GPUs EMBO 2018 - Revision history

Daniel Castaño at 10:18, 26 August 2018

2018-08-26T10:18:02Z

Daniel Castaño at 10:13, 26 August 2018

2018-08-26T10:13:18Z

Daniel Castaño at 09:24, 26 August 2018

2018-08-26T09:24:48Z

Daniel Castaño: /* Creation of the project */

2018-08-24T13:42:38Z

Creation of the project

Daniel Castaño at 13:42, 24 August 2018

2018-08-24T13:42:20Z

Daniel Castaño at 15:35, 22 August 2018

2018-08-22T15:35:13Z

Daniel Castaño at 15:15, 22 August 2018

2018-08-22T15:15:26Z

Daniel Castaño: Created page with " * Create a tutorial project
`dtutorial t -p ptest -M 100` * Adapt the project to be ran on a GPU environment without matlab
`dvput ptest destinatio..."`

2018-08-22T15:07:25Z Created page with " * Create a tutorial project <tt>dtutorial t -p ptest -M 100 </tt> * Adapt the project to be ran on a GPU environment without matlab <tt>dvput ptest destinatio..." New page * Create a tutorial project <tt>dtutorial t -p ptest -M 100 </tt> * Adapt the project to be ran on a GPU environment without matlab <tt>dvput ptest destination standalone_gpu</tt> * Passes a group of GPU identifiers <tt>dvput ptest gpu_identifier_set 0:3</tt> * Unfolds the project: <tt>dvunfold ptest</tt> It creates a script called <tt>ptest.sh</tt> that needs to be submitted on a GPU.

@@ Line 3: / Line 3: @@
 = Creation of the project =
-* Create a tutorial project <br />
+* Create a tutorial project  <br />
-  <tt>dtutorial t -p MYPROJECT -M 100 </tt>  <br />
+  <tt>dtutorial t -p ptest -M 100 </tt>  <br />
-This project contains 100 synthetic thermosomes.
+This project  <tt>ptest</tt>contains 100 synthetic thermosomes.
 * Adapt the project to be ran on a GPU environment <br />
-  <tt>dvput MYPROJECT destination matlab_gpu</tt>
+  <tt>dvput ptest destination matlab_gpu</tt>
 * Passes a group of GPU identifiers.  Assuming that we just want to use 2 GPUs: <br />
@@ Line 17: / Line 17: @@
   <tt>dvunfold ptest</tt>
-It creates a script called <tt>ptest.sh</tt> that needs to be submitted to the a GPU.
+It creates a script called <tt>ptest.m</tt> that needs to be submitted to the GPU.
 = Submission of the project =
 == Submission script model ==
-there is a sample script located in
+There is a sample submission script located in
   <tt> /g/embo2018/cryo06/Dynamo/test/submit.scrip </tt>

@@ Line 11: / Line 11: @@
 * Passes a group of GPU identifiers.  Assuming that we just want to use 2 GPUs: <br />
-  <tt>dvput ptest gpu_identifier_set  0:1</tt>
+  <tt>dvput ptest gpu_identifier_set  0:1</tt> <br />
 * Unfolds the project:
@@ Line 41: / Line 42: @@
 export LD_LIBRARY_PATH=$EBROOTGCC/lib64:$LD_LIBRARY_PATH
 module load CUDA/9.1.85_387.26-GCC-6.4.0-2.28
-echo "dvput MYPROJECT -gpu_identifier_set $CUDA_VISIBLE_DEVICES"  dcommands.sh
+echo $CUDA_VISIBLE_DEVICES
 echo "dvunfold MYPROJECT" >> dcommands.sh
 dynamo dcommands.sh
+chmod u=rxw ./$MYPROJECT.m
-chmod u=rxw ./MYPROJECT.m
+./$MYPROJECT.m
 </pre>

@@ Line 22: / Line 22: @@
 == Submission script model ==
 there is a sample script located in
-  <tt> path this and that </tt>
+  <tt> /g/embo2018/cryo06/Dynamo/test/submit.scrip </tt>
   <pre>
 #!/bin/bash
 #SBATCH -p gpu
 #SBATCH -N 1 #stay on a single node. remove for CPU jobs
-#SBATCH -J jobname   XXXX CHANGE THIS
+#SBATCH -J jobname    # change this
-#SBATCH --ntasks=7
+#SBATCH --ntasks=1;
 #SBATCH -o run.out          # STDOUT
 #SBATCH -e run.err          # STDERR
-#SBATCH --gres=gpu:2  XXXX CHANGE THIS
+#SBATCH --gres=gpu:2   # XXXX CHANGE THIS
 #SBATCH --mail-type=END,FAIL
-#SBATCH --mem=120GB
+#SBATCH --mem=12GB
 #SBATCH --time=0-03:00:00
 module load dynamo
+export LD_LIBRARY_PATH=$EBROOTGCC/lib64:$LD_LIBRARY_PATH
-echo "dvput MYPROJECT -gpu_identifier_set $CUDA_VISIBLE_DEVICES" > dcommands.sh
+module load CUDA/9.1.85_387.26-GCC-6.4.0-2.28
 echo "dvunfold MYPROJECT" >> dcommands.sh
 dynamo dcommands.sh
 chmod u=rxw ./MYPROJECT.m
-./myProject.m
+./MYPROJECT.m
 </pre>
@@ Line 52: / Line 54: @@
 You can copy the script to your local folder (where you have created the project) and edit it to match the requirements of the project. Basically, you need to change the number of GPUs, the name of the project.  Rename it to something you can identify later, like  <tt>ptest.script</tt>
 == Submit the script ==
 <tt>srun ptest.script</tt>

@@ Line 4: / Line 4: @@
 = Creation of the project =
 * Create a tutorial project <br />
-<tt>dtutorial t -p MYPROJECT -M 100 </tt>  <br />
+ <tt>dtutorial t -p MYPROJECT -M 100 </tt>  <br />
 This project contains 100 synthetic thermosomes.
 * Adapt the project to be ran on a GPU environment <br />
-<tt>dvput MYPROJECT destination matlab_gpu</tt>
+ <tt>dvput MYPROJECT destination matlab_gpu</tt>
 * Passes a group of GPU identifiers.  Assuming that we just want to use 2 GPUs: <br />
-<tt>dvput ptest gpu_identifier_set  0:1</tt>
+ <tt>dvput ptest gpu_identifier_set  0:1</tt>
 * Unfolds the project:
-<tt>dvunfold ptest</tt>
+ <tt>dvunfold ptest</tt>
 It creates a script called <tt>ptest.sh</tt> that needs to be submitted to the a GPU.

@@ Line 4: / Line 4: @@
 = Creation of the project =
 * Create a tutorial project <br />
-<tt>dtutorial t -p ptest -M 100 </tt>  <br />
+<tt>dtutorial t -p MYPROJECT -M 100 </tt>  <br />
 This project contains 100 synthetic thermosomes.
-* Adapt the project to be ran on a GPU environment without matlab <br />
+* Adapt the project to be ran on a GPU environment <br />
-<tt>dvput ptest destination standalone_gpu</tt>
+<tt>dvput MYPROJECT destination matlab_gpu</tt>
-* Passes a group of GPU identifiers <br />
+* Passes a group of GPU identifiers.  Assuming that we just want to use 2 GPUs: <br />
-<tt>dvput ptest gpu_identifier_set  0:3</tt>
+<tt>dvput ptest gpu_identifier_set  0:1</tt>
 * Unfolds the project:
@@ Line 36: / Line 36: @@
 #SBATCH --mem=120GB
 #SBATCH --time=0-03:00:00
 module load dynamo
-command
 </pre>