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[ptp-dev] LANL's Eclipse Cheat Sheet
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Attached is the cheat sheet Laura and I have for one of the clusters at LANL.
Hopefully, this will help Steve's configuration sheet.
Happy Labor Day!
Ginger
Created: 8/27/2011
Last Modified: 9/01/2011
Eclipse IDE for Parallel Application Developers (includes Incubating components)
Version: Indigo Release
Build id: 20110615-0604
----------------------------------------------------------------------------------------
Information on eclipse: http://wiki.eclipse.org/Main_Page
Documentation on eclipse Parallel Tools Platform (PTP)
http://eclipse.org/ptp/doc.php
http://wiki.eclipse.org/PTP/designs/2.x/launch_platform#Implementation_Details
PTP Help:
http://help.eclipse.org/indigo/index.jsp?topic=%2Forg.eclipse.ptp.doc.user%2Fhtml%2Ftoc.html
Instructions for Linux (32 or 64 bit) on Yellowrail.lanl.gov
As of 31 August 2011, Yellowrail has been set-up to be able to run eclipse. To manage
a sychronized project, eclipse needs Git to be installed on the remote cluster. This
has been done for yellowrail.
------------------------------------------------------------------------------------------
Getting Started
1. Set-up the following environment variables:
CVS_RSH=ssh,
http_proxy="http://proxyout.lanl.gov:8080";,
http_proxyPort=8080, and
no_proxy=localhost,127.0.0.0/8
(using tcsh, this can be done by adding the following lines to your .cshrc:
setenv CVS_RSH ssh
setenv http_proxy "http://proxyout.lanl.gov:8080";
setenv http_proxyPort 8080
setenv no_proxy localhost,127.0.0.0/8
)
If these environment variables are not set, all sorts of problems can ensue.
There will also be numerous problems if there are errors in your .cshrc
file on the remote system.
NOTE - for PTP developers, also add
setenv CVSROOT anonymous@xxxxxxxxxxxxxxx:/cvsroot/tools
2. Go to http://eclipse.org/downloads/
Download: Eclipse IDE for Parallel Application Developers
Notice that you need to choose the correct packages for your system
(Linux/Windows/Mac OS).
The following instructions are for an installation on a Linux System.
3. Install eclipse, which will create a directory named "eclipse":
If you want eclipse installed into a different directory than the one
downloaded to:
mv eclipse-parallel-indigo...tar.gz <installation_directory>
cd to <installation_directory>.
Unzip the file:
gunzip eclipse-parallel-indigo...tar.gz
Untar the file:
tar xvf eclipse-parallel-indigo...tar
4. Run eclipse:
cd <installation_directory>/eclipse
./eclipse&
Enter the path and name for a workspace directoryin the popup window
when requested. Eclipse works best when there is a different workspace
for each project, so be mindful of the name you choose.
To select a new workspace, in the eclipse application:
Choose menu item: File -> Switch Workspace
You may select from existing workspaces or enter a new one.
5. Verify settings:
In the eclipse application, select menu item:
Window -> Preferences -> Network Connections
The drop down <Active Provider> is <Native>
In the Proxy entries table, the last item is selected with
the following values:
HTTP proxyout.lanl.gov:8080 Native false
This is set automatically by the environment values in step 1.
6. Setup a Remote Environment:
In the eclipse application, select menu item:
Select Window -> Show View -> Other
Click [black triangle] by <Remote Tools> - expands the folder
Select <Remote Environments>
Click [OK]
In the Remote Environments tab,
Right Click [Remote Host]
Select [Create]
Enter the following:
Target Name: <Yellowrail>
Select Radio Button: Remote Host
Host: <yr-fe1.lanl.gov>
User: <your_moniker>
Select Radio Button: password based authentication
Password: (leave this blank, it requires your cryptocard password)
Click [Finish]
When Remote Host is expanded, there is a listing for Yellowrail.
7. Connecting to the Target Environment (Yellowrail):
This allows you to synchronize a project on Yellowrail and start batch jobs.
In the "Remote Environments" tab,
Right Click <Yellowrail>
Select <Edit> - pops up "Target Environment
Configuration" menu
Password: enter a password from your cryptocard
Click [Finish]
In the "Remote Environments" tab,
Click [green triangle] - pops up "Start the
Environment" window
The [green triangle] initiates a connection to Yellowrail.
The display in "Remote Environments" tab will change:
a [red square] is displayed; you can click this to stop the connection.
Remote Host -> Yellowrail's Status is Running
8. Create Resource Manager
To open the Parallel Runtime perspective:
Select Window -> Open Perspective -> Other... - pops up
"Open Perspective" menu
Select <Parallel Runtime>
Click [OK]
In the Resource Managers tab,
Right Click in this window
Select <Add Resource Manager...> - pops up
"Resource Manager Type" menu
Select <PBS-Generic-Batch>
Click [Next>]
Select Remote service provider: <Remote Tools]
Select Connection name: <Yellowrail]
Click [black triangle] by [Advanced Options]
Select Radio Button: [SSH port forwarding]
Click [Next>]
Unselect Box: [Same as control connection]
Select Remote service provided: <Remote Tools>
Select Connection name: <Yellowrail>
Click [black triangle] by [Advanced Options] - displays advanced options
Select Radio Button: <SSH port forwarding>
Click [Next>]
Unselect Box: Use default name and description
Enter:
Name: PBS-Generic-Batch-ProjectName - enter in a unique name
for each project.
Click [Finish]
The new resource manager "PBS-Generic-Batch-ProjectName (LML_JAXB)" is
displayed in the "Resource Managers" tab.
To start the Resource Manager (which is necessary to run a program on Yellowrail).
Right Click <PBS-Generic-Batch (LML_JAXB)>
Select <Start Resource Manager>
This starts the resource manager, so a batched job can be run on Yellowrail
in a synchronized project.
9. Create a Demo Synchronized Project
Select File -> New -> Project... - pops up "New Project" menu
Select Remote
Select Synchronized C/C++ Project - even for a Fortran Project!
Click [Next>] - pops up "New Synchronized
Project" menu
Enter the following:
Project name: FortranProject
Select <Demo - calculate Pi - Fortran using MPI>
Select <Linux GCC>
Click [Next>]
Enter the following:
Author: <Your Name>
Copyright notice: <Your copyright notice>
Greeting: Hello MPI PI Fortran World
Click [Next>]
Click [Next>]
Set Synchronization Provider: to <Git>
Set Remote Provider: to <Remote Tools>
Set Connection: to <Yellowrail>
Set Location: to <remote work-compile directory>
You can enter the directory information directly, or:
Select [Browse] - pops up a file selection menu
Select a work-compile directory on the remote system.
For this example: /panfs/scratch3/vol5/moniker/FortranProject
It's best to have space on /usr/projects/packages/.
Click [Finish]
The synchronized demo project is created. On Yellowrail, there is a copy of
the Makefile and source code in the location you selected
(/panfs/scratch3/vol5/moniker/FortranProject).
10. Run the demo synchronized project
In a terminal window, ssh onto Yellowrail (yr-fe1.lanl.gov):
Set-up the following in your .cshrc on Yellowrail (yr-fe1):
setenv CVS_RSH ssh
setenv PATH /usr/projects/packages/git-scm/got-1.7.5.4/bin:$PATH
module load intel-c
module load intel-f
module load openmpi-intel
On Yellowrail (yr-fe1):
cd /panfs/scratch3/vol5/moniker/FortranProject
mkdir bin
Go back to your eclipse window, and open FortranProject.f90:
Click [black triangle] by FortranProject - expands the folder
Click [black triangle] by src
Double Click [FortranProject.f90] - opens the file
Right Click on FortranProject.f90 - pops-up a menu
Select Run As -> Run Configurations...
Right Click [Parallel Application]
Select [New] - pops up a
"Run Configurations" menu
On the [Resources][Basic PBS Settings] tab,
Set Resource Manager: to <PBS-Generic-Batch>
Set Queue: to <Batch>
Total Memory Needed: to <30mb>
MPI Command: to <mpirun>
MPI Number of Cores to <3>
On the [Resources][Advanced PBS Settings] tab,
Set Queue: to [Batch]
On the [Resources][Import PBS Script] tab,
Select box: <Enable remote output file read>
Select box: <Enable remote error file read>
On the [Application} tab,
Parallel Project: FortranProject
Application Project:
/panfs/scratch3/vol5/moniker/FortranProject/bin/FortranProject
Click [Apply]
Click [Run]
11. To view status/results of batched job
On your Eclipse window:
Select Window -> Open Perspective -> Other - pops up a "Open Perspective" menu
Select [System Monitoring]
Click [OK] - opens up a "System Monitoring"
perspective
Click [Inactive jobs] tab - displays the status of all
eclipse's batched jobs
To view a batched job's error:
Right Click an inactive job - pops up a menu
Click [Get Job Error]
View [Console] tab in lower left corner for results
To view a batched job's output:
Right Click an inactive job - pops up a menu
Click [Get Job Output]
View [Console] tab in lower left corner for results
To view a batched job's status:
Right Click an inactive job - pops up a menu
Click [Refresh Job Status]
12. To create a new project:
Create a new workspace:
Select File -> Switch Workspace -> Other...
Workspace: /home/moniker/projects/cplusWorkpace - enter path and new name
for a workspace
Since this is a new workspace, you will need to repeat steps 6, 7, and 8 now.
Create a new project:
Select File -> New -> Project... - pops up "New Project" menu
Select <Remote>
Select <Synchronized C/C++ Project>
Click [Next>] - pops up "New Synchronized
Project" menu
Enter the following:
Project name: cplusProject
Select <Empty Project>
Select <Linux GCC>
Click [Next>]
Click [Next>]
Select Synchronization Provider: to <Git>
Select Remote Provider: to <Remote Tools>
Select Connection: to <Yellowrail>
Select Location: to <remote work-compile directory> [Browse]
You can enter the directory information directly, or:
Select [Browse] - pops up a file selection menu
Select a work-compile directory on the remote system.
For this example: /panfs/scratch3/vol5/moniker/FortranProject
Click [Finish]
The syncronized project is created. On Yellowrail, the specified workspace has been
created.
To create a source directory:
Select Window -> Open Perspective -> Other... - pops up "Open Perspective" menu
Select <C/C++>
Click [OK]
Right Click <cplusProject> - pops up a menu
Select New -> File - pops up "New Folder" menu
Enter the following:
Folder name: src
Click [Finish]
To create a C++ File:
Right Click <src> - pops up a menu
Select New -> Source File - pops up "New Source File" menu
Enter the following:
Source file: main.cpp
Click [Finish]
Then add your code...
You will have to add Makefiles and other tools for your project to compile and run.
