1.7. JobServer and TaskServer Administration and Configuration

download:pdf

1.7.1. Introduction

The JobServer is the middle tier of MedeA. It executes the jobs that are launched by the MedeA graphical user interface (the first tier). MedeA jobs encompass one or a series of MedeA tasks, i.e. the actual calculations. MedeA tasks are executed by the TaskServer. This section describes the JobServer and TaskServer management, administration, and configuration.

1.7.2. Checking, Starting, and Stopping JobServer and TaskServer

1.7.2.1. Checking JobServer and TaskServer

Before configuring your JobServer and TaskServer, first check whether they are up and running.

  1. Start a web browser (e.g. the Internet Explorer, Firefox) and point the address bar to http://localhost:32000 to see if the JobServer on your local computer is up and running.

    Hint

    “localhost” can be replaced with the IP address of a remote JobServer or its hostname.

  2. Open a browser and point the address bar to http://localhost:23000 to see if the TaskServer on your local computer is up and running.

  3. Open the MedeA GUI, click Jobs >> Select Server, and verify that local is chosen - this is the JobServer on the local computer.

  4. Click View and Control Jobs to see if the JobServer automatically opens.

    Note

    You can switch to other JobServers to examine if they are up and running

  5. On computers without the MedeA GUI or a web browser (or X-window) installed, such as HPC headnodes, you can use the following command-line options to check the JobServer and TaskServer statuses:

    • JobServer

      wget localhost:32000

      with MedeA 3.1 or newer:

      sudo systemctl status mdjobserver.service

      or with MedeA 3.0 or older:

      sudo /etc/init.d/mdjobserver status

    • TaskServer

      wget localhost:23000

      with MedeA 3.1 or newer:

      sudo systemctl status mdtaskserver.service

      or with MedeA 3.0 or older:

      sudo /etc/init.d/mdtaskserver status

1.7.2.2. Installing JobServer and TaskServer with MDMaintenance

If the JobServer and/or TaskServer had not been installed, follow these steps with MedeA 3.1 or newer:

  • Windows:

    • Open the Windows Start Menu fo find “MedeA Maintenance” in the the “Materials Design folder”
    • Right-click on the program >> More >> Run as administrator.
    • Mark the checkbox of Manage MD services and click the Start button.
    • Click Create Service buttons for JobServer and TaskServer, and then click Continue.
    • Open the URL http://localhost:32000 in a web browser to check whether the JobServer frontpage appears. If the JobServer frontpage is visible, then the JobServer is up and running.
    • Submit a job from MedeA GUI.

  • Linux with X-window:

    • Change to the <install_dir>/MD/Linux-x86_64 directory and find "MDMaintenance.x
    • Execute the program without sudo: ./MDMaintenance.x
    • Mark the checkbox of Manage MD services and click the Start button.
    • Enter your “Sudo password”, and click Check
    • Click the Create Service buttons for JobServer and TaskServer, and then click Continue.
    • Open the URL http://localhost:32000 in a web browser to check whether the JobServer frontpage appears. If the JobServer frontpage is visible, then the JobServer is up and running.
    • Submit a job from MedeA GUI.

  • Linux with command-line:

    Please refer to Subsection Command-line installation on Linux of the Section Installation from ISO.

1.7.2.3. Starting and Stopping the JobServer and TaskServer

If the JobServer and/or TaskServer had been installed but are down because of various reasons, follow these steps:

  • Windows:

    • Follow the steps in the previous subsection, but
    • Click Start Service buttons for JobServer and TaskServer, and then click Continue.
    • Open the URL http://localhost:32000 in a web browser to check whether the JobServer frontpage appears. If the JobServer frontpage is visible, then the JobServer is up and running.
    • Submit a job from MedeA GUI.

  • Linux with X-window:

    • Follow the steps in the previous subsection, but
    • Click the Start Service buttons for JobServer and TaskServer, and then click Continue.
    • Open the URL http://localhost:32000 in a web browser to check whether the JobServer frontpage appears. If the JobServer frontpage is visible, then the JobServer is up and running.
    • Submit a job from MedeA GUI.

  • Linux with command-line:

    • To start and stop the JobServer with MedeA 3.1 or newer:

      sudo systemctl start mdjobserver.service
sudo systemctl stop mdjobserver.service

    • To start and stop the TaskServer with MedeA 3.1 or newer:

      sudo systemctl start mdjobserver.service
sudo systemctl stop mdjobserver.service

    • To start and stop the JobServer with MedeA 3.0 or older:

      sudo /etc/init.d/mdjobserver start
sudo /etc/init.d/mdjobserver stop

    • To start and stop the TaskServer with MedeA 3.0 or older:

      sudo /etc/init.d/mdtaskserver start
sudo /etc/init.d/mdtaskserver stop

1.7.3. JobServer Administration and Configuration

The JobServer web page is primarily used for monitoring jobs. Please see the Monitoring a Running Job section for more information. Once on the JobServer page click the Administration tab to change the settings of the JobServer.

../../_images/jobserver_administration_page.png

On this page, you can set the Log Level. The default level is notice; however, this can be changed to debug if you are having issues configuring the JobServer. The Host address is the hostname or the IP address of the JobServer machine/computer and this name/address must be reachable from the TaskServer machine/computer. On local laptops and workstations, setting this variable to localhost or 127.0.0.1 is sufficient. For HPC headnodes, this variable is recommended to be the full hostname (i.e. with the domain name) or IP address. The Port is the port number via which the JobServer communicates. Though the default port number is 32000, you can change it to other numbers.

Warning

The port for the JobServer needs to be open through the firewall settings of the JobServer computer/machine. The JobServer has to be able to contact TaskServers via this port and TaskServers should be able to contact the JobServer via this port.

The Jobs directory is the directory where all the job folder and files are stored by their job id number. The default directory of the JobServer is the Jobs folder in the root of the installation directory, but you can change it to anywhere else. All the input and output files will be stored here after all the tasks have finished, see the next section TaskSever to learn how to administer tasks.

All of the above settings are saved in the configuration file (JobSever.options) located in the JobServer directory of the root installation directory. You can make changes to this file that will directly change the JobServer settings and appear on the JobServer page after the JobServer is restarted.

Warning

Incorrect settings in the JobSever.options will cause the JobServer to produce an error upon start and a JobServer malfunction. Please contact MD Support before changing this file.

MedeA stores job information in the MDJobs.db database file which is located in the Databases folder of the root installation directory. This database contains all the information displayed on the Jobs page. Jobs can be added to this database using the Import/Reconnect Jobs function of the Materials Design Maintenance program, see the section Using the Materials Design Maintenance Program for more information.

In the green bar are 5 sub-tabs:

  • Manage TaskServers: This page allows you to add and manage the TaskServers that this JobServer uses. Listed in a table at the bottom of the page are the registered TaskServers:

    ../../_images/image0017.png

    Click the Check button to check the communication between the JobServer and this particular TaskServer. Click the Change button to change the TaskServer domain name/IP address, port number, or make it active/inactive. You can also delete this TaskServer from the list.

  • Queues: This page controls the available MedeA queues on this JobServer to submit your jobs to:

    ../../_images/image0029.png

    Click the Change button to manage the settings:

    ../../_images/image0037.png

    • Queue: Name of this MedeA queue (this name will appear upon submitting jobs from the MedeA GUI to this JobServer)

    • Description: Description of this MedeA queue only for your information

    • Default Priority: 5 is the default value, 10 is the highest priority, while 1 is the lowest

      Note

      The priority is only effective within MedeA and does not affect the priority of queuing systems such as PBS, LSF, SLURM, GridEngine, etc.

    • Number of Cores: The default number of cores for new jobs. You can change the number of cores upon job submission to larger of smaller values.

      Note

      The maximum number of compute cores that a calculation, i.e. MedeA task is permitted to use, is determined by the TaskServer option Number of Parallel Cores, see the Section TaskServer Administration for more information.

    • Number of Jobs: The number of jobs this MedeA queue should simultaneously process by creating input files and queueing scripts and submitting calculations to TaskServers

    • Is Active: Whether this MedeA queue is active

    • TaskServers used by the queue: Manage the TaskServers for this queue so tasks submitted to this MedeA queue are executed by this TaskServers. If there is no TaskServer associated with this queue, then jobs submitted to this queue will not run and stay pending.

  • TaskServers

    Advanced settings on JobServer and TaskServer security. See Section the Sharing and Security for more information.

    Note

    To see a list of TaskServers for this JobServer, use the Manage TaskServer option

  • Users

    Advanced settings on JobServer and TaskServer security. See Section the Sharing and Security for more information.

  • Log

    Contains the JobServer log files which can be useful for debugging JobServer issues.

1.7.3.1. Administrative Rights

It is recommended to have MedeA JobServer and TaskServer running in the background. To install MedeA JobServer and TaskServer accordingly requires administrative rights during installation. Windows provides a mechanism, called Services, to accomplish that. On Linux, these service scripts are saved in the directory /etc/systemd/system. You can ask for temporary administrative rights or have your administrator install MedeA JobServer and TaskServer for you. see Section Run as Administrator for information about running programs as an administrator. Without administrative rights, JobServer and TaskServer can be started manually as interactive programs, see Section Running JobServer and TaskServer Scripts.

1.7.4. TaskServer Administration

The TaskServer is the end tier of MedeA that executes all the individual computations and calculations (tasks) needed to complete jobs. The MedeA TaskServer has several options on how to run your computational tasks, e.g. you can choose to run in serial, in parallel, or through a queuing system. You can limit the number of cores used on a specific TaskServer machine. This section describes what options are available to configure how tasks run.

In the following, please have a TaskServer installed that can be contacted through the JobServer links Home >> Administration >> Manage TaskServers or directly through the direct URL http://<taskserver>:23000 where <taskserver> can be localhost, your machine’s full hostname, or your machine IP address. Both, the sequence of links and the direct URL should open the following page:

../../_images/taskserver_administration_page.png

Note

To make any change of the TaskServer configuration options effective, click on the Apply button.

Click on the Administration tab in the brown navigation bar to proceed to the page with TaskServer configuration options:

The Control per number of drop-menu has two options:

  • Cores

    Follow-up options are:

    • Number of Parallel Cores: The maximum number of cores to use for all tasks.
    • Core limit type: Hard or Soft which allocates no more than available cores (Hard) or overload by a maximum of 50% (Soft), if necessary.

    The Number of Parallel Cores determines how many cores are available for all tasks running on this TaskServer. The default, set during installation, is the number of physical cores (no hyper-threading) on the TaskServer computer/machine. This is the right value for using mpi or direct mode. If you are using an external queuing system you may increase Number of Parallel Cores to the number of available cores. The Number of Parallel Cores is an upper limit and can be raised at run time in the job submission dialog, which shows the value set for a given queue as the default. If you have 10 compute nodes each with 24 cores, the Number of Parallel Cores variable can be set to 240.

  • Tasks

    ../../_images/image0046.png

    Follow-up options are:

    • Number of Parallel Cores: The maximum number of compute cores per task.
    • Simultaneous tasks: How many MedeA tasks (calculations) to run simultaneously.

The Queue Type determines how the executables of of the compute engines LAMMPS, GIBBS, VASP, MOPAC, and Gaussian are executed by the TaskServer. The following options are available:

  • direct: uses Intel MPI5 included in MedeA to run calculations (serial or parallel) interactively
  • mpi: uses Intel MPI5 included in MedeA to run serial or parallel jobs with an automatically generated script
  • PBS, LSF, GridEngine, SLURM, etc.: expects a file <templateQUEUE>.tcl in the directory <md_install_dir>/TaskServer/Tools
    • PBS (Linux): works with PBS, OpenPBS, or Torque
    • LSF (Windows/Unix/Linux)
    • GridEngine
    • SLURM
    • LoadLeveler
    • HPC: A placeholder for your queueing script
    • manual: supports running on remote systems with manual file transfer. See the Section Creating a Manual TaskServer and Queue for more information.

Attention

MedeA does not include any of the above external queuing systems. You will need to install, configure, and manage the external queuing systems. Furthermore, provide a working example batch script for the queuing system that you want to use. Send any working example batch script to MD Support . In return, you will receive a file <QUEUE>.tcl that your TaskServers can use to submit calculations to the HPC via the queuing system that you want to use.

To run e.g. with PBS, copy the file templatePBS.tcl in TaskServer/Tools to PBS.tcl and set the queue type to PBS in the TaskServer Administration page. The file PBS.tcl provides several parameters that can be fine-tuned to adapt the script to your HPC queueing environment. The script is general so it works with all compute engines in a general sense.

The Installation Directory is where the TaskServer is installed and cannot be changed from this Administration page.

The Working Directory is where the TaskServer creates temporary folders and files to run the calculations. This is a scratch directory as all relevant data are exported back to the JobServer upon completion of tasks.

The Port is the TaskServer port number. It is not recommended to change the Port that the TaskServer uses to communicate with the JobServer, unless there is a specific and inevitable reason for doing so.

With marking the checkbox of Save files temporarily and confirming with Apply task directories are kept temporarily for debugging purposes, such as configuring and tuning the submission to the external queueing system. Please note that this is a temporary switch and will be reset upon restarting the TaskServer.

In the green banner there are 3 sub-tabs:

  • Users

    Advanced settings on JobServer and TaskServer security. See Section the Sharing and Security for more information.

  • JobServers

    Advanced settings on JobServer and TaskServer security. See Section the Sharing and Security for more information.

  • Log

    Contains the TaskServer log files which can be useful for debugging TaskServer issues.

1.7.5. Managing JobServer and TaskServer Services on Linux

This section provides some additional notes on managing the JobServer and TaskServer services on Linux, including verifying automatic start of services on Linux, checking and managing firewall settings, and checking and setting system limits.

1.7.5.1. Verify Automatic Start of Services on Linux

Use your Linux distributions’ administration tools to verify that JobServer and TaskServer will start automatically after reboot. Check that the system service mdjobserver (if Installed) Starts automatically. On RPM-based systems (e.g. Ubuntu and Debian) the following commands are important:

chkconfig --list mdjobserver

mdjobserver 0:off    1:off    2:off    3:off    4:off   5:off    6:off

In this case, the system service mdjobserver is not going to start automatically. Let’s change this for run levels 3 and 5:

chkconfig --level 35 mdjobserver on

chkconfig --list mdjobserver

mdjobserver   0:off    1:off    2:off    3:on     4:off   5:on     6:off

Check that the system service mdtaskserver (if Installed) Starts automatically

chkconfig --list mdtaskserver

mdtaskserver   0:off    1:off    2:off    3:off    4:off   5:off    6:off

In this case, the system service mdtaskserver is not going to start automatically, change this for runlevels 3 and 5:

chkconfig --level 35 mdtaskserver on

chkconfig --list mdtaskserver

mdtaskserver   0:off    1:off    2:off    3:on     4:off   5:on     6:off

On SuSE Linux use the runlevel editor of YaST. With Debian-based systems such as Debian, Ubuntu, and Gentoo the installation of system services is part of installing the package mysqld.

1.7.5.2. Check Firewall Settings and Allow Connections for JobServer and TaskServer

If you have a firewall in place, make sure that the TaskServer can be reached from the JobServer. With iptables in place, the TaskServer port can be opened with the following commands.

iptables -I INPUT -p tcp --dport 23000 -j ACCEPT

You can restrict access to the TaskServer to a single JobServer by specifying a network address:

iptables -I INPUT -p tcp --dport 23000 -j ACCEPT -s <IP of JobServer>

Check the current set of rules in place - and please talk to your IT department:

iptables --list

Chain INPUT (policy ACCEPT)

target prot opt source destination

ACCEPT tcp – anywhere anywhere tcp dpt:23000

To keep the set of rules working after the next reboot, you need to save them. This depends on the Linux version and specifics of your installation.

  • RPM-based (RedHat/Centos/Fedora/SUSE):

    /etc/init.d/iptables save

    Similarly, you need to allow access on the JobServer from your GUI:

    iptables -I INPUT -p tcp --dport 32000 -j ACCEPT

  • Debian-based (Ubuntu/Debian/Mint):

    iptables-save > /etc/iptables/rules.v4

    or

    ip6tables-save > /etc/iptables/rules.v6

    to store IPv4 or IPv6 rules, respectively.

    To automatically load the rules upon booting computers, install the package iptables-persistent which is part of the default software repositories:

    sudo apt-get update

sudo apt-get install iptables-persistent

1.7.5.3. Check System Limits

Depending on model size and type of calculation, VASP and LAMMPS calculations can demand considerable amounts of memory, especially when running in parallel across many compute nodes. Please check whether the following properties are large enough, you can invoke the command ulimit -a in bash. The output of the command should be similar to

  • fsize: maximum file size: should be unlimited
  • memlock: maximum locked-in memory: 80-90% of total main memory
  • rss: maximum memory size: should be unlimited
  • nofile: number of open files: at least 20 per core
  • stack: (memory) stack size: 80-90% of total main memory
  • cpu: cpu time that can be used: should be unlimited
  • nproc: max. processed per user: set to at least 1000
  • as: virtual memory: should be unlimited
  • Locks: file locks: should be unlimited

Modify /etc/security/limits.conf to raise the impinging limits, here are examples:

* soft memlock unlimited

* hard memlock unlimited

* soft nofile 10240

* hard nofile 10240

* soft nproc 3153919

* hard nproc 3153919

download:pdf