{"id":1756,"date":"2014-08-08T09:43:07","date_gmt":"2014-08-08T09:43:07","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=1756"},"modified":"2017-03-14T11:09:57","modified_gmt":"2017-03-14T11:09:57","slug":"cp2k","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/cp2k\/","title":{"rendered":"CP2K"},"content":{"rendered":"

Overview<\/h2>\n

CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials.<\/p>\n

Version 2.5.1 is installed on the CSF. It was compiled with Intel Compilers 12.0.5 & MKL (with -msse4.1 and -axAVX) and support for MPI (no OpenMP). This software will not run on the AMD nodes, it is optimised for the Intel hardware.<\/p>\n

Version 2.6.0 is also available. Note that this version was not compiled on the CSF, instead the pre-compiled binary from the CP2K download site was installed. This version will only run on a maximum of 16 cores in smp.pe.<\/p>\n

Version 4.1 is available for distributed parallel use on all nodes, but will only run usefully across Infiniband-connected nodes, at least in modes like Quickstep which are very latency-sensitive. It is built with the add-ons<\/a> libint, libderiv, libxsmm, libxc, and ELPA; it may be possible to add others if required. (The way it is built sidesteps a bad performance problem<\/a> on Infiniband which you might see elsewhere.) There is a pure MPI binary, cp2k.popt, and an MPI+OpenMP one, cp2k.psmp, but running the latter properly still needs some investigation. See the parallel submission<\/a> recipe below for running the popt version.<\/p>\n

Restrictions on use<\/h2>\n

The software is open source under the GNU General Public License.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the appropriate modulefile. <\/p>\n

For version 4.1:<\/p>\n

\r\nmodule load apps\/gcc\/cp2k\/4.1\r\n<\/pre>\n
Potentials and bases can then be found in the directory pointed to by $CP2K_DATA.<\/p>\n
For version 2.6.0:<\/p>\n
\r\nmodule load apps\/binapps\/cp2k\/2.6.0\r\n<\/pre>\n
For version 2.5.1 on a single node jobs (2 to 24 cores)<\/p>\n
\r\nmodule load apps\/intel-12.0\/cp2k\/popt\/2.5.1\r\n<\/pre>\n
For version 2.5.1 jobs requiring two or more compute nodes ( 48+ cores in multiples of 24)<\/p>\n
\r\nmodule load apps\/intel-12.0\/cp2k\/popt\/2.5.1-ib\r\n<\/pre>\n
Running the application – version 2.6.1<\/h2>\n
Serial batch job submission<\/h3>\n
A serial version of CP2K has not been installed. CP2K should be run on 2 or more cores – see below.<\/p>\n
Parallel batch job submission – 2 to 24 cores<\/h3>\n
This version will only run on 2 or more processors up to a maximum of 24.<\/p>\n
    \n
  1. Load the appropriate modulefile<\/li>\n
  2. Create a directory (preferably in scratch) for your job. <\/li>\n
  3. Place all relevant files, e.g. input, in the directory.<\/li>\n
  4. Create a job submission script\/textfile, e.g:\n
    \r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n##Set current dir as the work directory\r\n#$ -cwd\r\n## Inherit login node including modulefile settings\r\n#$ -V\r\n## Submit to single node parallel environment and request up to 16 cores\r\n#$ -pe smp.pe 4\r\n\r\n## Run the executable specifying your input file. \r\n## The variable $NSLOTS automatically uses the no. of cores requested in the pe.\r\n\r\nexport OMP_NUM_THREADS=$NSLOTS\r\ncp2k.ssmp -i C.inp\r\n<\/pre>\n<\/li>\n
  5. Submit the job with: qsub scriptname<\/code> . Replacing ‘scriptname’ with the name of your file.>\/li>\n<\/ol>\n
    Running the application – version 2.5.1 and 4.1 (multi-node)<\/h2>\n
    Please do not run CP2K on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
    Serial batch job submission<\/h3>\n
    A serial version of CP2K has not been installed. CP2K should be run on 2 or more cores – see below.<\/p>\n
    Parallel batch job submission – 2 to 24 cores<\/h3>\n
      \n
    1. Load the appropriate modulefile<\/li>\n
    2. Create a directory (preferably in scratch) for your job. <\/li>\n
    3. Place all relevant files, e.g. input, in the directory.<\/li>\n
    4. Create a job submission script\/textfile, e.g:\n
      \r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n##Set current dir as the work directory\r\n#$ -cwd\r\n## Inherit login node including modulefile settings\r\n#$ -V\r\n## Submit to single node parallel environment and request up to 16 cores\r\n#$ -pe smp.pe 8\r\n\r\n## Run the executable specifying your input file. \r\n## The variable $NSLOTS automatically uses the no. of cores requested in the pe.\r\n\r\nmpirun -np $NSLOTS cp2k.popt -i H2O-32.inp\r\n<\/pre>\n<\/li>\n
    5. Submit the job with: qsub scriptname<\/code> . Replacing ‘scriptname’ with the name of your file.>\/li>\n<\/ol>\n
      Parallel batch job submission – 48 or more cores in multiples of 24<\/a><\/h3>\n
        \n
      1. You should have tested that your job scales well on 2-24 cores before using 48+<\/li>\n
      2. Load the appropriate modulefile<\/li>\n
      3. Create a directory (preferably in scratch) for your job. <\/li>\n
      4. Place all relevant files, e.g. input, in the directory.<\/li>\n
      5. Create a job submission script\/textfile, e.g:\n
        \r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n##Set current dir as the work directory\r\n#$ -cwd\r\n## Inherit login node including modulefile settings\r\n#$ -V\r\n## Multi-node environment uses 48 cores or more and in multiples of 24\r\n#$ -pe orte-24-ib.pe 48\r\n\r\n## Run the executable specifying your input file. \r\n## The variable $NSLOTS automatically uses the no. of cores requested in the pe.\r\n\r\nmpirun -np $NSLOTS cp2k.popt -i H2O-32.inp\r\n<\/pre>\n<\/li>\n
      6. Submit the job with: qsub scriptname<\/code> . Replacing ‘scriptname’ with the name of your file.<\/li>\n<\/ol>\n
        Further info<\/h2>\n