added examples for python R and GPU

docker/R/read/condor.submit

@@ -0,0 +1,11 @@
+should_transfer_files = Yes
+when_to_transfer_output = ON_EXIT_OR_EVICT
+transfer_input_files = read.R
+Universe = docker
+docker_image = r-base
+Executable = /usr/bin/Rscript
+Arguments = read.R /datos/ma0/test.txt
+Log = read_R_log.log
+Output = read_R_out.out
+Error = read_R_err.err
+Queue

docker/R/read/read.R

@@ -0,0 +1,4 @@
+args <- commandArgs(TRUE)
+data <- read.delim(args[1])
+print(data)
+

docker/R/read/read_R_log.log

@@ -0,0 +1,19 @@
+000 (050.000.000) 05/10 11:13:59 Job submitted from host: <192.168.27.25:9618?addrs=192.168.27.25-9618&noUDP&sock=1446571_f6bf_4>
+...
+001 (050.000.000) 05/10 11:14:01 Job executing on host: <192.168.27.17:9618?addrs=192.168.27.17-9618&noUDP&sock=27247_c111_3>
+...
+005 (050.000.000) 05/10 11:14:02 Job terminated.
+	(1) Normal termination (return value 0)
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Remote Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Local Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Total Remote Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Total Local Usage
+	49  -  Run Bytes Sent By Job
+	67  -  Run Bytes Received By Job
+	49  -  Total Bytes Sent By Job
+	67  -  Total Bytes Received By Job
+	Partitionable Resources :    Usage  Request Allocated 
+	   Cpus                 :        0        1         1 
+	   Disk (KB)            :       16        1     45972 
+	   Memory (MB)          :                 0      1024 
+...

docker/R/read/read_R_out.out

@@ -0,0 +1,2 @@
+[1] hello.world
+<0 rows> (or 0-length row.names)

docker/R/requirements/Dockerfile

@@ -0,0 +1,7 @@
+FROM r-base
+
+WORKDIR /code
+ADD install.R /code
+RUN Rscript install.R
+
+CMD ["Rscript"]

docker/R/requirements/compile_docker_image.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+if [ -z "$1" ]; then
+    echo "A name for the image is needed"
+    exit 1
+fi
+
+docker build -t 192.168.27.25:5000/$(whoami)/$1 .
+docker push 192.168.27.25:5000/$(whoami)/$1
+

docker/R/requirements/condor.submit

@@ -0,0 +1,11 @@
+should_transfer_files = Yes
+when_to_transfer_output = ON_EXIT_OR_EVICT
+transfer_input_files = requirements.R
+Universe = docker
+docker_image = 192.168.27.25:5000/ma0/plumber_test
+Executable = /usr/bin/Rscript
+Arguments = requirements.R
+Log = requirements_R_log.log
+Output = requirements_R_out.out
+Error = requirements_R_err.err
+Queue

docker/R/requirements/docker_stderror

@@ -0,0 +1,21 @@
+Unable to find image '192.168.27.25:5000/ma0/plumber_test:latest' locally
+latest: Pulling from ma0/plumber_test
+0656ed1d7f85: Already exists
+c753f78c1082: Already exists
+9b7d77a2fb38: Already exists
+f759fbe73258: Already exists
+5dbb370e90a3: Already exists
+77bb82bbd854: Already exists
+03cc54129ca4: Pulling fs layer
+821d7fd1ddb1: Pulling fs layer
+abf1a70cd42e: Pulling fs layer
+03cc54129ca4: Download complete
+821d7fd1ddb1: Verifying Checksum
+821d7fd1ddb1: Download complete
+03cc54129ca4: Pull complete
+821d7fd1ddb1: Pull complete
+abf1a70cd42e: Verifying Checksum
+abf1a70cd42e: Download complete
+abf1a70cd42e: Pull complete
+Digest: sha256:be7a2bdd848f4610f1ea5de4bb0c53d1c88d08a4b023cb791e640c9ad3dd9105
+Status: Downloaded newer image for 192.168.27.25:5000/ma0/plumber_test:latest

docker/R/requirements/install.R

@@ -0,0 +1 @@
+if(!require(plumber))install.packages("plumber")

docker/R/requirements/requirements.R

@@ -0,0 +1,3 @@
+library(plumber)
+plumb
+

docker/R/requirements/requirements_R_log.log

@@ -0,0 +1,19 @@
+000 (051.000.000) 05/10 12:05:50 Job submitted from host: <192.168.27.25:9618?addrs=192.168.27.25-9618&noUDP&sock=1446571_f6bf_4>
+...
+001 (051.000.000) 05/10 12:05:52 Job executing on host: <192.168.27.17:9618?addrs=192.168.27.17-9618&noUDP&sock=27247_c111_3>
+...
+005 (051.000.000) 05/10 12:05:56 Job terminated.
+	(1) Normal termination (return value 0)
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Remote Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Local Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Total Remote Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Total Local Usage
+	2015  -  Run Bytes Sent By Job
+	24  -  Run Bytes Received By Job
+	2015  -  Total Bytes Sent By Job
+	24  -  Total Bytes Received By Job
+	Partitionable Resources :    Usage  Request Allocated 
+	   Cpus                 :        0        1         1 
+	   Disk (KB)            :       18        1     45972 
+	   Memory (MB)          :                 0      1024 
+...

docker/R/requirements/requirements_R_out.out

@@ -0,0 +1,42 @@
+function (file, dir = ".") 
+{
+    dirMode <- NULL
+    if (!missing(file) && !missing(dir)) {
+        stop("You must set either the file or the directory parameter, not both")
+    }
+    else if (missing(file)) {
+        if (identical(dir, "")) {
+            stop("You must specify either a file or directory parameter")
+        }
+        dirMode <- TRUE
+        dir <- sub("/$", "", dir)
+        file <- list.files(dir, "^plumber\\.r$", ignore.case = TRUE, 
+            full.names = TRUE)
+        if (length(file) == 0) {
+            stop("No plumber.R file found in the specified directory: ", 
+                dir)
+        }
+    }
+    else {
+        dirMode <- FALSE
+    }
+    entrypoint <- list.files(dir, "^entrypoint\\.r$", ignore.case = TRUE)
+    if (dirMode && length(entrypoint) > 0) {
+        old <- setwd(dir)
+        on.exit(setwd(old))
+        x <- source(entrypoint)
+        pr <- x$value
+        if (!("plumber" %in% class(pr))) {
+            stop("entrypoint.R must return a runnable Plumber router.")
+        }
+        pr
+    }
+    else if (file.exists(file)) {
+        plumber$new(file)
+    }
+    else {
+        stop("File does not exist: ", file)
+    }
+}
+<bytecode: 0x55df34386588>
+<environment: namespace:plumber>

docker/R/write/condor.submit

@@ -0,0 +1,11 @@
+should_transfer_files = Yes
+when_to_transfer_output = ON_EXIT_OR_EVICT
+transfer_input_files = write.R
+Universe = docker
+docker_image = r-base
+Executable = /usr/bin/Rscript
+Arguments = write.R /datos/ma0/write_file.txt
+Log = write_R_log.log
+Output = write_R_out.out
+Error = write_R_err.err
+Queue

docker/R/write/docker_stderror

@@ -0,0 +1,27 @@
+Unable to find image 'r-base:latest' locally
+latest: Pulling from library/r-base
+0656ed1d7f85: Pulling fs layer
+c753f78c1082: Pulling fs layer
+9b7d77a2fb38: Pulling fs layer
+f759fbe73258: Pulling fs layer
+5dbb370e90a3: Pulling fs layer
+77bb82bbd854: Pulling fs layer
+f759fbe73258: Waiting
+77bb82bbd854: Waiting
+c753f78c1082: Download complete
+9b7d77a2fb38: Verifying Checksum
+9b7d77a2fb38: Download complete
+f759fbe73258: Verifying Checksum
+f759fbe73258: Download complete
+0656ed1d7f85: Download complete
+5dbb370e90a3: Download complete
+0656ed1d7f85: Pull complete
+c753f78c1082: Pull complete
+9b7d77a2fb38: Pull complete
+f759fbe73258: Pull complete
+5dbb370e90a3: Pull complete
+77bb82bbd854: Verifying Checksum
+77bb82bbd854: Download complete
+77bb82bbd854: Pull complete
+Digest: sha256:d0e69d45a36a60dfc7fd972f68fcbc154071018c79b7f44c28fe0e6032f94233
+Status: Downloaded newer image for r-base:latest

docker/R/write/write.R

@@ -0,0 +1,4 @@
+args <- commandArgs(TRUE)
+write("Hola mundo", args[1])
+
+

docker/R/write/write_R_log.log

@@ -0,0 +1,19 @@
+000 (049.000.000) 05/10 11:02:21 Job submitted from host: <192.168.27.25:9618?addrs=192.168.27.25-9618&noUDP&sock=1446571_f6bf_4>
+...
+001 (049.000.000) 05/10 11:02:23 Job executing on host: <192.168.27.17:9618?addrs=192.168.27.17-9618&noUDP&sock=27247_c111_3>
+...
+005 (049.000.000) 05/10 11:02:39 Job terminated.
+	(1) Normal termination (return value 0)
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Remote Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Local Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Total Remote Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Total Local Usage
+	899  -  Run Bytes Sent By Job
+	57  -  Run Bytes Received By Job
+	899  -  Total Bytes Sent By Job
+	57  -  Total Bytes Received By Job
+	Partitionable Resources :    Usage  Request Allocated 
+	   Cpus                 :        0        1         1 
+	   Disk (KB)            :       17        1     45972 
+	   Memory (MB)          :                 0      1024 
+...

docker/python/read/condor.submit

@@ -0,0 +1,11 @@
+should_transfer_files = Yes
+when_to_transfer_output = ON_EXIT_OR_EVICT
+transfer_input_files = read.py
+Universe = docker
+docker_image = python:3.7-alpine
+Executable = /usr/local/bin/python
+Arguments = read.py /datos/ma0/dummy_file.txt
+Log = read_python_log.log
+Output = read_python_out.out
+Error = read_python_err.err
+Queue

docker/python/read/docker_stderror

@@ -0,0 +1,23 @@
+Unable to find image 'python:3.7-alpine' locally
+3.7-alpine: Pulling from library/python
+bdf0201b3a05: Pulling fs layer
+59c926705abf: Pulling fs layer
+31ca6b067b5a: Pulling fs layer
+b18bc4e1c47b: Pulling fs layer
+7e244112a44c: Pulling fs layer
+b18bc4e1c47b: Waiting
+7e244112a44c: Waiting
+59c926705abf: Download complete
+bdf0201b3a05: Download complete
+bdf0201b3a05: Pull complete
+59c926705abf: Pull complete
+31ca6b067b5a: Verifying Checksum
+31ca6b067b5a: Download complete
+b18bc4e1c47b: Download complete
+7e244112a44c: Verifying Checksum
+7e244112a44c: Download complete
+31ca6b067b5a: Pull complete
+b18bc4e1c47b: Pull complete
+7e244112a44c: Pull complete
+Digest: sha256:a12943ec653051bab0c3a542cd99ef4b8f9c9253bfcdbfe291cfe5fea2c6008c
+Status: Downloaded newer image for python:3.7-alpine

docker/python/read/read.py

@@ -0,0 +1,12 @@
+import sys
+
+def read_dummy_file(file_name):
+    with open(file_name) as f:
+        data = f.read()
+        print(data)
+
+
+if __name__ == "__main__":
+    assert len(sys.argv) > 1
+    read_dummy_file(sys.argv[1])
+

docker/python/read/read.py.save

@@ -0,0 +1,3 @@
+def read_file():
+    with open("/datos/test/dummy_file.txt") as f:
+        dataf.read()

docker/python/read/read_python_log.log

@@ -0,0 +1,19 @@
+000 (055.000.000) 05/10 16:53:29 Job submitted from host: <192.168.27.25:9618?addrs=192.168.27.25-9618&noUDP&sock=1446571_f6bf_4>
+...
+001 (055.000.000) 05/10 16:53:30 Job executing on host: <192.168.27.17:9618?addrs=192.168.27.17-9618&noUDP&sock=27247_c111_3>
+...
+005 (055.000.000) 05/10 16:53:36 Job terminated.
+	(1) Normal termination (return value 0)
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Remote Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Local Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Total Remote Usage
+		Usr 0 00:00:00, Sys 0 00:00:00  -  Total Local Usage
+	802  -  Run Bytes Sent By Job
+	211  -  Run Bytes Received By Job
+	802  -  Total Bytes Sent By Job
+	211  -  Total Bytes Received By Job
+	Partitionable Resources :    Usage  Request Allocated 
+	   Cpus                 :        0        1         1 
+	   Disk (KB)            :       17        1     45972 
+	   Memory (MB)          :                 0      1024 
+...

docker/python/read/read_python_out.out

@@ -0,0 +1,2 @@
+data for test
+

docker/python/requirements/Dockerfile

@@ -0,0 +1,7 @@
+FROM python:3.7-alpine
+
+WORKDIR /code
+ADD requirements.txt /code
+RUN pip install -r requirements.txt
+
+CMD ["python"]

docker/python/requirements/compile_docker_image.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+if [ -z "$1" ]; then
+    echo "A name for the image is needed"
+    exit 1
+fi
+
+docker build -t 192.168.27.25:5000/$(whoami)/$1 .
+docker push 192.168.27.25:5000/$(whoami)/$1
+

docker/python/requirements/condor.submit

@@ -0,0 +1,11 @@
+should_transfer_files = Yes
+when_to_transfer_output = ON_EXIT_OR_EVICT
+transfer_input_files = requirements.py
+Universe = docker
+docker_image = 192.168.27.25:5000/ma0/django_test
+Executable = /usr/local/bin/python
+Arguments = requirements.py
+Log = requirements_python_log.log
+Output = requirements_python_out.out
+Error = requirements_python_err.err
+Queue

docker/python/requirements/requirements.py

@@ -0,0 +1,8 @@
+import django
+
+def check_django():
+    print(django.VERSION)
+
+if __name__ == "__main__":
+    check_django()
+

docker/python/requirements/requirements.txt

@@ -0,0 +1 @@
+django==2.2.0

docker/python/write/condor.submit

@@ -0,0 +1,11 @@
+should_transfer_files = Yes
+when_to_transfer_output = ON_EXIT_OR_EVICT
+transfer_input_files = write.py
+Universe = docker
+docker_image = python:3.7-alpine
+Executable = /usr/local/bin/python
+Arguments = write.py /datos/ma0/write_file.txt
+Log = write_python_log.log
+Output = write_python_out.out
+Error = write_python_err.err
+Queue

docker/python/write/write.py

@@ -0,0 +1,11 @@
+import sys
+
+def write_file(file_name):
+    with open(file_name, "w+") as f:
+        f.write("Dummy text")
+
+
+if __name__ == "__main__":
+    assert len(sys.argv) > 1
+    write_file(sys.argv[1])
+

gpu/add.cu

@@ -0,0 +1,55 @@
+#include <iostream>
+#include <math.h>
+
+// Kernel function to add the elements of two arrays
+__global__
+void add(int n, float *x, float *y)
+{
+  int index = threadIdx.x;
+  int stride = blockDim.x;
+  for (int i = index; i < n; i += stride)
+      y[i] = x[i] + y[i];
+}
+
+/*
+__global__
+void add(int n, float *x, float *y)
+{
+  for (int i = 0; i < n; i++)
+    y[i] = x[i] + y[i];
+}
+*/
+
+int main(void)
+{
+  int N = 1<<20;
+  float *x, *y;
+
+  // Allocate Unified Memory – accessible from CPU or GPU
+  cudaMallocManaged(&x, N*sizeof(float));
+  cudaMallocManaged(&y, N*sizeof(float));
+
+  // initialize x and y arrays on the host
+  for (int i = 0; i < N; i++) {
+    x[i] = 1.0f;
+    y[i] = 2.0f;
+  }
+
+  // Run kernel on 1M elements on the GPU
+  add<<<1, 256>>>(N, x, y);
+
+  // Wait for GPU to finish before accessing on host
+  cudaDeviceSynchronize();
+
+  // Check for errors (all values should be 3.0f)
+  float maxError = 0.0f;
+  for (int i = 0; i < N; i++)
+    maxError = fmax(maxError, fabs(y[i]-3.0f));
+  std::cout << "Max error: " << maxError << std::endl;
+
+  // Free memory
+  cudaFree(x);
+  cudaFree(y);
+  
+  return 0;
+}

gpu/condor.submit

@@ -0,0 +1,15 @@
+should_transfer_files = Yes
+when_to_transfer_output = ON_EXIT_OR_EVICT
+
+transfer_input_files=add.cu
+Executable = run.sh
+Universe   = vanilla
+Log        = add_log.log
+Output     = add_out.out
+Error      = add_err.err
+
+request_cpus = 1
+request_memory = 2G
+request_gpus = 1
+
+Queue 

gpu/run.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+export PATH=/usr/local/cuda-10.1/bin:/usr/local/cuda-10.1/NsightCompute-2019.1:${PATH}
+# Compilar codigo para GPU
+nvcc add.cu -o add_cuda
+# Ejecutar codigo
+nvprof ./add_cuda
+# Finalizada ejecucion
+