Merge pull request #40 from stigrj/turbomole

Add example script for TURBOMOLE calculations

applications/chemistry/TURBOMOLE/TURBOMOLE.rst

@@ -0,0 +1,104 @@
+.. _TURBOMOLE:
+
+============================
+The TURBOMOLE program system
+============================
+
+Information regarding the quantum chemistry program system TURBOMOLE.
+
+Related information
+===================
+
+.. toctree::
+ :maxdepth: 1
+
+ run_turbo.rst
+
+
+General Information
+===================
+
+Description
+-----------
+
+TURBOMOLE is a quantum chemical program package, initially developed in the
+group of Prof. Dr. Reinhart Ahlrichs at the University of Karlsruhe and at the
+Forschungszentrum Karlsruhe. In 2007, the TURBOMOLE GmbH (Ltd) was founded by
+the main developers of the program, and the company took over the responsibility
+for the coordination of the scientific development of the program, to which it
+holds all copy and intellectual property rights. 
+
+
+Online info from vendor
+-----------------------
+
+* Homepage: http://www.turbomole-gmbh.com
+* Documentation: http://www.turbomole-gmbh.com/turbomole-manuals.html
+
+
+License information
+-------------------
+
+Sigma2 holds a national TURBOMOLE license covering all computing centers in Norway.
+
+
+Citation
+--------
+
+When publishing results obtained with this software, please check with the
+developers web page in order to find the correct citation(s).
+
+
+TURBOMOLE on Stallo
+===================
+
+Usage
+-----
+
+To see which versions of TURBOMOLE are available
+
+.. code-block:: bash
+
+    $ module avail turbomole
+
+Note that the latest (as of May 2018) version 7.2 comes in three different
+parallelization variants
+
+* TURBOMOLE/7.2
+* TURBOMOLE/7.2.mpi
+* TURBOMOLE/7.2.smp
+
+where the latter two correspond to the old separation between distributed memory
+(mpi) and shared memory (smp) implementations that some users may know from
+previous versions of the program. We recommend, however, to use the new hybrid
+parallelization scheme (new in v7.2) provided by the ``TURBOMOLE/7.2`` module.
+
+In order to run efficiently in hybrid parallel the SLURM setup must be correct
+by specifying CPUs rather than tasks per node
+
+.. code-block:: bash
+
+    #SBATCH --nodes=2
+    #SBATCH --ntasks-per-node=1
+    #SBATCH --cpus-per-task=20
+
+i.e. do NOT specify ``--ntasks=40``. Also, some environment variables must be
+set in the run script
+
+.. code-block:: bash
+
+    export TURBOTMPDIR=/global/work/${USER}/${SLURM_JOBID}
+    export PARNODES=${SLURM_NNODES}
+    export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
+
+See the TURBOMOLE example for more details.
+
+NOTE: The new hybrid program (v7.2) will launch a separate server process in
+addition to the requested parallel processes, so if you run e.g. on 20 cores
+each on two nodes you will find one process consuming up to 2000% CPU on each
+node plus a single process on the first node consuming very little CPU.
+
+NOTE: We have found that the hybrid program (v7.2) runs efficiently only if
+*full* nodes are used, e.i. you should always ask for ``--cpus-per-node=20``,
+and scale the number of nodes by the size of the calculation.
+

applications/chemistry/TURBOMOLE/run_turbo.rst

@@ -0,0 +1,39 @@
+.. _turbomole_example:
+
+==========================
+TURBOMOL runscript example
+==========================
+
+.. include:: ../files/job_turbo.sh
+   :literal:
+
+
+TURBOMOL example on Stallo
+--------------------------
+
+The above runscript can be found on Stallo along with the necessary input files
+to perform a simple DFT calculation. To get access to the examples directory,
+load the ``notur`` module
+
+.. code-block:: bash
+
+    $ module load notur
+    $ cp -r $RUNEX/TURBOMOLE .
+
+From this directory you can submit the example script (you need to specify a
+valid account in the script first)
+
+.. code-block:: bash
+
+    $ sbatch job_turbo.sh
+
+
+The calculation should take less than 2 min, but may spend much more than this
+in the queue. Verify that the output file ``dscf.out`` ends with 
+
+.. code-block:: bash
+
+    **** dscf : all done ****
+
+Please refer to the TURBOMOLE manual for how to setup different types of
+calculations.

applications/chemistry/files/job_turbo.sh

@@ -0,0 +1,44 @@
+#!/bin/bash -l
+#SBATCH --job-name=turbomole
+#SBATCH --account=nnXXXXk
+#SBATCH --time=1:00:00
+#SBATCH --mem-per-cpu=1000MB
+#SBATCH --nodes=2
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=20
+#SBATCH --mail-type=ALL
+#SBATCH --partition=multinode
+
+# For TURBOMOLE v7.2:
+# --nodes           : scale by the size of the calculation
+# --ntasks-per-node : always a singel task per node
+# --cpus-per-task   : always full nodes
+
+# load modules
+module purge
+module load TURBOMOLE/7.2
+
+# TURBOMOLE needs this variable
+export TURBOTMPDIR=/global/work/${USER}/${SLURM_JOBID}
+workdir=${TURBOTMPDIR}
+submitdir=${SLURM_SUBMIT_DIR}
+
+# copy files to work
+mkdir -p $workdir
+cd $workdir
+cp $submitdir/* $workdir
+
+# set parallel environment
+export PARNODES=${SLURM_NNODES}
+export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
+
+# run jobex calculation
+dscf > dscf.out
+
+# copy files back
+mv * $submitdir
+
+# clean up
+rm -r $workdir
+
+exit 0

applications/sw_guides.rst

@@ -18,6 +18,7 @@ the module system, and information about changes in application software see :re
    chemistry/Schrodinger/Schrodinger
    chemistry/ORCA/ORCA
    chemistry/Molcas/Molcas
+   chemistry/TURBOMOLE/TURBOMOLE
 
    physics/COMSOL/COMSOL