ingest fedoraAdmin 2015-02-13T10:49:40.220Z eSciDoc object created addDatastream version-history fedoraAdmin 2015-02-13T10:49:40.300Z created modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:49:40.370Z modifyDatastreamByValue DC fedoraAdmin 2015-02-13T10:50:49.251Z modifyDatastreamByValue escidoc fedoraAdmin 2015-02-13T10:50:49.271Z modifyObject fedoraAdmin 2015-02-13T10:50:49.719Z touched modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:49.798Z modifyDatastreamByValue version-history fedoraAdmin 2015-02-13T10:50:49.822Z modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:49.850Z modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:54.058Z modifyDatastreamByValue version-history fedoraAdmin 2015-02-13T10:50:54.081Z modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:54.116Z modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:55.802Z modifyDatastreamByValue version-history fedoraAdmin 2015-02-13T10:50:55.835Z modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:55.867Z modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:56.495Z modifyDatastreamByValue version-history fedoraAdmin 2015-02-13T10:50:56.567Z modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:56.601Z modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:57.265Z modifyDatastreamByValue version-history fedoraAdmin 2015-02-13T10:50:57.294Z modifyDatastreamByValue RELS-EXT fedoraAdmin 2015-02-13T10:50:57.327Z Memory Optimization for the Octopus Scientific Code Alberdi-Rodriguez, J. Rubio, A. Oliveira, M. Charalampidou, A. Folias, D. Octopus is a software package for density-functional theory (DFT), and its time-dependent (TDDFT) variant. Linear Combination of the Atomic Orbitals (LCAO) is performed previous to the actual DFT run. LCAO is used to get an initial guess of densities, and therefore, to start with the Self Consistent Field (SCF) of the Ground-State (GS). System initialization and LCAO steps consume a large amount of memory and do not demonstrate good performance. In this study, extensive profiling has been performed, in order to identify large matrices and scaling behaviour of initialization and LCAO. Alternative implementations of LCAO in Octopus have been investigated in order to optimize memory usage and performance of LCAO approach. Use of ScaLAPACK library led to significant improvement of memory allocation and performance. Benchmark tests have been performed on MareNostrum III HPC system using various combinations of atomic systems’ sizes and numbers of CPU cores. Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F Theory Department, Max Planck Institute for the Structure and Dynamics of Matter, Max Planck SocietyTheory, Fritz Haber Institute, Max Planck SocietyNano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F http://purl.org/escidoc/metadata/ves/publication-types/paper Text escidoc:2095302 eng http://purl.org/escidoc/metadata/ves/publication-types/paper Text Alberdi-Rodriguez, J. Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F Rubio, A. Theory Department, Max Planck Institute for the Structure and Dynamics of Matter, Max Planck SocietyTheory, Fritz Haber Institute, Max Planck SocietyNano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F Oliveira, M. Charalampidou, A. Folias, D. Memory Optimization for the Octopus Scientific Code eng escidoc:2095302 2015 Octopus is a software package for density-functional theory (DFT), and its time-dependent (TDDFT) variant. Linear Combination of the Atomic Orbitals (LCAO) is performed previous to the actual DFT run. LCAO is used to get an initial guess of densities, and therefore, to start with the Self Consistent Field (SCF) of the Ground-State (GS). System initialization and LCAO steps consume a large amount of memory and do not demonstrate good performance. In this study, extensive profiling has been performed, in order to identify large matrices and scaling behaviour of initialization and LCAO. Alternative implementations of LCAO in Octopus have been investigated in order to optimize memory usage and performance of LCAO approach. Use of ScaLAPACK library led to significant improvement of memory allocation and performance. Benchmark tests have been performed on MareNostrum III HPC system using various combinations of atomic systems’ sizes and numbers of CPU cores. Alberdi-Rodriguez J. Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F escidoc:persistent22 Rubio A. Theory Department, Max Planck Institute for the Structure and Dynamics of Matter, Max Planck Society escidoc:2074320 Theory, Fritz Haber Institute, Max Planck Society escidoc:634547 Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F escidoc:persistent22 http://pubman.mpdl.mpg.de/cone/persons/resource/persons22028 Oliveira M. Charalampidou A. Folias D. Memory Optimization for the Octopus Scientific Code eng http://purl.org/escidoc/metadata/ves/review-methods/no-review Octopus is a software package for density-functional theory (DFT), and its time-dependent (TDDFT) variant. Linear Combination of the Atomic Orbitals (LCAO) is performed previous to the actual DFT run. LCAO is used to get an initial guess of densities, and therefore, to start with the Self Consistent Field (SCF) of the Ground-State (GS). System initialization and LCAO steps consume a large amount of memory and do not demonstrate good performance. In this study, extensive profiling has been performed, in order to identify large matrices and scaling behaviour of initialization and LCAO. Alternative implementations of LCAO in Octopus have been investigated in order to optimize memory usage and performance of LCAO approach. Use of ScaLAPACK library led to significant improvement of memory allocation and performance. Benchmark tests have been performed on MareNostrum III HPC system using various combinations of atomic systems’ sizes and numbers of CPU cores. Alberdi-Rodriguez J. Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F escidoc:persistent22 Rubio A. Theory Department, Max Planck Institute for the Structure and Dynamics of Matter, Max Planck Society escidoc:2074320 Theory, Fritz Haber Institute, Max Planck Society escidoc:634547 Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F escidoc:persistent22 http://pubman.mpdl.mpg.de/cone/persons/resource/persons22028 Oliveira M. Charalampidou A. Folias D. Memory Optimization for the Octopus Scientific Code eng 2015 http://purl.org/escidoc/metadata/ves/review-methods/no-review Octopus is a software package for density-functional theory (DFT), and its time-dependent (TDDFT) variant. Linear Combination of the Atomic Orbitals (LCAO) is performed previous to the actual DFT run. LCAO is used to get an initial guess of densities, and therefore, to start with the Self Consistent Field (SCF) of the Ground-State (GS). System initialization and LCAO steps consume a large amount of memory and do not demonstrate good performance. In this study, extensive profiling has been performed, in order to identify large matrices and scaling behaviour of initialization and LCAO. Alternative implementations of LCAO in Octopus have been investigated in order to optimize memory usage and performance of LCAO approach. Use of ScaLAPACK library led to significant improvement of memory allocation and performance. Benchmark tests have been performed on MareNostrum III HPC system using various combinations of atomic systems’ sizes and numbers of CPU cores. 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter pending Object created. ct Dr. Michael Grefe Dr. Michael Grefe Object created. pending ---1 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter pending Object created. ct Dr. Michael Grefe Dr. Michael Grefe Object created. pending 2015-02-13T10:49:40.230Z 1 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter pending Object created. ct Dr. Michael Grefe Dr. Michael Grefe ItemHandler.update() pending 2015-02-13T10:49:40.230Z 2 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter pending Object created. ct Dr. Michael Grefe Dr. Michael Grefe ItemHandler.update() pending 2015-02-13T10:50:49.798Z 2 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter submitted ct Dr. Michael Grefe Dr. Michael Grefe submitted 2015-02-13T10:50:49.798Z 2 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter submitted ct Dr. Michael Grefe Dr. Michael Grefe submitted 2015-02-13T10:50:54.058Z 2 hdl:11858/00-001M-0000-0024-C453-4 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter submitted ct Dr. Michael Grefe Dr. Michael Grefe submitted 2015-02-13T10:50:54.058Z 2 hdl:11858/00-001M-0000-0024-C453-4 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter submitted ct Dr. Michael Grefe Dr. Michael Grefe submitted 2015-02-13T10:50:55.802Z 2 hdl:11858/00-001M-0000-0024-C454-2 hdl:11858/00-001M-0000-0024-C453-4 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter submitted ct Dr. Michael Grefe Dr. Michael Grefe submitted 2015-02-13T10:50:55.802Z 2 hdl:11858/00-001M-0000-0024-C454-2 hdl:11858/00-001M-0000-0024-C453-4 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter submitted ct Dr. Michael Grefe Dr. Michael Grefe submitted 2015-02-13T10:50:56.495Z 2 hdl:11858/00-001M-0000-0024-C454-2 hdl:11858/00-001M-0000-0024-C454-2 hdl:11858/00-001M-0000-0024-C453-4 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter released ct Dr. Michael Grefe Dr. Michael Grefe released 2015-02-13T10:50:56.495Z 2 2 --- hdl:11858/00-001M-0000-0024-C454-2 hdl:11858/00-001M-0000-0024-C454-2 hdl:11858/00-001M-0000-0024-C453-4 1.3.10-SNAPSHOT Publications of the MPI for the Structure and Dynamics of Matter released ct Dr. Michael Grefe Dr. Michael Grefe released 2015-02-13T10:50:57.265Z 2 2 2015-02-13T10:50:57.265Z hdl:11858/00-001M-0000-0024-C454-2 2 2015-02-13T10:50:57.265Z released URL /ir/item/escidoc:2095302/resources/version-history#v2e1423824657206 released 2015-02-13T10:50:57.265Z escidoc-internal escidoc:2073774 escidoc-internal escidoc:2095302 URL /ir/item/escidoc:2095302/resources/version-history#v2e1423824656439 assignVersionPid 2015-02-13T10:50:55.867Z versionPid assigned escidoc-internal escidoc:2073774 escidoc-internal escidoc:2095302 URL /ir/item/escidoc:2095302/resources/version-history#v2e1423824655750 assignObjectPid 2015-02-13T10:50:54.116Z objectPid assigned escidoc-internal escidoc:2073774 escidoc-internal escidoc:2095302 URL /ir/item/escidoc:2095302/resources/version-history#v2e1423824654002 submitted 2015-02-13T10:50:54.058Z escidoc-internal escidoc:2073774 escidoc-internal escidoc:2095302 URL /ir/item/escidoc:2095302/resources/version-history#v2e1423824649778 update 2015-02-13T10:50:49.798Z ItemHandler.update() escidoc-internal escidoc:2073774 escidoc-internal escidoc:2095302 1 2015-02-13T10:49:40.230Z pending Object created. 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