arteymix

Slurm Primer!

I decided to write this primer to encourage the usage the lab members to use our compute cluster.

We don’t really do distribute computing with tasks that run across nodes/processes and inter-communicate. Thus, I’ll focus on the case where only one task is asked (i.e. --tasks=1).

Slurm vocabulary

arteymix

package ubic.gemma.persistence.util;

import org.springframework.beans.factory.DisposableBean;
import org.springframework.beans.factory.FactoryBean;

import javax.annotation.OverridingMethodsMustInvokeSuper;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;

arteymix

import requests
import pandas as pd
from tqdm import tqdm
from os.path import join
from functools import wraps

def unpaginate(endpoint):
    """Unpaginate a paginated Spring endpoint by yielding from the pages content"""
    @wraps(endpoint)
    def f(*args, page_size=20):

arteymix

#!/usr/bin/env python

#
# Converts the CADD format to VCF
#

import sys
import csv

print('''##fileformat=VCFv4.2

arteymix

project('test', 'c', 'vala')

glib_dep = dependency('glib-2.0')
config = configure_file(input: 'build.vala',
                        output: 'build.vala',
                        configuration: configuration_data())

executable('main', ['main.vala', config],
           dependencies: [glib_dep])

arteymix

class ErrorHandler {
    public signal void publish (Error err);
    private static ErrorHandler _default;
    public static ErrorHandler get_default () {
      if (_default == null) {
              _default = new ErrorHandler ();
      }
      return _default;
    }
}

arteymix

/* gocl-0.2.vapi generated by vapigen, do not modify. */

[CCode (cprefix = "Gocl", gir_namespace = "Gocl", gir_version = "0.2", lower_case_cprefix = "gocl_")]
namespace Gocl {
	[CCode (cheader_filename = "gocl.h", type_id = "gocl_buffer_get_type ()")]
	public class Buffer : GLib.Object, GLib.Initable {
		[CCode (has_construct_function = false)]
		public Buffer (Gocl.Context context, uint flags, size_t size, uint64 host_ptr);
		public unowned Gocl.Context get_context ();
		public unowned Gocl.Event map (Gocl.Queue queue, Gocl.BufferMapFlags map_flags, size_t offset, size_t size, GLib.List<Gocl.Event>? event_wait_list);

arteymix

TOOLS := meson mesonconf mesonintrospect wraptool

all: $(TOOLS)

%: %.py
	cp meson.py __main__.py
	zip $@.zip __main__.py mesonbuild/**/*.py
	echo '#!/usr/bin/env python3' > $@
	cat $@.zip >> $@
	chmod +x $@

arteymix

using GLib;

[ModuleInit]
public Type simple_init (TypeModule type_module) 
{
	return typeof (CustomSimple);
}

public class CustomSimple : Simple
{

arteymix

using Gtk;
Button button;

public static int main (string[] args) {
	Gtk.init (ref args);

	var window = new Window ();
	window.title = "Count without blocking the UI";
	window.border_width = 10;
	window.window_position = WindowPosition.CENTER;