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Use Software Available in Modules

This guide describes when and how to use software, using MPI as an example, that is available as pre-installed modules on the HTC system.

To best understand the below information, users should already have an understanding of:

Using the command line to: navigate within directories, create/copy/move/delete files and directories, and run their intended programs (aka "executables").
The CHTC's Intro to Running HTCondor Jobs

Overview

General Software Policies
Using Pre-Installed Software in Modules
Installing Software on the HTC System
Example: Using an MPI module in HTC Jobs

1. General Software Policies

In CHTC, we install a minimal set of software for use on our systems. On the HTC System, CHTC staff manage installations of the following types of programs:

Compilation tools and common dependencies (e.g. MPI, different GCC versions)
Software that requires a shared license (e.g. COMSOL)

Information on how to access CHTC-managed installations is in the next section of this guide.

2. Using Pre-Installed Software in Modules

All software on the HTC system that is installed by CHTC staff is available via a tool called “modules”.

A. See Available Software Modules

There are two ways to search through the software modules on the HTC system:

View all modules This command will show all software modules available:
```
[alice@submit]$ module avail
```
Search for specific modules If you are searching for a specific software module, you can use the module spider command with part of the software name. For example, to search for Open MPI modules, you would type:
```
[alice@submit]$ module spider openmpi
```

B. Load Software in Modules

Once you find a software module that you want to use, you need to “load” it into your command line environment to make it active, filling in module_name with the name you found through one of the above steps.

[alice@submit]$ module load module_name

When to Load Modules

You can load modules to compile code (see below). If you do this, make sure to load the same modules as part of your job script before running the main command.

You can also load modules to run specific software. If done for interactive testing, this should be done in an interactive job; otherwise, the module should be loaded in the job submit file.

C. Unload Software in Modules

If you no longer want to use a specific software installation, you can “unload” the software module with the following command:

[alice@submit]$ module unload module_name

If you want to clear your command line environment and start over, run the following:

[alice@submit]$ module purge

3. Installing Software on the HTC System

A. Overview

Unless you are using a licensed software program provided via modules, you are able to compile and install the software you need on the HTC System.

Compilation can be done via an interactive job as described in our HTC Compiling or Testing Code with an Interactive Job guide. If using CHTC’s provided compilation tools via modules, make sure to load the needed modules before compiling and to load the same modules in your job submission.

For groups that would like to share software installations among group members, please contact us about getting a shared “group” directory.

If you are new to software installation, see the section below for a more step-by-step description of the process.

B. Step by Step Process

The process for installing software is described in more detail in our Compiling or Testing Code with an Interactive Job

Start an Interactive Job - it is necessary to build software in an interactive job as noted in Compiling or Testing Code with an Interactive Job
Download Source Code - download the source code for your desired program. You should only need the source code until the software is properly installed, but if desired, you may keep a zipped copy of the source code in your workspace.
Read the Docs - try to find the installation instructions, either online or in the downloaded source code. In particular, you’ll want to note if there are any special requirements for dependencies like MPI or the compiler needed.
Load Modules - if you are using software modules to help you build your code, load them now. Keep track of what you use so that you can load them in your job submit file later. We also recommend doing a module purge before loading your compiling modules to make sure you’re starting from a clean environment.
Install - most scientific software follows the three step installation process of configure - make - make install.
1. configure- this step checks for tools and requirements needed to compile the code. This is the step where you set the final installation location of a program. The option for setting this location is typically called the “prefix”; a common syntax is: $ ./configure --prefix=/home/user. This is where you will want to set the installation location to be your /home directory.
2. make - this step compiles and links the code, turning it from human-readable source code to compiled binary code. This is usually the most time consuming step of the installation process.
3. make install - this step copies compiled files to the final installation location (usually specified in the configure step).

4. Example: Using an MPI module in HTC Jobs

Below is the process of setting up HTC jobs that use the MPI modules to run. This process can be modified for other software available in modules as well.

Before you begin, review our below discussion of MPI requirements and use cases, to make sure that our multi-core MPI capabilities are the right solution for your computing problem.

Once you know that you need to run multi-core jobs that use MPI on our HTC system, you will need to do the following:

Compile your code using our MPI module system
Create a script to that loads the MPI module you used for compiling, and then runs your code
Make sure your submit file has certain key requirements

A. Requirements and Use Cases

Most jobs on CHTC's HTC system are run on one CPU (sometimes called a "processor", or "core") and can be executed without any special system libraries. However, in some cases, it may be advantageous to run a single program on multiple CPUs (also called multi-core), in order to speed up single computations that cannot be broken up and run as independent jobs.

Running on multiple CPUs can be enabled by the parallel programming standard MPI. For MPI jobs to compile and run, CHTC has a set of MPI tools installed to a shared location that can be accessed via software modules.

B. View MPI Modules on the HTC System

MPI tools are accessible on the HTC system through software "modules", which are tools to access and activate a software installation. To see which MPI packages are supported in the HTC, you can type the following command from the submit server:

[alice@submit]$ module avail

Your software may require newer versions of MPI libraries than those available via our modules. If this is the case, send an email to chtc@cs.wisc.edu, to find out if we can install that library into the module system.

C. Submitting MPI jobs

1. Compile MPI Code

You can compile your program by submitting an interactive build job to one of our compiling servers. Do not compile code on the submit server, as doing so may cause performance issues. The interactive job is essentially a regular HTCondor job, but without an executable; you are the one running the commands instead (in this case, to compile the program).

Instructions for submitting an interactive build/compile job are available on our interactive submission guide. The only line in the submit file that you need to change is transfer_input_files to reflect all the source files on which your program depends. Otherwise, go through the steps described in that guide until immediately after running condor_submit -i.

Once your interactive job begins on one of our compiling servers, you can confirm which MPI modules are available to you by typing:

[alice@build]$ module avail

Choose the module you want to use and load it with the following command:

[alice@build]$ module load mpi_module

where mpi_module is replaced with the name of the MPI module you'd like to use.

After loading the module, compile your program. If your program is organized in directories, make sure to create a tar.gz file of anything you want copied back to the submit server. Once typing exit the interactive job will end, and any *files* created during the interactive job will be copied back to the submit location for you.

If your MPI program is especially large (more than 100 MB, compiled), or if it can only run from the exact location to which it was installed, you may also need to take advantage of CHTC's shared software location or our public web proxy called Squid. Email CHTC's Research Computing Facilitators at chtc@cs.wisc.edu if this is the case.

2. Script For Running MPI Jobs

To run your newly compiled program within a job, you need to write a script that loads an MPI module and then runs the program, like so:

#!/bin/bash

# The following three commands are **REQUIRED** to enable modules, and then to load the appropriate MP/MPI module
export PATH
. /etc/profile.d/modules.sh
module load mpi_module

# Untar your program installation, if necessary
tar -xzf my_install.tar.gz

# Command to run your OpenMP/MPI program
# (This example uses mpirun, other programs
# may use mpiexec, or other commands)
mpirun -np 8 ./path/to/myprogram

Replace mpi_module with the name of the module you used to compile your code, myprogram with the name of your program, and X with the number of CPUs you want the program to use. There may be additional options or flags necessary to run your particular program; make sure to check the program's documentation about running multi-core processes.

3. Submit File Requirements

There are several important requirements to consider when writing a submit file for multicore jobs. They are shown in the sample submit file below and include:

Require access to MPI modules. To ensure that your job will have access to CHTC software modules, including MPI modules, you must include the following in your submit file.
```
requirements = (HasChtcSoftware == true)
```
The script you wrote above (shown as run_mpi.sh below) should be your submit file "executable", and your compiled program and any files should be listed in transfer_input_files.

A sample submit file for multi-core jobs is given below:

# multicore.sub
# A sample submit file for running a single multicore (8 cores) job
executable = run_mpi.sh
# arguments = (if you want to pass any to the shell script)

## Specify the name of HTCondor's log, standard error, and standard out files
log = mc_$(Cluster).log
output = mc_$(Cluster).out
error = mc_$(Cluster).err

# Tell HTCondor how to handle input files
should_transfer_files = YES
transfer_input_files = (this should be a comma separate list of input files if needed)

# Requirement for accessing new set of modules
requirements = ( HasChtcSoftware == true ) 

## Request resources needed by your job
request_cpus = 8
request_memory = 8GB
request_disk = 2GB

queue

After the submit file is complete, you can submit your jobs using condor_submit.