your system, but you can force it to use a particular scheduler using the --with-scheduler option. Supported values include SGE and LSF:
$ ./configure --with-scheduler=SGE
or
$ ./configure --with-scheduler=LSF
For Sun Grid Engine you must specify the parallel environment for multi-core jobs using the --with-pe option:
$ ./configure --with-pe=smp
If you wish to disable the environment modules integration then use the flag --without-modules:
$ ./configure --without-modules
If the boost library and/or job scheduler library and header files are installed in a non-standard place you need to add compiler options to find these files. Use CPPFLAGS to specify header file locations:
$ ./configure CPPFLAGS="-I/boost/include/dir -I/scheduler/include/dir"
Use LDFLAGS to specify library locations:
$ ./configure LDFLAGS="-L/boost/lib/dir -L/scheduler/lib/dir"
Note that if you use shared libraries and they are in a non-standard location then you may have to set LD_LIBRARY_PATH prior to running sjm.
To see all of the available options run:
$ ./configure --help
To build from a git repository, you must have GNU autoconf and automake installed. First run the following command and then continue with the instructions above:
$ sh bootstrap.sh
See doc/MANUAL.txt for usage instructions. You can run a quick test like this:
$ sjm -i doc/example.sjm
Note that the integration with environment modules requires a helper script called run_with_env that is installed as part of the package. The installation directory is hardwired into the sjm binary at compile time and must be the same on your compute nodes. If you need to override that value you can set the environment variable RUN_WITH_ENV to the full path of the script prior to running sjm. For example:
$ export RUN_WITH_ENV=/full/path/for/run_with_env $ sjm ...
If you want to use SJM with a job scheduler that isn't currently supported you will need to write a C++ adapter class. Use src/sge.hh and src/sge.cc as an example. Then add references to the new adapter class in configure.ac, src/Makefile.am and src/job_mon.hh. Please contribute your changes so other people can benefit!
SJM is distributed under the BSD 3-clause licence. See COPYING for the full license.
Please send comments, suggestions, bug reports and bug fixes to [email protected].
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