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(→‎Intel C/C++ CDT Plugin)
(information about usage on cedar and graham)
 
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}}
 
}}
  
−
=Introduction=
+
=Eclipse on new Compute Canada clusters=
  
−
Sharcnet provides a module for the Eclipse SDK based on the download-able Eclipse Classic 4.2.2 package. Once the module is loaded and the eclipse gui is up and running, users can easily install any of the available add-on packages found in the left hand column of the package comparison [http://www.eclipse.org/downloads/compare.php table].  The installation procedure is explained in the General Notes section below ie) for the purpose of customizing and extended eclipses capability to ones programming needs.
+
Eclipse has been installed on the new Compute Canada clusters cedar and graham as a module.
 +
 
 +
To use it, connect with a graphical interface enabled (ssh -Y ...) and execute:
 +
 
 +
module load eclipse
 +
eclipse
 +
 
 +
The information below refers to Eclipse usage on SHARCNET clusters. Some of this functionality has not yet been enabled on cedar and graham. If you find you need this functionality on the new clusters as well, please email help@sharcnet.ca
 +
 
 +
=Introduction to Eclipse on SHARCNET clusters=
 +
 
 +
Sharcnet provides a module for the <i>Eclipse for Parallel Application Developers</i> Release.  Once the module is loaded and the eclipse gui is up and running, users can easily install any of the available add-on packages found in the left hand column of the package comparison [http://www.eclipse.org/downloads/compare.php table] to customize and extend their eclipse environment.  The installation procedure for additional software into eclipse is explained in the general nodes section below.
  
 
=Version Selection=
 
=Version Selection=
  
−
<pre>module load eclipse/4.2.2</pre>
+
<pre>module load eclipse/4.6.2
 +
eclipse</pre>
  
 
=Job Submission=
 
=Job Submission=
  
−
Not applicable.
+
Eclipse is intended for interactive use outside of the queue therefore this section is not applicable.
  
−
=Example Job=
+
=Example Usage=
  
−
Not applicable.
+
==Serial Program==
 +
 
 +
Eclipse provides sample project for getting started such as hello world.  Once the Intel Compilers have been added as described below the following button click seqeuence should allow you to load up Hello World to test compiling with the Intel C++ compiler, where \ simply indicates a line break:
 +
 
 +
<pre>
 +
File->New->Project->C/C++->C/C++ Project->C++ Managed Build->Executable-> \
 +
  Hello World C++ Project->Intel C++ Compiler->Prject Name: test1->Finish
 +
</pre>
 +
 
 +
==Parallel Program==
 +
 
 +
To get started see the eclipse [http://help.eclipse.org/mars/nav/59 Parallel Development User Guide].  To find help building openmpi parallel programs click <i>Running Parallel Programs</i> then scroll down the the <b>PTP supported Target System Configurations</b> table and click <i>Open MPI-Generic-Interactive</i>.  More detailed usage instructions to provide user guidance will be provided here asap.
  
 
=General Notes=
 
=General Notes=
  
−
==Preparation (first time use only)==
+
Before beginning to use Eclipse the following steps should be done since there is limited space under home which otherwise would be used by default.
  
 
<pre>
 
<pre>
Line 29: Line 52:
 
2) mkdir -p /work/$USER/eclipse/workspace
 
2) mkdir -p /work/$USER/eclipse/workspace
 
3) ln -s /work/$USER/eclipse/.eclipse ~/.eclipse
 
3) ln -s /work/$USER/eclipse/.eclipse ~/.eclipse
−
4) ln -s /work/$USER/eclipse/workspace workspace
+
4) ln -s /work/$USER/eclipse/workspace ~/workspace
 
</pre>
 
</pre>
  
−
==Running Eclipse (on a devel node)==
+
Note that Step 4) assumes you specify your <i>workspace</i> under your home directory, adjust accordingly.
 +
 
 +
==Interactive Use==
 +
 
 +
===On VDI Workstation===
 +
 
 +
<pre>
 +
0) Install tigervnc client on your desktop
 +
1) Start tigervnc client application
 +
2) Connect to vdi-centos6.user.sharcnet.ca
 +
3) open a terminal window
 +
4) module load intel/16.0.4 eclipse/4.6.2
 +
5) eclipse
 +
</pre>
 +
 
 +
Note that tigervnc can be download from [http://tigervnc.org/].  Additional documentation regarding howto use vncviewer maybe found  in section <i>1.2.1 vncviewer (Windows, MacOS, and Fedora)</i> of the sharcnet [https://www.sharcnet.ca/help/index.php/Remote_Graphical_Connections wiki].
 +
 
 +
===On Devel Node===
 +
 
 +
Please note that its not recommended to run graphical application on sharcnet clusters over ssh due to performance issues.  When a program is available on vdi or viz workstations, its best to run it there instead since vnc can be used.
  
 
<pre>
 
<pre>
 
1) ssh -Y orca.sharcnet.ca
 
1) ssh -Y orca.sharcnet.ca
 
2) ssh -Y orc-dev1
 
2) ssh -Y orc-dev1
−
3) module load eclipse
+
3) module unload intel mkl
−
4) eclipse
+
4) module load intel/16.0.4
 +
5) module load eclipse/4.6.2
 +
6) eclipse
 
</pre>
 
</pre>
  
−
==Installing New Software Into Eclipse==
+
==Using Eclipse==
  
−
===Intel C/C++ CDT Plugin===
+
===Installing the Integration===
  
−
An overview how to add the intel compiler and intel debugger integrations into eclipse is provided [http://software.intel.com/sites/products/documentation/doclib/iss/2013/compiler/cpp-lin/GUID-77395CD9-9BDF-4BB4-A01C-5BB2C4F03310.htm here].  Another similar article by intel (reproduced below) is provided [http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/GUID-B74312A7-4771-40FA-B35B-B8B2A49083E4.htm  here].  Intel also provides an online tutorial [http://software.intel.com/en-us/articles/intel-c-compiler-for-linux-using-intel-compilers-with-the-eclipse-ide-pdf/ here].  
+
The intel article [https://software.intel.com/en-us/articles/intel-c-compiler-for-linux-using-intel-compilers-with-the-eclipse-ide-pdf" Using Intel® C++ Compiler with the Eclipse IDE on Linux] explains in detail how to configure eclipse to use any of the intel compiler versions installed on linux. The main step which might not be obvious is adding the repository once you click the <i>Add->Local</i> buttons, you should specify a repository root directory such as  <i>/opt/sharcnet/intel/16.0.4/ide_support_2016/eclipse/compiler_xe</i> by clicking File System in the left had menu of the finder window that appears and traversing down the tree.  Once the compiler is added it will be available the next time you run eclipse, as can be confirmed by scrolling through <i>help --> Installed Software</i> and you should see:
  
 
<pre>
 
<pre>
−
To install the integrations for C/C++, it is recommended to download the Eclipse package for C/C++
+
Name                          Version          I                                            Provider
−
developers that comes with CDT already installed. To debug Fortran applications, you need to install
+
Intel C++ Compiler          16.0.0.201607221  com.intel.compiler.composerxe.feature.group  Intel Corporation
−
Photran project plug-ins in addition to the CDT plug-ins as follows:
+
  C/C++ Developement Tools   9.2.0.2016120613  org.eclipse.cdt.feature.group                Eclipse CDT
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  1. Start Eclipse and select Help > Install new software.
+
</pre>
−
  2. Select Indigo from the list of available software sites. A list of available plug-ins is displayed.
+
−
  3. Expand the node Programming Languages and check the checkbox for Fortran Development Tools (Photran).
+
−
You must have a working X Window System environment to use the debugger integrations for Eclipse.
+
−
To add the Intel® Debugger integrations to your Eclipse configuration:
+
−
   1. Start Eclipse.
+
−
  2. Select or create a workspace. For example, select or create a makefile project with already existing code. For more information see the Eclipse New Project wizard. Makefiles need to contain a rule "all:" to build the whole project.
+
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  3. Select Help > Install New Software.
+
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  4. Next to the Work with field, Click the Add button. The Add Site dialog opens.
+
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  5. Click the Local button and browse to the appropriate Intel CDT integration directory:
+
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          * install_dir/eclipse_support/cdt8.0/eclipse
+
−
  6. Click OK.
+
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  7. Make sure Group items by category is not checked.
+
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  8. Select the Intel Debugger (IDB) integration of your choice and click Next.
+
−
  9. Follow the installation instructions.
+
−
  10. When asked if you want to restart Eclipse, select Yes.
+
  
−
When Eclipse restarts, you can create and work with CDT projects that use the Intel C++ compiler.
+
You should also see new fortran entries under PTP Fortran Support.
 +
 +
<pre>
 +
Name                                      Version          I                                          Provider
 +
PTP Fortran Support                   9.1.1.201612062209 org.eclipse.ptp.fortran.feature.group Eclipse PTP
 +
  Fortran Development Tools (Photran)      9.1.1.201612062125 org.eclipse.photran.feature.group Eclipse PTP
 +
  Linux Intel(R) Fortran Compiler Support  9.1.1.201612062125 org.eclipse.photran.intel.feature.group Eclipse PTP
 
</pre>
 
</pre>
  
−
===Intel Photran IDE Plugin===
+
Its not necessary to install Fortran Development Tools (Photran) since its included in [https://eclipse.org/ptp PTP].
 +
 
 +
===Using the Integration===
 +
 
 +
The intel article reminds us to source compilervars.[csh|sh] before starting eclipse so the compiler commands are found.  Its sufficient to load the corresponding intel sharcnet module before starting eclipse as follows:
 +
 
 +
<pre>
 +
module unload intel mkl
 +
module load intel/16.0.4
 +
module load eclipse/4.6.2
 +
eclipse
 +
</pre>
 +
 
 +
===Installing Plugins===
  
 
This section shows the basic procedure for installing additional (eclipse provided) packages into eclipse. The installation of Photran (the Fortran IDE plugin for Eclipse) which works with the intel compiler and most other compilers is used as an example. Many other packages can similarly be installed.  Since the eclipse download repository is external to the sharcnet network, package installation must be done on iqaluk or a viz station and not on a devel node. Once the required add-on packages are installed they are available on any other sharcnet system where eclipse might be started.  Note that the packages are installed under your <i>~/.eclipse</i> directory hence significant disk space consumption could occur depending how many packages are added.
 
This section shows the basic procedure for installing additional (eclipse provided) packages into eclipse. The installation of Photran (the Fortran IDE plugin for Eclipse) which works with the intel compiler and most other compilers is used as an example. Many other packages can similarly be installed.  Since the eclipse download repository is external to the sharcnet network, package installation must be done on iqaluk or a viz station and not on a devel node. Once the required add-on packages are installed they are available on any other sharcnet system where eclipse might be started.  Note that the packages are installed under your <i>~/.eclipse</i> directory hence significant disk space consumption could occur depending how many packages are added.
  
 
<pre>
 
<pre>
−
1)  ssh -Y iqaluk.sharcnet.ca
+
1)  Connect to vdi-centos6.user.sharcnet.ca
−
2)  module load eclipse
+
2)  module load eclipse/4.6.2
 
3)  eclipse (start workbench)
 
3)  eclipse (start workbench)
 
4)  select the default workspace /home/myusername/workspace then click Ok
 
4)  select the default workspace /home/myusername/workspace then click Ok
 
5)  click Help on top pull down menu, then click Install New Software
 
5)  click Help on top pull down menu, then click Install New Software
−
6)  for "Work with:" enter http://download.eclipse.org/releases/juno/ --> click Add
+
6)  from the pulldown select  ...
−
7)  for "Name:" enter juno422
+
    The Eclipse Project Updates - http://download.eclipse.org/eclipse/updates/4.6
−
8)  for "Location:" enter http://download.eclipse.org/releases/juno/ --> click Ok
+
7)  from the "Available Software" menu click something like ...
−
9)  from the "Available Software" menu click the Programming Languages pulldown tick
+
     Plugin development tools
−
     check boxes "Linux Intel Compiler Support" and "Fortran Development Tools"
+
8) Click finish to commit the installation and wait to finish.
−
10) click Next --> click Next again --> Review and Agree to license agreement
+
 
</pre>
 
</pre>
 +
 +
Note in step 6 you can see what packages are already installed by clicking "What is already installed?"
  
 
==Querying Installed Packages==
 
==Querying Installed Packages==
  
 +
1) Start eclipse<br>
 +
2) click Help on top pull down menu<br>
 +
3) click About Eclipse<br>
 
<pre>
 
<pre>
−
1) Start eclipse
+
Version: Neon.2 Release (4.6.2)
−
2) click Help on top pull down menu
+
Build id: 20161208-0600
−
3) click About Eclipse SDK
+
</pre>
−
4) click Installation Details button.
+
4) click <i>Installation Details</i>
 +
All packages relating to the base installation will be displayed:
 +
<pre>
 +
Eclipse for Parallel Application Developers  64bit-linux
 +
Tools for C, C++, Fortran, and UPC, including MPI, OpenMP,
 +
OpenACC, a parallel debugger, and remotely building, running
 +
and monitoring applications...
 
</pre>
 
</pre>
−
Note that Eclipse SDK will appear as the first entry, and is the sharcnet eclipse module. Any other packages shown were manually installed by the user.
 
  
 
=References=
 
=References=
Line 106: Line 163:
 
o Eclipse Documentation<br>
 
o Eclipse Documentation<br>
 
http://help.eclipse.org/
 
http://help.eclipse.org/
 +
 +
o Eclipse Wiki<br>
 +
http://wiki.eclipse.org/
  
 
o Eclipse Download Area<br>
 
o Eclipse Download Area<br>
Line 112: Line 172:
 
o Compare Eclipse Meta Packages<br>
 
o Compare Eclipse Meta Packages<br>
 
http://www.eclipse.org/downloads/compare.php
 
http://www.eclipse.org/downloads/compare.php
 +
 +
o CDT Documentation<br>
 +
http://www.eclipse.org/cdt/documentation.php
 +
 +
o Eclipse PTP<br>
 +
http://wiki.eclipse.org/ptp/
 +
 +
o Photran - An Integrated Development Environment and Refactoring Tool for Fortran<br>
 +
http://www.eclipse.org/photran/
 +
 +
o Fortran Development User Guide<br>
 +
http://help.eclipse.org/mars/index.jsp?topic=%2Forg.eclipse.photran.doc.user%2Fhtml%2Ftoc.html

Latest revision as of 16:08, 31 October 2017

ECLIPSE
Description: The Eclipse Platform, and Plug-in Development Environment.
SHARCNET Package information: see ECLIPSE software page in web portal
Full list of SHARCNET supported software


Eclipse on new Compute Canada clusters

Eclipse has been installed on the new Compute Canada clusters cedar and graham as a module.

To use it, connect with a graphical interface enabled (ssh -Y ...) and execute: 

module load eclipse
eclipse

The information below refers to Eclipse usage on SHARCNET clusters. Some of this functionality has not yet been enabled on cedar and graham. If you find you need this functionality on the new clusters as well, please email help@sharcnet.ca

Introduction to Eclipse on SHARCNET clusters

Sharcnet provides a module for the Eclipse for Parallel Application Developers Release. Once the module is loaded and the eclipse gui is up and running, users can easily install any of the available add-on packages found in the left hand column of the package comparison table to customize and extend their eclipse environment. The installation procedure for additional software into eclipse is explained in the general nodes section below.

Version Selection

module load eclipse/4.6.2
eclipse

Job Submission

Eclipse is intended for interactive use outside of the queue therefore this section is not applicable.

Example Usage

Serial Program

Eclipse provides sample project for getting started such as hello world. Once the Intel Compilers have been added as described below the following button click seqeuence should allow you to load up Hello World to test compiling with the Intel C++ compiler, where \ simply indicates a line break: 

File->New->Project->C/C++->C/C++ Project->C++ Managed Build->Executable-> \
   Hello World C++ Project->Intel C++ Compiler->Prject Name: test1->Finish

Parallel Program

To get started see the eclipse Parallel Development User Guide. To find help building openmpi parallel programs click Running Parallel Programs then scroll down the the PTP supported Target System Configurations table and click Open MPI-Generic-Interactive. More detailed usage instructions to provide user guidance will be provided here asap.

General Notes

Before beginning to use Eclipse the following steps should be done since there is limited space under home which otherwise would be used by default. 

1) mkdir -p /work/$USER/eclipse/.eclipse
2) mkdir -p /work/$USER/eclipse/workspace
3) ln -s /work/$USER/eclipse/.eclipse ~/.eclipse
4) ln -s /work/$USER/eclipse/workspace ~/workspace

Note that Step 4) assumes you specify your workspace under your home directory, adjust accordingly.

Interactive Use

On VDI Workstation

0) Install tigervnc client on your desktop
1) Start tigervnc client application
2) Connect to vdi-centos6.user.sharcnet.ca
3) open a terminal window
4) module load intel/16.0.4 eclipse/4.6.2
5) eclipse

Note that tigervnc can be download from [1]. Additional documentation regarding howto use vncviewer maybe found in section 1.2.1 vncviewer (Windows, MacOS, and Fedora) of the sharcnet wiki.

On Devel Node

Please note that its not recommended to run graphical application on sharcnet clusters over ssh due to performance issues. When a program is available on vdi or viz workstations, its best to run it there instead since vnc can be used. 

1) ssh -Y orca.sharcnet.ca
2) ssh -Y orc-dev1
3) module unload intel mkl
4) module load intel/16.0.4
5) module load eclipse/4.6.2 
6) eclipse

Using Eclipse

Installing the Integration

The intel article " Using Intel® C++ Compiler with the Eclipse IDE on Linux explains in detail how to configure eclipse to use any of the intel compiler versions installed on linux. The main step which might not be obvious is adding the repository once you click the Add->Local buttons, you should specify a repository root directory such as /opt/sharcnet/intel/16.0.4/ide_support_2016/eclipse/compiler_xe by clicking File System in the left had menu of the finder window that appears and traversing down the tree. Once the compiler is added it will be available the next time you run eclipse, as can be confirmed by scrolling through help --> Installed Software and you should see: 

Name                          Version           I                                            Provider
Intel C++ Compiler           16.0.0.201607221   com.intel.compiler.composerxe.feature.group  Intel Corporation
  C/C++ Developement Tools    9.2.0.2016120613  org.eclipse.cdt.feature.group                Eclipse CDT

You should also see new fortran entries under PTP Fortran Support. 

Name                                       Version           I                                           Provider
PTP Fortran Support	                   9.1.1.201612062209	org.eclipse.ptp.fortran.feature.group	 Eclipse PTP
  Fortran Development Tools (Photran)      9.1.1.201612062125	org.eclipse.photran.feature.group	 Eclipse PTP
  Linux Intel(R) Fortran Compiler Support  9.1.1.201612062125	org.eclipse.photran.intel.feature.group	 Eclipse PTP

Its not necessary to install Fortran Development Tools (Photran) since its included in PTP.

Using the Integration

The intel article reminds us to source compilervars.[csh|sh] before starting eclipse so the compiler commands are found. Its sufficient to load the corresponding intel sharcnet module before starting eclipse as follows: 

module unload intel mkl
module load intel/16.0.4
module load eclipse/4.6.2 
eclipse

Installing Plugins

This section shows the basic procedure for installing additional (eclipse provided) packages into eclipse. The installation of Photran (the Fortran IDE plugin for Eclipse) which works with the intel compiler and most other compilers is used as an example. Many other packages can similarly be installed. Since the eclipse download repository is external to the sharcnet network, package installation must be done on iqaluk or a viz station and not on a devel node. Once the required add-on packages are installed they are available on any other sharcnet system where eclipse might be started. Note that the packages are installed under your ~/.eclipse directory hence significant disk space consumption could occur depending how many packages are added. 

1)  Connect to vdi-centos6.user.sharcnet.ca
2)  module load eclipse/4.6.2
3)  eclipse (start workbench)
4)  select the default workspace /home/myusername/workspace then click Ok
5)  click Help on top pull down menu, then click Install New Software
6)  from the pulldown select  ...
    The Eclipse Project Updates - http://download.eclipse.org/eclipse/updates/4.6
7)  from the "Available Software" menu click something like ...
    Plugin development tools
8)  Click finish to commit the installation and wait to finish.

Note in step 6 you can see what packages are already installed by clicking "What is already installed?"

Querying Installed Packages

1) Start eclipse
2) click Help on top pull down menu
3) click About Eclipse

Version: Neon.2 Release (4.6.2)
Build id: 20161208-0600

4) click Installation Details All packages relating to the base installation will be displayed: 

Eclipse for Parallel Application Developers   64bit-linux
Tools for C, C++, Fortran, and UPC, including MPI, OpenMP,
OpenACC, a parallel debugger, and remotely building, running
and monitoring applications...

References

o Eclipse Homepage
http://www.eclipse.org/

o Eclipse Documentation
http://help.eclipse.org/

o Eclipse Wiki
http://wiki.eclipse.org/

o Eclipse Download Area
http://www.eclipse.org/downloads/

o Compare Eclipse Meta Packages
http://www.eclipse.org/downloads/compare.php

o CDT Documentation
http://www.eclipse.org/cdt/documentation.php

o Eclipse PTP
http://wiki.eclipse.org/ptp/

o Photran - An Integrated Development Environment and Refactoring Tool for Fortran
http://www.eclipse.org/photran/

o Fortran Development User Guide
http://help.eclipse.org/mars/index.jsp?topic=%2Forg.eclipse.photran.doc.user%2Fhtml%2Ftoc.html

Retrieved from "https://sharcnet.ca/help/index.php?title=ECLIPSE&oldid=15943"