Request History

• Restore to current request
• data/admin/allowurl.txt
• posts/findByTag/18
• robots.txt

Session

• 0(null)

Request

Cake Params

• plugin(null)
• controllerposts
• actionview
• named(empty)
• pass(array)
  • 023
  • 1How to install and use the environment modules system

Post data

No post data.

Query string

No querystring data.

Cookie

To view Cookies, add CookieComponent to Controller

Current Route

• keys(array)
  • 0controller
  • 1action
• options(array)
  • defaultRoute(true)
• defaults(array)
  • plugin(null)
• template/:controller/:action/*

Sql Logs

Logs

View Variables

• meta_keywordsLinux, Blog, Post, Ivo Filot
• meta_descriptionHow to install and use the environment modules system
• title_for_layoutHow to install and use the environment modules system
• tags(array)
  • 0(array)
    • Tag(array)
      • id18
      • nameLinux
      • iconpictonic-os-linux_1_
      • colorwarning
    • Post(array)
      • 0(array)
        • id18
        • titleSystem status lights on your Raspberry Pi using the PiGlow module and systemd
        • content## System status lights Recently I wanted to use my [Raspberry Pi](http://www.raspberrypi.org/), a cheap and small computer device for hobby projects, for making a wireless radio. Wireless at least in the sense that it connects to the internet via a wifi dongle. I like my device to have some kind of interface, but I found a TFT screen a bit too expensive, so I decided to buy a [Pimoroni PiGlow](http://shop.pimoroni.com/products/piglow). The PiGlow is a small add on board for the Raspberry Pi that provides 18 individually controllable LEDs, which are placed in a three-legged swirling pattern and consists of red, orange, amber, green, blue and white LEDs. Turning these LEDs on and off from the command line is fairly easy using the [Wiring Pi](http://wiringpi.com/download-and-install/) library. What I wanted was that when my Pi boots, it shows which services were running using these lights, in the following way: * Red lights: Filesystems are enabled * Orange lights: Wireless networking is enabled * Amber lights: SSH daemon is enabled * Green lights: Apache (HTTP) server is enabled <img src="http://www.ivofilot.nl/images/5/front-pi.jpg" width="500" class="img-rounded" /> ## Configuration The way I configured this behaviour was by writing my own [systemd service scripts](https://wiki.archlinux.org/index.php/systemd#Writing_custom_.service_files). For example, the file below defines the service that lights up the red LEDs when the filesystem is enabled. <pre> <code class="bash"> [Unit] Description=PiGlow Enabling Red1 Lights Requires=local-fs.target After=local-fs.target [Service] Type=oneshot ExecStart=/usr/local/bin/piglow_color red0 25 [Install] RequiredBy=local-fs.target </code> </pre> Each service scripts has three sections, which are [unit], [service] and [install]. The [unit] section contains a description, it defines a requirement and an order. The requirement keyword ensures that this service starts when the service local-fs.target starts. By defining the after keyword as well, this service will only be started after local-fs.target has started and not simultaneously. The [service] attribute defines the type of service. Here, I have used the oneshot type. This means that the service is started by running an executable, which immediately exits, in contrast to for instance a daemon service, which keeps running in the background. Finally, the [install] attribute configures how this service should be installed. Installation is done by <pre> <code class="bash"> systemctl enable piglow.color.red.service </code> </pre> Note that piglow.color.red.service should be the filename where you have written your service script. Place such files in /etc/systemd/system. Similarly, for the green LEDs (which light up when the Apache server is enabled), I wrote the following script: <pre> <code class="bash"> [Unit] Description=PiGlow Enabling Green Lights Requires=httpd.service After=httpd.service [Service] Type=oneshot ExecStart=/usr/local/bin/piglow_color green 10 [Install] RequiredBy=httpd.service </code> </pre> Up next, I want the white LEDs to fade in and out when the device has any sofware updates ready to install. But I will dedicate another post on that topic. :-) <img src="http://www.ivofilot.nl/images/4/piglow-on-off.jpg" width="500" class="img-rounded" />
        • watched5786
        • active(true)
        • created2014-06-24 00:00:00
        • modified2015-06-30 17:32:13
      • 1(array)
        • id23
        • titleHow to install and use the environment modules system
        • content# Introduction Let us think about the way we run programs from the terminal. If we want to list the content of a directory, we simply type ```ls```. Why does this work? You probably know the answer: Because the program ```ls``` is residing in the ```/bin/ls``` folder and that folder is in the ```$PATH``` variable. In fact, you can check this by typing: <pre> <code class="bash"> which ls </code> </pre> and <pre> <code class="bash"> echo $PATH </code> </pre> What now if we have multiple versions of a particular program. For instance, we could have multiple versions installed of the GNU compiler. How would you then distinguish the programs? One could then append the version number to the binaries, like so: * gcc-4.7.4-i686 * gcc-4.8.4-i686 and place all the folders where these executables reside in , in the ```$PATH``` variable. Let me now propose an alternative, which is often implemented in computational clusters. It is called [Modules Environment](http://modules.sourceforge.net/). Using this tool, you simply type ```module avail``` to check which programs are installed on the system and if you would like to use a particular program, let's say gcc-4.8.4, you would type ```module load gcc-4.8.4```. The Environment Modules tool will then *prepend* the folder where the executables of gcc-4.8.4 reside in to the ```$PATH``` variable so that when you type ```gcc```, you will automatically use *that particular version*. Pretty nifty tool right? Well, you can use it on your local system as well and in this blog post I will explain you how. # Installation Download the tarball <pre> <code class="bash"> wget http://sourceforge.net/projects/modules/files/latest/download?source=files -O modules-3.2.10.tar.gz </code> </pre> and extract it <pre> <code class="bash"> tar -xvzf modules-3.2.10.tar.gz </code> </pre> You need to have the tcl libraries installed, on Debian this can be done via: <pre> <code class="bash"> sudo apt-get install tcl-dev </code> </pre> Next, run ```configure``` like so <pre> <code class="bash"> ./configure --with-module-path=/opt/modulefiles --prefix=/opt/modules-3.2.10 </code> </pre> Feel free to change the paths mentioned above to something suitable for your system. (Though the ```/opt``` folder is meant to place installed programs in. [Read more about the Linux directory structure here](http://www.thegeekstuff.com/2010/09/linux-file-system-structure/)). After configuring, run ```make``` and ```make install```. <pre> <code class="bash"> make sudo make install </code> </pre> Lastly, you need to initialize the Environment Modules every time you load ```bash```. On Debian, this is done by adding two lines to ```/etc/profile``` (a file that is run every time you run ```bash```). Open ```/etc/profile``` <pre> <code class="bash"> sudo nano /etc/profile </code> </pre> and add at the bottom of the file <pre> <code class="bash"> # load the modules source /opt/modules-3.2.10/Modules/3.2.10/init/bash </code> </pre> And you are all set up. If you now log out and back in, and type ```modules avail```, you should see something like this <pre> <code class="bash"> --------- /opt/gcc-4.7.2/modules-3.2.10/Modules/versions --------- 3.2.10 ---- /opt/gcc-4.7.2/modules-3.2.10/Modules/3.2.10/modulefiles ---- dot module-info null module-git modules use.own </code> </pre> # Configuration In the file ```/opt/modules-3.2.10/Modules/3.2.10/init/.modulespath``` a list of directories are given in which ```modules``` will search for module files. Personally, I don't like the default directories given there, and I tend to change it to something like this: <pre> <code class="bash"> # # This file defines the initial setup for the module files search path. # Comments may be added anywhere, which begin on # and continue until the # end of the line # Each line containing a single path will be added to the MODULEPATH # environment variable. You may add as many as you want - just # limited by the maximum variable size of your shell. # /opt/modulefiles </code> </pre> and I then put in ```/opt/modulefiles``` all my module files. To exemplify, let us assume that we have two different versions of gcc installed, being 4.7.2 and 4.8.3. We then need to create two modulefiles as such ```/opt/modulefiles/gnu-gcc-4.7.2``` <pre> <code class="bash"> #%Module1.0##################################################################### ## ## null modulefile ## ## modulefiles/null. Generated from null.in by configure. ## # for Tcl script use only set root /opt/gcc-4.7.2 prepend-path PATH $root/bin prepend-path LD_LIBRARY_PATH $root/lib prepend-path LD_LIBRARY_PATH $root/lib64 </code> </pre> and ```/opt/modulefiles/gnu-gcc-4.8.3``` <pre> <code class="bash"> #%Module1.0##################################################################### ## ## null modulefile ## ## modulefiles/null. Generated from null.in by configure. ## # for Tcl script use only set root /opt/gcc-4.8.3 prepend-path PATH $root/bin prepend-path LD_LIBRARY_PATH $root/lib prepend-path LD_LIBRARY_PATH $root/lib64 </code> </pre> If you would now run ```module avail```, (assuming you have a similar ```.modulespath``` as mine) you would see something like this <pre> <code class="bash"> -------- /opt/modulefiles -------- gnu-gcc-4.7.2 gnu-gcc-4.8.3 </code> </pre> If I would now like to use gcc-4.7.2 to compile, I would type ```module load gnu-gcc-4.7.2``` and have the bin directories of ```gcc-4.7.2``` appended to my ```$PATH``` ensuring that I use the right compiler. More advanced configuration would actually modify the modulefiles in such a way that when gcc-4.7.2 is loaded and you would run ```module load 4.8.3``` that then a conflict error would be given.
        • watched6425
        • active(true)
        • created2015-02-22 12:07:00
        • modified2015-06-30 17:24:46
      • 2(array)
        • id25
        • titleCreating a local queuing system on Linux Debian using Torque
        • content# Introduction Imagine you would like to perform a large series of calculation. Obviously, you would not run the complete series of calculations at the same time. In principle, you would like to start as many jobs as the number of processors on your computer can handle and start the next job in the series when the previous job has finished. You could write your own program for this, but there are many of such programs available. In this blog post, I will show you how to install and use Torque. Although Torque can be set up to run in a computer cluster, I will show you how you can install and use it on just a single machine. This tutorial is written for Linux Debian, but should in principle also work for Linux Ubuntu and with (hopefully) small modifications for the other distributions. # Compiling Torque Download the tarball from the website. Extract, compile and install it on your machine. <pre> <code class="bash"> wget http://www.adaptivecomputing.com/index.php?wpfb_dl=2868 -O torque-5.1.0.tar.gz cd torque-5.1.0 ./configure --prefix=/opt/gcc-4.7.2/torque-5.1.0 make -j5 sudo make install </code> </pre> # Installing the daemons Torque uses four daemons that have to be loaded at boot time. Copy their ```init.d``` scripts to the ```/etc/init.d``` folder like so <pre> <code class="bash"> sudo cp contrib/init.d/debian.trqauthd /etc/init.d/trqauthd sudo cp contrib/init.d/debian.pbs_mom /etc/init.d/pbs_mom sudo cp contrib/init.d/debian.pbs_server /etc/init.d/pbs_server sudo cp contrib/init.d/debian.pbs_sched /etc/init.d/pbs_sched </code> </pre> and add these to the boot procedure <pre> <code class="bash"> sudo update-rc.d pbs_mom defaults sudo update-rc.d pbs_server defaults sudo update-rc.d pbs_sched defaults sudo update-rc.d trqauthd defaults </code> </pre> # Configuring the server and the nodes Next, we would like to set our machine as both the server as well as the (only) node. Start the ```trqauthd``` daemon <pre> <code class="bash"> sudo /etc/init.d/trqauthd start </code> </pre> Log in as root and add the binary folders of Torque to the path. <pre> <code class="bash"> su export PATH=/opt/gcc-4.7.2/torque-5.1.0/sbin:/opt/gcc-4.7.2/torque-5.1.0/bin:$PATH ./torque.setup root </code> </pre> If you get an error like the following <pre> <code class="bash"> qmgr obj= svr=default: Bad ACL entry in host list MSG=First bad host: </code> </pre> check your ```/etc/hosts``` file and change the directives in there. Torque only reads the first two columns to match the hostname with an IP adress. Add your machine to the list of nodes by editing ```/var/spool/torque/server_priv/nodes```. You have to specify the number of cores in your machine after the ```np=``` directive. <pre> <code class="bash"> localhost np=6 </code> </pre> Edit ```/var/spool/torque/mom_priv/config``` and set your machine as the ```$pbsserver```. Also configure the bitmap for the logging events. <pre> <code class="bash"> $pbsserver ST-A1771 $logevent 225 </code> </pre> Please note that in the above file, `ST-A1771` should be replaced by the name of your local machine. Moreover, this name should match an IP address which can be configured in `/etc/hosts`. (thanks to `danielmejia55_at_gmail_dot_com` for mentioning this, see comments below) Start pbs_mom. <pre> <code class="bash"> /etc/init.d/pbs_mom start </code> </pre> In order for every user to submit files to the queuing system and check the current status of the queue, you would like that every user has the ```bin``` folder of Torque in their ```$PATH``` variable. As such, add the Torque binaries folder to the PATH in ```/etc/profile``` <pre> <code class="bash"> echo 'export PATH=/opt/gcc-4.7.2/torque-5.1.0/bin:$PATH' >> /etc/profile </code> </pre> Finally, log out as root (CTRL+D) # Checking the installation To check that everything is correctly configured, run <pre> <code class="bash"> pbsnodes -a </code> </pre> If you do not get something like this, you can try to reset ```pbs_server```. (see below) <pre> <code class="bash"> state = free power_state = Running np = 6 ntype = cluster status = rectime=1424867568,cpuclock=OnDemand:1998MHz,varattr=,jobs=,state=free,netload=6890398942,gres=,loadave=0.00,ncpus=4,physmem=8066840kb,availmem=11324404kb,totmem=11970324kb,idletime=240,nusers=1,nsessions=2,sessions=3336 27395,uname=Linux ST-A1771 3.2.0-4-amd64 #1 SMP Debian 3.2.65-1+deb7u1 x86_64,opsys=linux mom_service_port = 15002 mom_manager_port = 15003 </code> </pre> To reset ```pbs_server```, run <pre> <code class="bash"> sudo /etc/init.d/pbs_server restart </code> </pre> Also start the scheduler <pre> <code class="bash"> sudo /etc/init.d/pbs_sched start </code> </pre> And test a job by running <pre> <code class="bash"> echo "sleep 30" | qsub </code> </pre> When you run <pre> <code class="bash"> qstat </code> </pre> you should see something like <pre> <code class="bash"> Job ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 0.ST-A1771 STDIN ivo 0 R batch </code> </pre> **Note**: `danielmejia55_at_gmail_dot_com` has noted (see comments below) that if you encounter an error that certain queue directives are missing, that you need to set these first. He has kindly provided the settings he has used. # Submission files Below, an example submission file for a multiprocessor job is given. In the submission file, you specify the name of the job after the ```PBS -N``` directive, the number of nodes and the number of processors per node and finally the maximum time the job is allowed to run. Typically, you would like to run the job in the same folder as where the jobfile is residing. To do so, you can use the ```$PBS_O_WORKDIR``` variable. Furthermore, you can use the ```$PBS_NP``` variable to pass the number of processes to the ```mpirun``` program. <pre> <code class="bash"> #!/bin/bash # #This is an example script example.sh # #These commands set up the Torque Environment for your job: #PBS -N TestJob #PBS -l nodes=1:ppn=4,walltime=00:12:00 pwd cd $PBS_O_WORKDIR pwd #print the time and date date mpirun -np $PBS_NP ./testjob #print the time and date again date </code> </pre>
        • watched11584
        • active(true)
        • created2015-03-03 15:50:39
        • modified2015-06-30 17:22:47
      • 3(array)
        • id32
        • titleHow to compile VASP 5.4.1 using the Intel compilers
        • content
        • watched0
        • active(false)
        • created2015-11-04 00:00:00
        • modified2015-11-03 16:38:25
• relatedposts(array)
  • 0(array)
    • id25
    • titleCreating a local queuing system on Linux Debian using Torque
    • content# Introduction Imagine you would like to perform a large series of calculation. Obviously, you would not run the complete series of calculations at the same time. In principle, you would like to start as many jobs as the number of processors on your computer can handle and start the next job in the series when the previous job has finished. You could write your own program for this, but there are many of such programs available. In this blog post, I will show you how to install and use Torque. Although Torque can be set up to run in a computer cluster, I will show you how you can install and use it on just a single machine. This tutorial is written for Linux Debian, but should in principle also work for Linux Ubuntu and with (hopefully) small modifications for the other distributions. # Compiling Torque Download the tarball from the website. Extract, compile and install it on your machine. <pre> <code class="bash"> wget http://www.adaptivecomputing.com/index.php?wpfb_dl=2868 -O torque-5.1.0.tar.gz cd torque-5.1.0 ./configure --prefix=/opt/gcc-4.7.2/torque-5.1.0 make -j5 sudo make install </code> </pre> # Installing the daemons Torque uses four daemons that have to be loaded at boot time. Copy their ```init.d``` scripts to the ```/etc/init.d``` folder like so <pre> <code class="bash"> sudo cp contrib/init.d/debian.trqauthd /etc/init.d/trqauthd sudo cp contrib/init.d/debian.pbs_mom /etc/init.d/pbs_mom sudo cp contrib/init.d/debian.pbs_server /etc/init.d/pbs_server sudo cp contrib/init.d/debian.pbs_sched /etc/init.d/pbs_sched </code> </pre> and add these to the boot procedure <pre> <code class="bash"> sudo update-rc.d pbs_mom defaults sudo update-rc.d pbs_server defaults sudo update-rc.d pbs_sched defaults sudo update-rc.d trqauthd defaults </code> </pre> # Configuring the server and the nodes Next, we would like to set our machine as both the server as well as the (only) node. Start the ```trqauthd``` daemon <pre> <code class="bash"> sudo /etc/init.d/trqauthd start </code> </pre> Log in as root and add the binary folders of Torque to the path. <pre> <code class="bash"> su export PATH=/opt/gcc-4.7.2/torque-5.1.0/sbin:/opt/gcc-4.7.2/torque-5.1.0/bin:$PATH ./torque.setup root </code> </pre> If you get an error like the following <pre> <code class="bash"> qmgr obj= svr=default: Bad ACL entry in host list MSG=First bad host: </code> </pre> check your ```/etc/hosts``` file and change the directives in there. Torque only reads the first two columns to match the hostname with an IP adress. Add your machine to the list of nodes by editing ```/var/spool/torque/server_priv/nodes```. You have to specify the number of cores in your machine after the ```np=``` directive. <pre> <code class="bash"> localhost np=6 </code> </pre> Edit ```/var/spool/torque/mom_priv/config``` and set your machine as the ```$pbsserver```. Also configure the bitmap for the logging events. <pre> <code class="bash"> $pbsserver ST-A1771 $logevent 225 </code> </pre> Please note that in the above file, `ST-A1771` should be replaced by the name of your local machine. Moreover, this name should match an IP address which can be configured in `/etc/hosts`. (thanks to `danielmejia55_at_gmail_dot_com` for mentioning this, see comments below) Start pbs_mom. <pre> <code class="bash"> /etc/init.d/pbs_mom start </code> </pre> In order for every user to submit files to the queuing system and check the current status of the queue, you would like that every user has the ```bin``` folder of Torque in their ```$PATH``` variable. As such, add the Torque binaries folder to the PATH in ```/etc/profile``` <pre> <code class="bash"> echo 'export PATH=/opt/gcc-4.7.2/torque-5.1.0/bin:$PATH' >> /etc/profile </code> </pre> Finally, log out as root (CTRL+D) # Checking the installation To check that everything is correctly configured, run <pre> <code class="bash"> pbsnodes -a </code> </pre> If you do not get something like this, you can try to reset ```pbs_server```. (see below) <pre> <code class="bash"> state = free power_state = Running np = 6 ntype = cluster status = rectime=1424867568,cpuclock=OnDemand:1998MHz,varattr=,jobs=,state=free,netload=6890398942,gres=,loadave=0.00,ncpus=4,physmem=8066840kb,availmem=11324404kb,totmem=11970324kb,idletime=240,nusers=1,nsessions=2,sessions=3336 27395,uname=Linux ST-A1771 3.2.0-4-amd64 #1 SMP Debian 3.2.65-1+deb7u1 x86_64,opsys=linux mom_service_port = 15002 mom_manager_port = 15003 </code> </pre> To reset ```pbs_server```, run <pre> <code class="bash"> sudo /etc/init.d/pbs_server restart </code> </pre> Also start the scheduler <pre> <code class="bash"> sudo /etc/init.d/pbs_sched start </code> </pre> And test a job by running <pre> <code class="bash"> echo "sleep 30" | qsub </code> </pre> When you run <pre> <code class="bash"> qstat </code> </pre> you should see something like <pre> <code class="bash"> Job ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 0.ST-A1771 STDIN ivo 0 R batch </code> </pre> **Note**: `danielmejia55_at_gmail_dot_com` has noted (see comments below) that if you encounter an error that certain queue directives are missing, that you need to set these first. He has kindly provided the settings he has used. # Submission files Below, an example submission file for a multiprocessor job is given. In the submission file, you specify the name of the job after the ```PBS -N``` directive, the number of nodes and the number of processors per node and finally the maximum time the job is allowed to run. Typically, you would like to run the job in the same folder as where the jobfile is residing. To do so, you can use the ```$PBS_O_WORKDIR``` variable. Furthermore, you can use the ```$PBS_NP``` variable to pass the number of processes to the ```mpirun``` program. <pre> <code class="bash"> #!/bin/bash # #This is an example script example.sh # #These commands set up the Torque Environment for your job: #PBS -N TestJob #PBS -l nodes=1:ppn=4,walltime=00:12:00 pwd cd $PBS_O_WORKDIR pwd #print the time and date date mpirun -np $PBS_NP ./testjob #print the time and date again date </code> </pre>
    • watched11584
    • active(true)
    • created2015-03-03 15:50:39
    • modified2015-06-30 17:22:47
    • comments3
  • 1(array)
    • id18
    • titleSystem status lights on your Raspberry Pi using the PiGlow module and systemd
    • content## System status lights Recently I wanted to use my [Raspberry Pi](http://www.raspberrypi.org/), a cheap and small computer device for hobby projects, for making a wireless radio. Wireless at least in the sense that it connects to the internet via a wifi dongle. I like my device to have some kind of interface, but I found a TFT screen a bit too expensive, so I decided to buy a [Pimoroni PiGlow](http://shop.pimoroni.com/products/piglow). The PiGlow is a small add on board for the Raspberry Pi that provides 18 individually controllable LEDs, which are placed in a three-legged swirling pattern and consists of red, orange, amber, green, blue and white LEDs. Turning these LEDs on and off from the command line is fairly easy using the [Wiring Pi](http://wiringpi.com/download-and-install/) library. What I wanted was that when my Pi boots, it shows which services were running using these lights, in the following way: * Red lights: Filesystems are enabled * Orange lights: Wireless networking is enabled * Amber lights: SSH daemon is enabled * Green lights: Apache (HTTP) server is enabled <img src="http://www.ivofilot.nl/images/5/front-pi.jpg" width="500" class="img-rounded" /> ## Configuration The way I configured this behaviour was by writing my own [systemd service scripts](https://wiki.archlinux.org/index.php/systemd#Writing_custom_.service_files). For example, the file below defines the service that lights up the red LEDs when the filesystem is enabled. <pre> <code class="bash"> [Unit] Description=PiGlow Enabling Red1 Lights Requires=local-fs.target After=local-fs.target [Service] Type=oneshot ExecStart=/usr/local/bin/piglow_color red0 25 [Install] RequiredBy=local-fs.target </code> </pre> Each service scripts has three sections, which are [unit], [service] and [install]. The [unit] section contains a description, it defines a requirement and an order. The requirement keyword ensures that this service starts when the service local-fs.target starts. By defining the after keyword as well, this service will only be started after local-fs.target has started and not simultaneously. The [service] attribute defines the type of service. Here, I have used the oneshot type. This means that the service is started by running an executable, which immediately exits, in contrast to for instance a daemon service, which keeps running in the background. Finally, the [install] attribute configures how this service should be installed. Installation is done by <pre> <code class="bash"> systemctl enable piglow.color.red.service </code> </pre> Note that piglow.color.red.service should be the filename where you have written your service script. Place such files in /etc/systemd/system. Similarly, for the green LEDs (which light up when the Apache server is enabled), I wrote the following script: <pre> <code class="bash"> [Unit] Description=PiGlow Enabling Green Lights Requires=httpd.service After=httpd.service [Service] Type=oneshot ExecStart=/usr/local/bin/piglow_color green 10 [Install] RequiredBy=httpd.service </code> </pre> Up next, I want the white LEDs to fade in and out when the device has any sofware updates ready to install. But I will dedicate another post on that topic. :-) <img src="http://www.ivofilot.nl/images/4/piglow-on-off.jpg" width="500" class="img-rounded" />
    • watched5786
    • active(true)
    • created2014-06-24 00:00:00
    • modified2015-06-30 17:32:13
    • comments1
• post(array)
  • Post(array)
    • id23
    • titleHow to install and use the environment modules system
    • content# Introduction Let us think about the way we run programs from the terminal. If we want to list the content of a directory, we simply type ```ls```. Why does this work? You probably know the answer: Because the program ```ls``` is residing in the ```/bin/ls``` folder and that folder is in the ```$PATH``` variable. In fact, you can check this by typing: <pre> <code class="bash"> which ls </code> </pre> and <pre> <code class="bash"> echo $PATH </code> </pre> What now if we have multiple versions of a particular program. For instance, we could have multiple versions installed of the GNU compiler. How would you then distinguish the programs? One could then append the version number to the binaries, like so: * gcc-4.7.4-i686 * gcc-4.8.4-i686 and place all the folders where these executables reside in , in the ```$PATH``` variable. Let me now propose an alternative, which is often implemented in computational clusters. It is called [Modules Environment](http://modules.sourceforge.net/). Using this tool, you simply type ```module avail``` to check which programs are installed on the system and if you would like to use a particular program, let's say gcc-4.8.4, you would type ```module load gcc-4.8.4```. The Environment Modules tool will then *prepend* the folder where the executables of gcc-4.8.4 reside in to the ```$PATH``` variable so that when you type ```gcc```, you will automatically use *that particular version*. Pretty nifty tool right? Well, you can use it on your local system as well and in this blog post I will explain you how. # Installation Download the tarball <pre> <code class="bash"> wget http://sourceforge.net/projects/modules/files/latest/download?source=files -O modules-3.2.10.tar.gz </code> </pre> and extract it <pre> <code class="bash"> tar -xvzf modules-3.2.10.tar.gz </code> </pre> You need to have the tcl libraries installed, on Debian this can be done via: <pre> <code class="bash"> sudo apt-get install tcl-dev </code> </pre> Next, run ```configure``` like so <pre> <code class="bash"> ./configure --with-module-path=/opt/modulefiles --prefix=/opt/modules-3.2.10 </code> </pre> Feel free to change the paths mentioned above to something suitable for your system. (Though the ```/opt``` folder is meant to place installed programs in. [Read more about the Linux directory structure here](http://www.thegeekstuff.com/2010/09/linux-file-system-structure/)). After configuring, run ```make``` and ```make install```. <pre> <code class="bash"> make sudo make install </code> </pre> Lastly, you need to initialize the Environment Modules every time you load ```bash```. On Debian, this is done by adding two lines to ```/etc/profile``` (a file that is run every time you run ```bash```). Open ```/etc/profile``` <pre> <code class="bash"> sudo nano /etc/profile </code> </pre> and add at the bottom of the file <pre> <code class="bash"> # load the modules source /opt/modules-3.2.10/Modules/3.2.10/init/bash </code> </pre> And you are all set up. If you now log out and back in, and type ```modules avail```, you should see something like this <pre> <code class="bash"> --------- /opt/gcc-4.7.2/modules-3.2.10/Modules/versions --------- 3.2.10 ---- /opt/gcc-4.7.2/modules-3.2.10/Modules/3.2.10/modulefiles ---- dot module-info null module-git modules use.own </code> </pre> # Configuration In the file ```/opt/modules-3.2.10/Modules/3.2.10/init/.modulespath``` a list of directories are given in which ```modules``` will search for module files. Personally, I don't like the default directories given there, and I tend to change it to something like this: <pre> <code class="bash"> # # This file defines the initial setup for the module files search path. # Comments may be added anywhere, which begin on # and continue until the # end of the line # Each line containing a single path will be added to the MODULEPATH # environment variable. You may add as many as you want - just # limited by the maximum variable size of your shell. # /opt/modulefiles </code> </pre> and I then put in ```/opt/modulefiles``` all my module files. To exemplify, let us assume that we have two different versions of gcc installed, being 4.7.2 and 4.8.3. We then need to create two modulefiles as such ```/opt/modulefiles/gnu-gcc-4.7.2``` <pre> <code class="bash"> #%Module1.0##################################################################### ## ## null modulefile ## ## modulefiles/null. Generated from null.in by configure. ## # for Tcl script use only set root /opt/gcc-4.7.2 prepend-path PATH $root/bin prepend-path LD_LIBRARY_PATH $root/lib prepend-path LD_LIBRARY_PATH $root/lib64 </code> </pre> and ```/opt/modulefiles/gnu-gcc-4.8.3``` <pre> <code class="bash"> #%Module1.0##################################################################### ## ## null modulefile ## ## modulefiles/null. Generated from null.in by configure. ## # for Tcl script use only set root /opt/gcc-4.8.3 prepend-path PATH $root/bin prepend-path LD_LIBRARY_PATH $root/lib prepend-path LD_LIBRARY_PATH $root/lib64 </code> </pre> If you would now run ```module avail```, (assuming you have a similar ```.modulespath``` as mine) you would see something like this <pre> <code class="bash"> -------- /opt/modulefiles -------- gnu-gcc-4.7.2 gnu-gcc-4.8.3 </code> </pre> If I would now like to use gcc-4.7.2 to compile, I would type ```module load gnu-gcc-4.7.2``` and have the bin directories of ```gcc-4.7.2``` appended to my ```$PATH``` ensuring that I use the right compiler. More advanced configuration would actually modify the modulefiles in such a way that when gcc-4.7.2 is loaded and you would run ```module load 4.8.3``` that then a conflict error would be given.
    • watched6425
    • active(true)
    • created2015-02-22 12:07:00
    • modified2015-06-30 17:24:46
    • comments0
• comments(empty)
• $request->data(empty)
• $this->validationErrors(array)
  • Post(empty)
  • Comment(empty)
  • Tag(empty)
  • PostsTag(empty)
  • ParentComment(empty)
• Loaded Helpers(array)
  • 0Auth
  • 1Navbar
  • 2Download
  • 3Flag
  • 4Markdown
  • 5Number
  • 6SimpleGraph
  • 7DebugTimer
  • 8Toolbar
  • 9Html
  • 10Form
  • 11Session
  • 12HtmlToolbar

App Constants

CakePHP Constants

PHP Environment

Included Files

Include Paths

• 0/customers/e/2/e/ivofilot.nl/httpd.www/lib
• 2/usr/share/php
• 3-> /customers/e/2/e/ivofilot.nl/httpd.www/lib/Cake/

Included Files

• core(array)
  • Behavior(array)
    • 0CORE/Model/Behavior/TreeBehavior.php
  • Cache(array)
    • 0CORE/Cache/Cache.php
    • 1CORE/Cache/Engine/FileEngine.php
    • 2CORE/Cache/CacheEngine.php
  • Component(array)
    • 0CORE/Controller/Component/SessionComponent.php
    • 1CORE/Controller/Component/AuthComponent.php
    • 2CORE/Controller/Component/Auth/FormAuthenticate.php
    • 3CORE/Controller/Component/Auth/BaseAuthenticate.php
  • Config(array)
    • 0CORE/Config/routes.php
    • 1CORE/Config/config.php
  • Controller(array)
    • 0CORE/Controller/Controller.php
    • 1CORE/Controller/ComponentCollection.php
    • 2CORE/Controller/Component.php
  • Datasource(array)
    • 0CORE/Model/Datasource/CakeSession.php
    • 1CORE/Model/Datasource/Database/Mysql.php
    • 2CORE/Model/Datasource/DboSource.php
    • 3CORE/Model/Datasource/DataSource.php
  • Error(array)
    • 0CORE/Error/exceptions.php
    • 1CORE/Error/ErrorHandler.php
  • I18n(array)
    • 0CORE/I18n/I18n.php
    • 1CORE/I18n/L10n.php
  • Log(array)
    • 0CORE/Log/CakeLog.php
    • 1CORE/Log/LogEngineCollection.php
    • 2CORE/Log/Engine/FileLog.php
    • 3CORE/Log/Engine/BaseLog.php
    • 4CORE/Log/CakeLogInterface.php
  • Model(array)
    • 0CORE/Model/Model.php
    • 1CORE/Model/BehaviorCollection.php
    • 2CORE/Model/ConnectionManager.php
    • 3CORE/Model/ModelBehavior.php
  • Network(array)
    • 0CORE/Network/CakeRequest.php
    • 1CORE/Network/CakeResponse.php
  • Other(array)
    • 0CORE/bootstrap.php
    • 1CORE/basics.php
    • 2CORE/Core/App.php
    • 3CORE/Core/Configure.php
    • 4CORE/Core/CakePlugin.php
    • 5CORE/Event/CakeEventListener.php
    • 6CORE/Event/CakeEvent.php
    • 7CORE/Event/CakeEventManager.php
    • 8CORE/Core/CakeObject.php
  • Routing(array)
    • 0CORE/Routing/Dispatcher.php
    • 1CORE/Routing/Filter/AssetDispatcher.php
    • 2CORE/Routing/DispatcherFilter.php
    • 3CORE/Routing/Filter/CacheDispatcher.php
    • 4CORE/Routing/Router.php
    • 5CORE/Routing/Route/CakeRoute.php
    • 6CORE/Routing/Route/PluginShortRoute.php
  • Utility(array)
    • 0CORE/Utility/Hash.php
    • 1CORE/Utility/Inflector.php
    • 2CORE/Utility/ObjectCollection.php
    • 3CORE/Utility/Debugger.php
    • 4CORE/Utility/CakeText.php
    • 5CORE/Utility/ClassRegistry.php
    • 6CORE/Utility/Set.php
  • View(array)
    • 0CORE/View/HelperCollection.php
• app(array)
  • Config(array)
    • 0APP/Config/core.php
    • 1APP/Config/bootstrap.php
    • 2APP/Config/routes.php
    • 3APP/Config/database.php
  • Controller(array)
    • 0APP/Controller/PostsController.php
    • 1APP/Controller/AppController.php
  • Model(array)
    • 0APP/Model/Post.php
    • 1APP/Model/AppModel.php
    • 2APP/Model/Comment.php
    • 3APP/Model/Tag.php
  • Other(array)
    • 0APP/webroot/index.php
• plugins(array)
  • DebugKit(array)
    • Component(array)
      • 0DebugKit/Controller/Component/ToolbarComponent.php
    • Plugin(array)
      • 0DebugKit/Lib/DebugMemory.php
      • 1DebugKit/Lib/Panel/HistoryPanel.php
      • 2DebugKit/Lib/DebugPanel.php
      • 3DebugKit/Lib/Panel/SessionPanel.php
      • 4DebugKit/Lib/Panel/RequestPanel.php
      • 5DebugKit/Lib/Panel/SqlLogPanel.php
      • 6DebugKit/Lib/Panel/TimerPanel.php
      • 7DebugKit/Lib/Panel/LogPanel.php
      • 8DebugKit/Lib/Log/Engine/DebugKitLog.php
      • 9DebugKit/Lib/Panel/VariablesPanel.php
      • 10DebugKit/Lib/Panel/EnvironmentPanel.php
      • 11DebugKit/Lib/Panel/IncludePanel.php
      • 12DebugKit/Lib/DebugTimer.php
  • Markdown(array)
    • Config(array)
      • 0Markdown/Config/bootstrap.php
    • Plugin(array)
      • 0Markdown/Lib/Error/MarkdownExceptions.php