hpc documentation - technical:generic:gaussian-linda-integration

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====== Integration of TCPLinda+Gaussian on Caviness ======

This document contains a summary of the steps necessary to tightly-integrate Gaussian multi-node parallelism (TCPLinda) in our Slurm clusters.

===== Scheduling =====

The current infrastructure for Gaussian jobs expects submissions like

<code bash>
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=<C>
#SBATCH --mem=<M> OR --mem-per-cpu=<M>
</code>

The allocated CPU core ids are used to construct a ''GAUSS_CDEF'' environment variable and the on-node memory limit -- minus fixed/per-core overhead -- produces a value for ''GAUSS_MDEF''.

<note important>The infrastructure also sets ''GAUSS_GDEF'' if a GPU-enabled version of Gaussian is being used on a node with GPUs allocated to the job.</note>

For multi-node Gaussian jobs, the submission profile would be expected to change to:

<code bash>
#SBATCH --nodes=<N>
#SBATCH --ntasks-per-node=<T>
#SBATCH --cpus-per-task=<C>
#SBATCH --mem=<M> OR --mem-per-cpu=<M>
</code>

Each //task// would equate with a TCPLinda worker, and each worker would have <C> cores for SMP parallelism.  The ''GAUSS_WDEF'' environment variable would need to be set accordingly; e.g. for ''SLURM_JOB_NODELIST=r00n[00-02]'', ''SLURM_TASKS_PER_NODE=2'', and ''SLURM_CPUS_PER_TASK=18'' the environment would contain:

^Variable^Value^
|''GAUSS_WDEF''|''r00n00:2,r00n01:2,r00n02:2''|
|''GAUSS_CDEF''|Not set|
|''GAUSS_PDEF''|''=$SLURM_CPUS_PER_TASK''|
|''GAUSS_MDEF''|Memory per task - overhead FIXME|

Since Slurm will not in general allocate the same <C> CPU core ids to each task, the now-deprecated ''GAUSS_PDEF'' CPU count must be used; otherwise, ''srun'' will communicate the same ''GAUSS_CDEF'' to each task and cores will fail to be bound.  If future versions of Gaussian remove the ''GAUSS_PDEF'' functionality entirely, it will be necessary either to allocate entire nodes (at 1 task-per-node) or the Linda worker startup will need to be wrapped by a script that reconfigures ''GAUSS_CDEF'' on-the-fly.  The latter is probably beneficial, as it would also allow ''GAUSS_MDEF'' and ''GAUSS_GDEF'' to be customized -- which would be extremely important for heterogenous job allocations.

===== TCPLinda Worker Startup =====

The ''linda_rsh'' script is used by TCPLinda to execute a remote command on a node participating in the job.  By default it uses ''rsh'' or ''ssh'' to connect to the remote host.  But on a Slurm cluster the ''srun'' command must be used for proper job containment and accounting.

The ''linda_rsh'' script would require modification to **only** make use of ''srun''.  Since TCPLinda executes one instance of ''linda_rsh'' per Linda task, the job's batch step would perform ((<N>*<T>)-1) invocations of ''linda_rsh''.  Each such invocation will be made against a specific hostname (pulled from ''GAUSS_WDEF'').  The ''srun'' command would alter e.g. the ''ssh'' formula

<code bash>
/usr/bin/ssh -x $host $user -n "$@"
</code>

to

<code bash>
srun --nodes=1 --ntasks=1 --cpus-per-task=${SLURM_CPUS_PER_TASK:-1} --nodelist=$host "$@"
</code>

Each TCPLinda worker (beyond the primary Gaussian process in the batch step) would be a separate job step in the final accounting of the job.