{"type":"doc","content":[{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"minLevel":{"value":"1"},"maxLevel":{"value":"6"},"include":{"value":""},"outline":{"value":"false"},"indent":{"value":""},"style":{"value":"none"},"exclude":{"value":""},"type":{"value":"list"},"class":{"value":""},"printable":{"value":"true"}},"macroMetadata":{"macroId":{"value":"4972261c-78df-4eb3-8ff7-4cb6d8d19d93"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"520fc739-657a-48e5-a199-18a435fc5a8d"}},{"type":"heading","attrs":{"level":1},"content":[{"text":"Overview ","type":"text"}]},{"type":"paragraph","content":[{"text":"OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT) , norm-conserving pseudopotentials and pseudo-atomic localized basis functions. ","type":"text"}]},{"type":"paragraph","content":[{"text":"Website: ","type":"text"},{"type":"inlineCard","attrs":{"url":"https://www.openmx-square.org/index.html"}},{"text":" ","type":"text"}]},{"type":"paragraph"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Presentation","type":"text"}]},{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"widget","parameters":{"macroParams":{"overlay":{"value":"youtube"},"_template":{"value":"com/atlassian/confluence/extra/widgetconnector/templates/youtube.vm"},"width":{"value":"400px"},"url":{"value":"https://www.youtube.com/watch?v=kLNNx4aUW2k"},"height":{"value":"300px"}},"macroMetadata":{"macroId":{"value":"2b6db9c41ffb0198a217f4b1fa457f136ddb07d81320b24978bd4ad1d386f552"},"schemaVersion":{"value":"1"},"placeholder":[{"type":"image","data":{"url":"/plugins/servlet/widgetconnector/placeholder?thumb=https://img.youtube.com/vi/kLNNx4aUW2k/mqdefault.jpg&overlay=youtube&width=400&height=300"}}],"title":"Widget Connector"}},"localId":"e8db13ec-6219-4ed6-94bc-15a156e5ac63"}},{"type":"paragraph","content":[{"text":"PDF: ","type":"text"},{"type":"mediaInline","attrs":{"id":"6840ed6a-bab5-4116-bf2a-6bcc92684ab9","collection":"contentId-3180331009"}},{"text":" ","type":"text"}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Build","type":"text"}]},{"type":"paragraph","content":[{"text":"Download the version 3.9 and keep the data folder, ","type":"text"},{"text":"DFT_DATA19","type":"text","marks":[{"type":"code"}]},{"text":". ","type":"text"}]},{"type":"codeBlock","content":[{"text":"wget https://www.openmx-square.org/openmx3.9.tar.gz\ntar xfp openmx3.9.tar.gz\ncd openmx3.9\nrm -rf source","type":"text"}]},{"type":"paragraph","content":[{"text":"Download and extract the version 3.962, ","type":"text"},{"type":"mediaInline","attrs":{"id":"85bbcc85-f609-413c-9dc8-ed9923d8d260","collection":"contentId-3180331009"}},{"text":" .","type":"text"}]},{"type":"codeBlock","content":[{"text":"tar xfp source3.962.tar.gz\ncd source3.962","type":"text"}]},{"type":"paragraph","content":[{"text":"Note: don’t use the v3.9.9, but the 3.962 in the competition.","type":"text"}]},{"type":"paragraph"},{"type":"paragraph","content":[{"text":"Edit the ","type":"text"},{"text":"makefile","type":"text","marks":[{"type":"code"}]},{"text":" for the compilers and MPI on the system you will be using. The following shows the differences between the modified makefile and the original one:","type":"text"}]},{"type":"codeBlock","content":[{"text":"$ diff makefile makefile.orig\n9,12c9,12\n< # MKLROOT = /opt/intel/mkl\n< CC = mpicc -O3 -march=core-avx2 -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw -diag-disable=10441\n< FC = mpif90 -O3 -march=core-avx2 -ip -no-prec-div -qopenmp -diag-disable=10441\n< LIB= -mkl -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64\n---\n> MKLROOT = /opt/intel/mkl\n> CC = mpicc -O3 -xHOST -ip -no-prec-div -qopenmp -I/opt/intel/mkl/include/fftw/\n> FC = mpif90 -O3 -xHOST -ip -no-prec-div -qopenmp\n> LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lifcore -liomp5 -lpthread -lm -ldl\n249c249\n< $(FC) $(OBJS) $(LIB) -lm -nofor-main -o openmx\n---\n> $(CC) $(OBJS) $(LIB) -lm -o openmx","type":"text"}]},{"type":"paragraph","content":[{"text":"To build openmx using openmpi module on PSC.","type":"text"}]},{"type":"codeBlock","content":[{"text":"module load openmpi/4.0.5-nvhpc22.9\n\nexport OMPI_CC=icc\nexport OMPI_FC=ifort\nmake install","type":"text"}]},{"type":"paragraph","content":[{"text":"If everything goes well, there will be an executable called ","type":"text"},{"text":"openmx","type":"text","marks":[{"type":"code"}]},{"text":" in the ","type":"text"},{"text":"../work","type":"text","marks":[{"type":"code"}]},{"text":" directory. (See also ","type":"text"},{"text":"Installation tips","type":"text","marks":[{"type":"link","attrs":{"href":"https://openmx-square.org/openmx_man3.9/node14.html"}}]},{"text":".)","type":"text"}]},{"type":"paragraph","content":[{"text":"You can build your openmpi with latest Intel compilers or use any other MPI.","type":"text"}]},{"type":"paragraph","content":[{"text":"You will also need (at the same level where your ","type":"text"},{"text":"work","type":"text","marks":[{"type":"code"}]},{"text":" and ","type":"text"},{"text":"source3.962","type":"text","marks":[{"type":"code"}]},{"text":" directories are), the ","type":"text"},{"text":"DFT_DATA19","type":"text","marks":[{"type":"code"}]},{"text":" directory that contains the database needed by OpenMX.","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"Sample output:","type":"text"}]},{"type":"codeBlock","content":[{"text":"The number of threads in each node for OpenMP parallelization is 1.\n\n\n*******************************************************\n*******************************************************\n Welcome to OpenMX Ver. 3.9.23\n Copyright (C), 2002-2019, T. Ozaki\n OpenMX comes with ABSOLUTELY NO WARRANTY.\n This is free software, and you are welcome to\n redistribute it under the constitution of the GNU-GPL.\n*******************************************************\n*******************************************************\n\nAutomatic determination of Kerker_factor: 1.072808181156\n\n\n Your input file was normally read.\n The system includes 3 species and 64 atoms.\n\n*******************************************************\n PAO and VPS\n*******************************************************\n\n PAOs of species C were normally found.\n PAOs of species N were normally found.\n...\nThe SCF was achieved at MD= 1\n\n*******************************************************\n MD or geometry opt. at MD = 1\n*******************************************************\n\n\noutputting data on grids to files...\n\n\n***********************************************************\n***********************************************************\n Computational Time (second)\n***********************************************************\n***********************************************************\n\n Min_ID Min_Time Max_ID Max_Time\n Total Computational Time = 387 271.764 0 272.818\n readfile = 8 2.722 344 2.733\n truncation = 105 3.859 6 4.736\n MD_pac = 507 0.003 27 0.006\n ...","type":"text"}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Tasks and Submissions","type":"text"}]},{"type":"paragraph","content":[{"text":" You can practice building and running with a tiny input, Methane, below.","type":"text"}]},{"type":"codeBlock","content":[{"text":"cd ../work\n# Copy the input here\nmpirun -np <# procs> ./openmx Methane.dat","type":"text"}]},{"type":"mediaGroup","content":[{"type":"media","attrs":{"id":"299a96c5-ca3c-480b-b056-14d787ba6deb","collection":"contentId-3180331009","type":"file"}}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Run the application on 4 CPU nodes with the NVC input and submit the results in the team’s folder. Try varying the number of OpenMP threads per MPI rank for your optimal run. Submit the std outputs.","type":"text"}]}]}]},{"type":"mediaGroup","content":[{"type":"media","attrs":{"id":"d95a14a9-8556-4cdc-b0ca-00b755687d1d","collection":"contentId-3180331009","type":"file"}}]},{"type":"orderedList","attrs":{"order":2},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Run MPI Profiler to profile the application. Which three MPI calls are mostly used? Include your results in the team's interview ppt slides.","type":"text"}]}]}]},{"type":"paragraph"},{"type":"orderedList","attrs":{"order":3},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Visualize the results, create a short video that demonstrate the given input via OpenMXViewer (","type":"text"},{"type":"inlineCard","attrs":{"url":"https://www.openmx-square.org/viewer/"}},{"text":" just drag and drop). Include it in the team’s interview ppt slides. If you use have an X (Twitter) account, please tag the video/photo with your team name and the hashtags “#ISC25 #ISC25_SCC” prior to the team interview.","type":"text"}]}]}]},{"type":"paragraph"}],"version":1}

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