Prato Workshop 2018 - Revision history

Raffaele Coray at 13:20, 2 December 2024

2024-12-02T13:20:08Z

2018-04-12T12:31:23Z

Compiling Dynamo for the GPU

2018-04-12T12:15:06Z

Run Dynamo projects in a different shell

2018-04-12T12:14:53Z

Computers

2018-04-12T12:14:31Z

Computers

2018-04-12T09:48:02Z

General Introduction

2018-04-12T09:26:57Z

Computers

2018-04-12T07:43:05Z

Materials

2018-04-12T07:42:01Z

Program

2018-04-12T06:33:33Z

Computers

← Older revision		Revision as of 13:20, 2 December 2024
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		+	[[Category:WalkthroughsSpecific]]
		+
	This page describes the contents of the practical hands-on sessions in Diamond (11th-12th November 2018).		This page describes the contents of the practical hands-on sessions in Diamond (11th-12th November 2018).

@@ Line 28: / Line 28: @@
 === Compiling  ''Dynamo'' for the GPU===
-You only need to do  this if you want to use the  GPU projects:
+You only need to do  this if you want to '''compile''  the  GPU projects:
-  <tt> export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6</tt>
+  <tt>export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6</tt>
   <tt>export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH</tt>
   <tt>cd ~/ws/opt</tt>

@@ Line 21: / Line 21: @@
 * Open a new Linux terminal
 * Activate ''Dynamo''
-* ''If''' you are going to use a GPU, you need to make the CUDA libraries visible:
+* ''If'' you are going to use a GPU, you need to make the CUDA libraries visible:
   <tt>export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH</tt>
 *go to the folder containing the project.  Type the name of the project executable (extension .exe). For a project called <tt>myProject</tt>:

@@ Line 21: / Line 21: @@
 * Open a new Linux terminal
 * Activate ''Dynamo''
-* If you are going to use a GPU, you need to make the CUDA libraries visible:
+* ''If''' you are going to use a GPU, you need to make the CUDA libraries visible:
-<tt>export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH</tt>
+ <tt>export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH</tt>
 *go to the folder containing the project.  Type the name of the project executable (extension .exe). For a project called <tt>myProject</tt>:
   <tt>./myProject.exe</tt>

@@ Line 21: / Line 21: @@
 * Open a new Linux terminal
 * Activate ''Dynamo''
 *go to the folder containing the project.  Type the name of the project executable (extension .exe). For a project called <tt>myProject</tt>:
   <tt>./myProject.exe</tt>

@@ Line 83: / Line 83: @@
 Working on your own:
-* Basic [[Starters guide | walkthrough]]:  on synthetic data. Covers creating a catalogue, picking particles, launching a project. (~1.5 hours)
+* Basic [[Starters guide | walkthrough (Starters guide)]]:  on synthetic data. Covers creating a catalogue, picking particles, launching a project. (~1.5 hours)
 * Related materials (not covered in this course):

@@ Line 17: / Line 17: @@
 === Run ''Dynamo'' projects in a different shell ===
 It is inconvenient to run projects in the ''Dynamo'' console. Instead, do the following:
 * Open a new Linux terminal
@@ Line 31: / Line 32: @@
   <tt>sudo make clean </tt>
   <tt>sudo make all</tt>
 == Materials ==

@@ Line 53: / Line 53: @@
 *	Dynamo_03_projects.pdf
 General operation of the GUI that creates alignment projects.
-*	Dynamo_04_starters.pdf
+*	'''Dynamo_04_starters.pdf'''
 Walkthrough with synthetic data
-*	Dynamo_05_advanced.pdf
+*	'''Dynamo_05_advanced.pdf'''
 A single slide with the basic concepts in  Dynamo.
 *	Dynamo_06_membranes.pdf
@@ Line 61: / Line 61: @@
 *	Dynamo_07_filaments.pdf
 Creation of filaments in the tomogram browser.
-*	Dynamo_08_lattices.pdf
+*	'''Dynamo_08_lattices.pdf'''
 Walkthrough on extraction of particles in densely populated vesicles.
 == Program ==

@@ Line 8: / Line 8: @@
 To activate ''Dynamo''
   <tt> activate_dynamo </tt>
@@ Line 27: / Line 26: @@
 You only need to do  this if you want to use the  GPU projects:
   <tt>export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH</tt>
   <tt>cd ~/ws/opt</tt>