diff --git a/Compendium_attachments/AlphaCentauri/example_pytorch_image_recognition.zip b/Compendium_attachments/AlphaCentauri/example_pytorch_image_recognition.zip new file mode 100644 index 0000000000000000000000000000000000000000..46538b2de73e25e5f8519c1a05ecb3cd71f1c057 Binary files /dev/null and b/Compendium_attachments/AlphaCentauri/example_pytorch_image_recognition.zip differ diff --git a/Compendium_attachments/BigDataFrameworks:ApacheSparkApacheFlinkApacheHadoop/SparkExample.ipynb b/Compendium_attachments/BigDataFrameworks:ApacheSparkApacheFlinkApacheHadoop/SparkExample.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..ffe1aa174859fe6697f65af7ce7bd09d526e4bc1 --- /dev/null +++ b/Compendium_attachments/BigDataFrameworks:ApacheSparkApacheFlinkApacheHadoop/SparkExample.ipynb @@ -0,0 +1,136 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "echo $SPARK_HOME\n", + "echo $JAVA_HOME\n", + "hostname" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "import os\n", + "os.environ['PYSPARK_PYTHON'] = sys.executable\n", + "os.environ['SPARK_CONF_DIR'] = os.environ['HOME'] + '/cluster-conf-' + os.environ['SLURM_JOBID'] + '/spark'" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!SHELL=/bin/bash bash framework-configure.sh spark $SPARK_HOME/conf " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!start-all.sh" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "#import findspark\n", + "#findspark.init()\n", + "import platform\n", + "import pyspark\n", + "from pyspark import SparkContext" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "sc = SparkContext(master=\"spark://\"+platform.node()+\":7077\", appName=\"RDD basic functions App\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "#your Spark workflow code here, the following is just an example:\n", + "datafile = sc.textFile(\"SparkExample.ipynb\")\n", + "firstTenItems = datafile.take(10)\n", + "for item in firstTenItems:\n", + " print(item)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "sc.stop()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!stop-all.sh" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!ps -ef | grep -i java" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "haswell-py3.6-spark", + "language": "python", + "name": "haswell-py3.6-spark" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.10" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/Compendium_attachments/BigDataFrameworks:ApacheSparkApacheFlinkApacheHadoop/example-spark.sbatch b/Compendium_attachments/BigDataFrameworks:ApacheSparkApacheFlinkApacheHadoop/example-spark.sbatch new file mode 100644 index 0000000000000000000000000000000000000000..5a418a9c5e98f70b027618a4da1158010619556b --- /dev/null +++ b/Compendium_attachments/BigDataFrameworks:ApacheSparkApacheFlinkApacheHadoop/example-spark.sbatch @@ -0,0 +1,27 @@ +#!/bin/bash +#SBATCH --time=00:03:00 +#SBATCH --partition=haswell +#SBATCH --nodes=1 +#SBATCH --exclusive +#SBATCH --mem=60G +#SBATCH -J "example-spark" + +ml Spark + +function myExitHandler () { + stop-all.sh +} + +#configuration +. framework-configure.sh spark $SPARK_HOME/conf + +#register cleanup hook in case something goes wrong +trap myExitHandler EXIT + +start-all.sh + +spark-submit --class org.apache.spark.examples.SparkPi $SPARK_HOME/examples/jars/spark-examples_2.11-2.4.4.jar 1000 + +stop-all.sh + +exit 0 diff --git a/Compendium_attachments/DataAnalyticsWithR/Launcher.png b/Compendium_attachments/DataAnalyticsWithR/Launcher.png new file mode 100644 index 0000000000000000000000000000000000000000..fd50be1824655ef7e39c2adf74287fa14a716148 Binary files /dev/null and b/Compendium_attachments/DataAnalyticsWithR/Launcher.png differ diff --git a/Compendium_attachments/DataAnalyticsWithR/RPSOCK.R b/Compendium_attachments/DataAnalyticsWithR/RPSOCK.R new file mode 100644 index 0000000000000000000000000000000000000000..fbf7cad3593d87cfb910b38651b29a9b0d08c6d0 --- /dev/null +++ b/Compendium_attachments/DataAnalyticsWithR/RPSOCK.R @@ -0,0 +1,31 @@ +library(parallel) + +# here some function that needs to be executed in parallel +average <- function(size){ + norm_vector <- rnorm(n=size, mean=mu, sd=sigma) + return(mean(norm_vector)) +} + +# variable initialization +mu <- 1.0 +sigma <- 1.0 +vector_length <- 10^7 +n_repeat <- 100 +sample_sizes <- rep(vector_length, times=n_repeat) + +# cluster setup + +# get number of available nodes (should be the = "ntask") +mynodes = 8 +print(paste("The cluster of size", threads, "will be setup...")) + +# initialize cluster +cl <- makeCluster(mynodes, type="PSOCK", outfile="") + +# distribute required variables for the execution over the cluster +clusterExport(cl, list("mu","sigma")) + +list_of_averages <- parLapply(X=sample_sizes, fun=average, cl=cl) + +# shut down the cluster +print(paste("Program finished")) diff --git a/Compendium_attachments/DataAnalyticsWithR/Rmpi.R b/Compendium_attachments/DataAnalyticsWithR/Rmpi.R new file mode 100644 index 0000000000000000000000000000000000000000..c2dd8410a5ea22f6fe78b61b1ed00ab369ec7a34 --- /dev/null +++ b/Compendium_attachments/DataAnalyticsWithR/Rmpi.R @@ -0,0 +1,34 @@ +library(Rmpi) +library(parallel) + +# here some function that needs to be executed in parallel +average <- function(size){ + norm_vector <- rnorm(n=size, mean=mu, sd=sigma) + return(mean(norm_vector)) +} + +# variable initialization +mu <- 1.0 +sigma <- 1.0 +vector_length <- 10^7 +n_repeat <- 100 +sample_sizes <- rep(vector_length, times=n_repeat) + +# cluster setup + +# get number of available MPI ranks +threads = mpi.universe.size()-1 +print(paste("The cluster of size", threads, "will be setup...")) + +# initialize MPI cluster +cl <- makeCluster(threads, type="MPI", outfile="") + +# distribute required variables for the execution over the cluster +clusterExport(cl, list("mu","sigma")) + +list_of_averages <- parLapply(X=sample_sizes, fun=average, cl=cl) + +# shut down the cluster +#snow::stopCluster(cl) # usually it hangs over here with OpenMPI > 2.0. In this case this command may be avoided, SLURM will clean up after the job finishes + + diff --git a/Compendium_attachments/DataAnalyticsWithR/Rmpi_c.R b/Compendium_attachments/DataAnalyticsWithR/Rmpi_c.R new file mode 100644 index 0000000000000000000000000000000000000000..3e4ba3c5ebb66b1295bd671544facd0052a67efc --- /dev/null +++ b/Compendium_attachments/DataAnalyticsWithR/Rmpi_c.R @@ -0,0 +1,17 @@ +library(Rmpi) + +# initialize an Rmpi environment +ns <- mpi.universe.size()-1 +mpi.spawn.Rslaves(nslaves=ns) + +# send these commands to the slaves +mpi.bcast.cmd( id <- mpi.comm.rank() ) +mpi.bcast.cmd( ns <- mpi.comm.size() ) +mpi.bcast.cmd( host <- mpi.get.processor.name() ) + +# all slaves execute this command +mpi.remote.exec(paste("I am", id, "of", ns, "running on", host)) + +# close down the Rmpi environment +mpi.close.Rslaves(dellog = FALSE) +mpi.exit() diff --git a/Compendium_attachments/DataAnalyticsWithR/TensorflowMNIST.R b/Compendium_attachments/DataAnalyticsWithR/TensorflowMNIST.R new file mode 100644 index 0000000000000000000000000000000000000000..fbc1ca165673ddc4ae3eb08739fd605b04f858cf --- /dev/null +++ b/Compendium_attachments/DataAnalyticsWithR/TensorflowMNIST.R @@ -0,0 +1,80 @@ +library(tensorflow) +library(keras) + +# Data Preparation + +batch_size <- 128 +num_classes <- 10 +epochs <- 12 + +# Input image dimensions + +img_rows <- 28 +img_cols <- 28 + +# The data, shuffled and split between train and test sets + +mnist <- dataset_mnist() +x_train <- mnist$train$x +y_train <- mnist$train$y +x_test <- mnist$test$x +y_test <- mnist$test$y + +# Redefine dimension of train/test inputs + +x_train <- array_reshape(x_train, c(nrow(x_train), img_rows, img_cols, 1)) +x_test <- array_reshape(x_test, c(nrow(x_test), img_rows, img_cols, 1)) +input_shape <- c(img_rows, img_cols, 1) + +# Transform RGB values into [0,1] range + +x_train <- x_train / 255 +x_test <- x_test / 255 + +cat('x_train_shape:', dim(x_train), '\n') +cat(nrow(x_train), 'train samples\n') +cat(nrow(x_test), 'test samples\n') + +# Convert class vectors to binary class matrices + +y_train <- to_categorical(y_train, num_classes) +y_test <- to_categorical(y_test, num_classes) + +# Define Model + +model <- keras_model_sequential() %>% + layer_conv_2d(filters = 32, kernel_size = c(3,3), activation = 'relu', + input_shape = input_shape) %>% + layer_conv_2d(filters = 64, kernel_size = c(3,3), activation = 'relu') %>% + layer_max_pooling_2d(pool_size = c(2, 2)) %>% + layer_dropout(rate = 0.25) %>% + layer_flatten() %>% + layer_dense(units = 128, activation = 'relu') %>% + layer_dropout(rate = 0.5) %>% + layer_dense(units = num_classes, activation = 'softmax') + +# Compile model + +model %>% compile( + loss = loss_categorical_crossentropy, + optimizer = optimizer_adadelta(), + metrics = c('accuracy') +) + +# Train model + +model %>% fit( + x_train, y_train, + batch_size = batch_size, + epochs = epochs, + validation_split = 0.2 +) + + +scores <- model %>% evaluate( + x_test, y_test, verbose = 0 +) + +# Output metrics +cat('Test loss:', scores[[1]], '\n') +cat('Test accuracy:', scores[[2]], '\n') diff --git a/Compendium_attachments/DataAnalyticsWithR/environments.png b/Compendium_attachments/DataAnalyticsWithR/environments.png new file mode 100644 index 0000000000000000000000000000000000000000..15076eb14f822a26b80730f1cba2c244a15e326f Binary files /dev/null and b/Compendium_attachments/DataAnalyticsWithR/environments.png differ diff --git a/Compendium_attachments/DataAnalyticsWithR/lapply.R b/Compendium_attachments/DataAnalyticsWithR/lapply.R new file mode 100644 index 0000000000000000000000000000000000000000..84849396caf89acc584daf75ce0b41909f88d310 --- /dev/null +++ b/Compendium_attachments/DataAnalyticsWithR/lapply.R @@ -0,0 +1,24 @@ +#create small dataset +name <- c("1", "2", "3", "4", "5") +age <- c(6, 7, 4, 5, 6) +growth <- c(100, 107, 85, 93, 99) +weight <- c(20, 23, 16, 19, 20) +children <- data.frame(name, age, growth, weight) + +#The kmeans function is now wrapped in a custom parallel function +#that takes the number of starting positions (nstart) as its sole parameter +parallel.function <- function(i) {kmeans( children, centers=4, nstart=i )} + +#Each of the four invocations of lapply winds up calling kmeans, +#but each call to kmeans only does 25 starts instead of the full 100 +results <- lapply( c(25, 25, 25, 25), FUN=parallel.function ) + + +#for the k-means result with the absolute lowest value for results$tot.withinss use the which.min() function alue. +#for thw which.min() for the input vecor) use tot.withinss.sapply returns a vector comprised of each tot.withinss value from the list of k-means objects +temp.vector <- sapply( results, function(result) { result$tot.withinss } ) + +#to get the index of temp.vector that contains the minimum value +result <- results[[which.min(temp.vector)]] + +print(result) diff --git a/Compendium_attachments/DataAnalyticsWithR/multicore.R b/Compendium_attachments/DataAnalyticsWithR/multicore.R new file mode 100644 index 0000000000000000000000000000000000000000..8404bc5e59b93aafd21ba5abf105728f0e2e2d1c --- /dev/null +++ b/Compendium_attachments/DataAnalyticsWithR/multicore.R @@ -0,0 +1,22 @@ +library(parallel) + +# here some function that needs to be executed in parallel +average <- function(size){ + norm_vector <- rnorm(n=size, mean=mu, sd=sigma) + return(mean(norm_vector)) +} + +# variable initialization +mu <- 1.0 +sigma <- 1.0 +vector_length <- 10^7 +n_repeat <- 100 +sample_sizes <- rep(vector_length, times=n_repeat) + + +# shared-memory version +threads <- as.integer(Sys.getenv("SLURM_CPUS_ON_NODE")) +# here the name of the variable depends on the correct sbatch configuration +# unfortunately the built-in function gets the total number of physical cores without looking on SLURM configuration + +list_of_averages <- mclapply(X=sample_sizes, FUN=average, 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b/Compendium_attachments/FEMSoftware/Rot-modell-BenjaminGroeger.inp @@ -0,0 +1,189 @@ +*Heading +** Job name: Rot-modell Model name: Model-1 +** Generated by: Abaqus/CAE 2016 +*Preprint, echo=NO, model=NO, history=NO, contact=NO +** +** PARTS +** +*Part, name=Part-1 +*Node + 1, 98.0785294, -19.5090313, 0. + 2, 108.150925, -21.5125561, 0. + 3, 119.31588, -23.7334042, 0. + 4, 131.691895, -26.1951466, 0. + 5, 145.410339, -28.923914, 0. + 6, 160.616821, -31.9486732, 0. + 7, 177.472763, -35.3015251, 0. + 8, 196.157059, -39.0180626, 0. + 9, 99.1444855, -13.052619, 0. + 10, 109.326355, -14.3930874, 0. + 11, 120.612656, -15.8789568, 0. + 12, 133.123184, -17.5259991, 0. + 13, 146.990723, -19.351696, 0. + 14, 162.362473, -21.3754253, 0. + 15, 179.401611, -23.6186695, 0. + 16, 198.288971, -26.105238, 0. + 17, 99.7858887, -6.54031277, 0. + 18, 110.03363, -7.21198511, 0. + 19, 121.392944, -7.95651388, 0. + 20, 133.984406, -8.78180218, 0. + 21, 147.941666, -9.69660854, 0. + 22, 163.412857, 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generate + 1, 42, 1 +*Orientation, name=Ori-1, system=CYLINDRICAL + 0., 0., 0., 0., 0., 1. +3, 0. +** Section: Section-1 +*Shell Section, elset=_PickedSet14, material=Material-1, orientation=Ori-1 +5., 5 +*End Part +** +** +** ASSEMBLY +** +*Assembly, name=Assembly +** +*Instance, name=Part-1-1, part=Part-1 +*End Instance +** +*Nset, nset=_PickedSet4, internal, instance=Part-1-1 + 1, 2, 3, 4, 5, 6, 7, 8, 49, 50, 51, 52, 53, 54, 55, 56 +*Elset, elset=_PickedSet4, internal, instance=Part-1-1 + 1, 2, 3, 4, 5, 6, 7, 36, 37, 38, 39, 40, 41, 42 +*Nset, nset=_PickedSet5, internal, instance=Part-1-1, generate + 1, 56, 1 +*Elset, elset=_PickedSet5, internal, instance=Part-1-1, generate + 1, 42, 1 +*Nset, nset="_T-Part-1-1-Datum csys-1", internal +_PickedSet4, +*Transform, nset="_T-Part-1-1-Datum csys-1", type=C + 0., 0., 0., 0., 0., 1. +*End Assembly +** +** MATERIALS +** +*Material, name=Material-1 +*Density + 7.8e-09, +*Elastic +210000., 0.29 +** 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By default, graphics are left aligned. **Note:** It is crucial to +have `{: align="center"}` on a new line.