{"type":"doc","content":[{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"minLevel":{"value":"1"},"maxLevel":{"value":"7"},"type":{"value":"flat"},"separator":{"value":"pipe"}},"macroMetadata":{"macroId":{"value":"c087fa00340ee106821099be4ca45337"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"23e40f33-46f7-4f38-b662-c9e7f86b19d4"}},{"type":"heading","attrs":{"level":2},"content":[{"text":"Overview","type":"text"}]},{"type":"paragraph","content":[{"text":"The Vienna Ab initio Simulation Package (VASP), is a package for performing ab initio quantum mechanical calculations using either Vanderbilt pseudopotentials, or the projector augmented wave method and a plane wave basis set.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"VASP Homepage","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/"}}]},{"text":": Access to VASP News, Wiki, Support Forum and Portal","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"VASP ","type":"text"},{"text":"Wiki: Menu","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/wiki/index.php/The_VASP_Manual"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Please consult the VASP ","type":"text"},{"text":"FAQ","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/info/faq/"}}]},{"text":" for more details regards licensing.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"For Example: ","type":"text"},{"text":"To whom are VASP licenses given?","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"VASP licenses are given to well-defined research groups only. They are not department-or institution-wide, also they are not personal licenses. All members of a VASP-group have to work in the same organizational unit (Department, Institute) at the same location.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"VASP-licenses are not transferable from one research institution to another one. Any transfer of a license to another group at the same research institution has to be approved by the VASP Software GmbH explicitly.","type":"text"}]}]}]}]}]}]}]}]}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"Using","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"NOTE:","type":"text","marks":[{"type":"strong"}]},{"text":" VASP is NOT publicly available to users across the clusters. Instead, there are local installations per project with each project having its own license agreement. If ARCC comes across users abusing the licensing agreement we will have to act on it.","type":"text"}]}]}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"Multicore","type":"text"}]},{"type":"paragraph","content":[{"text":"Note","type":"text","marks":[{"type":"strong"}]},{"text":": Although ARCC can assist in the ","type":"text"},{"text":"functional","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" setup and running of VASP on the cluster, we do leave the ","type":"text"},{"text":"science","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" up to the researchers.","type":"text"}]},{"type":"paragraph","content":[{"text":"With this in mind, there are a number of pages on the VASP Wiki that make suggestions on how best to configure simulation inputs with respect to nodes/cores, as well as memory considerations.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"VASP Wiki:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"NCORE","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/wiki/index.php/NCORE"}}]},{"text":": determines the number of compute cores that work on an individual orbital. Default: ","type":"text"},{"text":"NCORE = 1","type":"text","marks":[{"type":"code"}]},{"text":" ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"NPAR","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/wiki/index.php/NPAR"}}]},{"text":" determines the number of bands that are treated in parallel. Default: NPAR = number of cores ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Performance issues, try NCORE, KPAR, ALGO, LREAL","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/wiki/index.php/Performance_issues,_try_NCORE,_KPAR,_ALGO,_LREAL"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Not enough memory","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/wiki/index.php/Not_enough_memory"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Memory requirements","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/wiki/index.php/Memory_requirements"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"These are just a few, please look through the VASP Wiki for others. If you find further details, please pass them onto us and we can add them to this page.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"ISTART","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/wiki/index.php/ISTART"}}]},{"text":": Related to starting a job and determines whether or not to read the ","type":"text"},{"text":"WAVECAR","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.vasp.at/wiki/index.php/WAVECAR"}}]},{"text":" file.","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Others:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Yale: CRC: ","type":"text"},{"text":"VASP","type":"text","marks":[{"type":"link","attrs":{"href":"https://docs.ycrc.yale.edu/clusters-at-yale/guides/vasp/"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"NSC: ","type":"text"},{"text":"Selecting the Right Number of Cores for a VASP Calculation","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.nsc.liu.se/~pla/blog/2015/01/12/vasp-how-many-cores/"}}]}]}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Installation Guidelines","type":"text"}]},{"type":"paragraph","content":[{"text":"The basic process is to unpack the provided source tar file. Copy and update an appropriate ","type":"text"},{"text":"arch/makefile.include.","type":"text","marks":[{"type":"code"}]},{"text":" file, and then build.","type":"text"}]},{"type":"paragraph","content":[{"text":"Below is an example using a ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" that ARCC believes is suitable. By all means select and try a different ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" but you will need to select appropriate compilers and related libraries, as well as updating the ","type":"text"},{"text":"makefile.include","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"With the example below, you will need to update ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" appropriately.","type":"text"}]}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"MedicineBow: Version 6.3.2","type":"text"}]},{"type":"expand","attrs":{"title":"General Process:"},"content":[{"type":"codeBlock","content":[{"text":"# We suggest building this software underneath your related project, so it can be shared across that project, \n# specifically under /project//software/.\n[]$ tar -xf vasp.6.3.2.tar\n[]$ cd vasp.6.3.2/\n[]$ cp arch/makefile.include.gnu_omp .\n[]$ mv makefile.include.gnu_omp makefile.include\n\n# Update the makefile.include file.\n\n[]$ module load gcc/14.2.0 openmpi/5.0.5 fftw/3.3.10-ompi openblas/0.3.24 netlib-scalapack/2.2.0-ompi wannier90/3.1.0 hdf5/1.14.3__hl_True__fortran_True-ompi\n[]$ make all\n[]$ ls bin/\nvasp_gam vasp_ncl vasp_std ","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"You need to update the ","type":"text"},{"text":"makefile.include","type":"text","marks":[{"type":"code"}]},{"text":" file. The following modifications have been made:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Commented out native compiling.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Have explicitly added the paths to ","type":"text"},{"text":"openblas","type":"text","marks":[{"type":"code"}]},{"text":", ","type":"text"},{"text":"scalapack","type":"text","marks":[{"type":"code"}]},{"text":" and ","type":"text"},{"text":"fftw","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Building with, and thus adding paths to, ","type":"text"},{"text":"hdf5","type":"text","marks":[{"type":"code"}]},{"text":" and ","type":"text"},{"text":"wannier90","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The ","type":"text"},{"text":"wannier90","type":"text","marks":[{"type":"code"}]},{"text":" library typically installs the actual library file in its parent folder, and not a sub ","type":"text"},{"text":"lib/","type":"text","marks":[{"type":"code"}]},{"text":" folder. This modifies the ","type":"text"},{"text":"makefile.include","type":"text","marks":[{"type":"code"}]},{"text":" to: ","type":"text"},{"text":"LLIBS += -L$(WANNIER90_ROOT)/ -lwannier","type":"text","marks":[{"type":"code"}]},{"text":" i.e the ","type":"text"},{"text":"lib","type":"text","marks":[{"type":"code"}]},{"text":" folder is not included.","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Compiling ","type":"text"},{"text":"fftlib","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]}]}]}]},{"type":"expand","attrs":{"title":"makefile.include"},"content":[{"type":"codeBlock","content":[{"text":"# Default precompiler options\nCPP_OPTIONS = -DHOST=\\\"LinuxGNU\\\" \\\n -DMPI -DMPI_BLOCK=8000 -Duse_collective \\\n -DscaLAPACK \\\n -DCACHE_SIZE=4000 \\\n -Davoidalloc \\\n -Dvasp6 \\\n -Duse_bse_te \\\n -Dtbdyn \\\n -Dfock_dblbuf \\\n -D_OPENMP\n\nCPP = gcc -E -C -w $*$(FUFFIX) >$*$(SUFFIX) $(CPP_OPTIONS)\n\nFC = mpif90 -fopenmp\nFCL = mpif90 -fopenmp\n\nFREE = -ffree-form -ffree-line-length-none\n\nFFLAGS = -w -ffpe-summary=none\n\nOFLAG = -O2\nOFLAG_IN = $(OFLAG)\nDEBUG = -O0\n\nOBJECTS = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o\nOBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o\nOBJECTS_O2 += fft3dlib.o\n\n# For what used to be vasp.5.lib\nCPP_LIB = $(CPP)\nFC_LIB = $(FC)\nCC_LIB = gcc\nCFLAGS_LIB = -O\nFFLAGS_LIB = -O1\nFREE_LIB = $(FREE)\n\nOBJECTS_LIB = linpack_double.o\n\n# For the parser library\nCXX_PARS = g++\nLLIBS = -lstdc++\n\n##\n## Customize as of this point! Of course you may change the preceding\n## part of this file as well if you like, but it should rarely be\n## necessary ...\n##\n\n# When compiling on the target machine itself, change this to the\n# relevant target when cross-compiling for another architecture\n# VASP_TARGET_CPU ?= -march=native\n# FFLAGS += $(VASP_TARGET_CPU)\n\n# For gcc-10 and higher (comment out for older versions)\nFFLAGS += -fallow-argument-mismatch\n\n# BLAS and LAPACK (mandatory)\nOPENBLAS_ROOT ?= /apps/u/spack/gcc/14.2.0/openblas/0.3.24-52ip5la/\nBLASPACK = -L$(OPENBLAS_ROOT)/lib -lopenblas\n\n# scaLAPACK (mandatory)\nSCALAPACK_ROOT ?= /apps/u/spack/gcc/14.2.0/netlib-scalapack/2.2.0-dbchdg6/\nSCALAPACK = -L$(SCALAPACK_ROOT)/lib -lscalapack\n\nLLIBS += $(SCALAPACK) $(BLASPACK)\n\n# FFTW (mandatory)\nFFTW_ROOT ?= /apps/u/spack/gcc/14.2.0/fftw/3.3.10-mk3sml6/\nLLIBS += -L$(FFTW_ROOT)/lib -lfftw3 -lfftw3_omp\nINCS += -I$(FFTW_ROOT)/include\n\n# HDF5-support (optional but strongly recommended)\n#CPP_OPTIONS+= -DVASP_HDF5\nHDF5_ROOT ?= /apps/u/spack/gcc/14.2.0/hdf5/1.14.3-2frri7c/\nLLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran\nINCS += -I$(HDF5_ROOT)/include\n\n# For the VASP-2-Wannier90 interface (optional)\nCPP_OPTIONS += -DVASP2WANNIER90\nWANNIER90_ROOT ?= /apps/u/opt/gcc/14.2.0/wannier90/3.1.0/\nLLIBS += -L$(WANNIER90_ROOT)/ -lwannier\n\n# For the fftlib library (recommended)\nCPP_OPTIONS+= -Dsysv\nFCL += fftlib.o\nCXX_FFTLIB = g++ -fopenmp -std=c++11 -DFFTLIB_THREADSAFE\nINCS_FFTLIB = -I./include -I$(FFTW_ROOT)/include\nLIBS += fftlib\nLLIBS += -ldl","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Note","type":"text","marks":[{"type":"strong"}]},{"text":": If you wish to use a different ","type":"text"},{"text":"make.include.your_choice","type":"text","marks":[{"type":"code"}]},{"text":" or try another process, then you’ll need to ","type":"text"},{"text":"module load","type":"text","marks":[{"type":"code"}]},{"text":" potentially a different compiler, and build core libraries if not built for that chosen compiler.","type":"text"}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Suggested Module File Creation","type":"text"}]},{"type":"paragraph","content":[{"text":"If you have installed under say: ","type":"text"},{"text":"/project//software/vasp.6.3.2/","type":"text","marks":[{"type":"code"}]},{"text":" you could create the following:","type":"text"}]},{"type":"expand","attrs":{"title":"Module file creation process:"},"content":[{"type":"codeBlock","content":[{"text":"[]$ cd /project//software/\n[]$ mkdir modules\n[]$ cd modules\n[]$ mkdir vasp\n[]$ cd vasp\n[]$ vim 6.3.2.lua","type":"text"}]}]},{"type":"expand","attrs":{"title":"6.3.2.lua"},"content":[{"type":"codeBlock","content":[{"text":"whatis([[Name : vasp]])\nwhatis([[Version : 6.3.2]])\nwhatis([[Short description : The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. ]])\n\nhelp([[\nvasp : 6.3.2\nThe Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.\nhttps://vasp.at/\n]])\n\nif not isloaded(\"gcc/14.2.0\") then\n load(\"gcc/14.2.0\")\nend\n\nif not isloaded(\"openmpi/5.0.5\") then\n load(\"openmpi/5.0.5\")\nend\n\nif not isloaded(\"fftw/3.3.10-ompi\") then\n load(\"fftw/3.3.10-ompi\")\nend\n\nif not isloaded(\"openblas/0.3.24\") then\n load(\"openblas/0.3.24\")\nend\n\nif not isloaded(\"netlib-scalapack/2.2.0-ompi\") then\n load(\"netlib-scalapack/2.2.0-ompi\")\nend\n\nif not isloaded(\"wannier90/3.1.0\") then\n load(\"wannier90/3.1.0\")\nend\n\nif not isloaded(\"hdf5/1.14.3__hl_True__fortran_True-ompi\") then\n load(\"hdf5/1.14.3__hl_True__fortran_True-ompi\")\nend\n\nprepend_path(\"PATH\", \"/project//software/vasp.6.3.2/bin\")","type":"text"}]}]},{"type":"expand","attrs":{"title":"To use module file:"},"content":[{"type":"codeBlock","content":[{"text":"[]$ module purge\n[]$ module use /project//software/modules\n[]$ module avail\n-------------------- /project//software/modules ---------------------\n vasp/6.3.2\n...\n\n[]$ module load vasp/6.3.2","type":"text"}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Installation: Potential Issues","type":"text"}]},{"type":"heading","attrs":{"level":5},"content":[{"text":"Bin Folder Executables: Permission Denied","type":"text"}]},{"type":"paragraph","content":[{"text":"If you get an error of the form:","type":"text"}]},{"type":"codeBlock","content":[{"text":"... /project//software/vasp.6.3.2/bin/vasp_std: Permission denied","type":"text"}]},{"type":"paragraph","content":[{"text":"Once built, the files in the ","type":"text"},{"text":"bin","type":"text","marks":[{"type":"code"}]},{"text":" folder should be ","type":"text"},{"text":"executable","type":"text","marks":[{"type":"em"}]},{"text":". Check they have the ","type":"text"},{"text":"x","type":"text","marks":[{"type":"code"}]},{"text":" permission defined for the groups:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[bin]$ ls -al\n-rwxrwxr-x 1

19190336 Oct 7 14:32 vasp_gam\n-rwxrwxr-x 1

19547024 Oct 7 14:39 vasp_ncl\n-rwxrwxr-x 1

19481464 Oct 7 14:25 vasp_std","type":"text"}]},{"type":"paragraph","content":[{"text":"If you don’t then use ","type":"text"},{"text":"chmod ugo+x ","type":"text","marks":[{"type":"code"}]},{"text":" to update.","type":"text"}]}],"version":1}

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