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gpu_isac [2020/05/29 18:08]
fschoenfeld 		gpu_isac [2020/06/18 11:11]
fschoenfeld
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   - **Untar the archive** using ''tar -xf GPU_ISAC_CHIMERA.tar''.   - **Untar the archive** using ''tar -xf GPU_ISAC_CHIMERA.tar''.
   - **Check CUDA path variables** using:   - **Check CUDA path variables** using:
-    - ''echo $PATH'' Does it contain the path to your **cuda/bin** folder?+    - <code>echo $PATH</code> Does it contain the path to your **cuda/bin** folder?
     - ''echo $LD_LIBRARY_PATH'' Does it contain the path to your **cuda/lib64** folder?     - ''echo $LD_LIBRARY_PATH'' Does it contain the path to your **cuda/lib64** folder?
     - If the path variables do **not** contain these path variables, you can add them like so:     - If the path variables do **not** contain these path variables, you can add them like so:
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   - **Adjust sparx libraries** to work with the C++/CUDA library we just compiled:   - **Adjust sparx libraries** to work with the C++/CUDA library we just compiled:
     - ''cd ../eman2/sparx/libpy''     - ''cd ../eman2/sparx/libpy''
-    - ''sed -i.bkp "s|/home/schoenf/work/code/cuISAC/cuda|$(realpath ../../../cuda)|g" applications.py'' +    - ''sed -i.bkp <nowiki>"</nowiki>s|/home/schoenf/work/code/cuISAC/cuda|$(realpath ../../../cuda)|g<nowiki>"</nowiki> applications.py'' 
-    - ''sed -i.bkp2 's|statistics.sum_oe( data, "a", CTF, EMData(), myid=myid|statistics.sum_oe( data, "a", CTF, EMData()|g' applications.py ''+    - ''sed -i.bkp2 's|statistics.sum_oe( data, <nowiki>"</nowiki>a<nowiki>"</nowiki>, CTF, EMData(), myid=myid|statistics.sum_oe( data, <nowiki>"</nowiki>a<nowiki>"</nowiki>, CTF, EMData()|g' applications.py ''
   - **Set the correct libraries and environment:**   - **Set the correct libraries and environment:**
     - ''cd ../bin'' (we are now in the **/eman2/sparx/bin** folder of your GPU ISAC installation folder)     - ''cd ../bin'' (we are now in the **/eman2/sparx/bin** folder of your GPU ISAC installation folder)
     - ''ln -rs ../libpy/* .'' (don't forget the dot at the end)     - ''ln -rs ../libpy/* .'' (don't forget the dot at the end)
-    - ''sed -i.bkp "s|/home/schoenf/applications/sphire/v1.1/envs/sphire_1.3/bin|$(dirname $(which sphire))|g" sxisac2_gpu.py'' +    - ''sed -i.bkp <nowiki>"</nowiki>s|/home/schoenf/applications/sphire/v1.1/envs/sphire_1.3/bin|$(dirname $(which sphire))|g<nowiki>"</nowiki> sxisac2_gpu.py'' 
-    - ''sed -i.bkp2 "s/^\(.*options, args.*\)$/\1\n    os.environ['CUDA_VISIBLE_DEVICES'] = options.gpu_devices\n options.gpu_devices = ','.join(map(str, range(len(options.gpu_devices.split(',')))))/g" sxisac2_gpu.py''+    - ''sed -i.bkp2 <nowiki>"</nowiki>s/^\(.*options, args.*\)$/\1\n    os.environ['CUDA_VISIBLE_DEVICES'] = options.gpu_devices\n options.gpu_devices = ','.join(map(str, range(len(options.gpu_devices.split(',')))))/g<nowiki>"</nowiki> sxisac2_gpu.py'' 
  
 ===== Usage ===== ===== Usage =====
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 An example call to use GPU ISAC looks as follows: An example call to use GPU ISAC looks as follows:
  
-**''mpirun''**''-np 6''**''/path/to/sxisac2_gpu.py''**''bdb:path/to/stack out_dir --CTF –radius=160  +<code> 
---target_radius=29 --target_nx=76 --img_per_grp=100 --minimum_grp_size=60 -thld_err=0.7+mpirun -np 6 /path/to/sxisac2_gpu.py bdb:path/to/stack out_dir --CTF -–radius=160 --target_radius=29 --target_nx=76 --img_per_grp=100 --minimum_grp_size=60 --thld_err=0.7 --center_method=0 --gpu_devices=0,1 
 +</code> 
 + 
 +More readable: 
 + 
 +<code> 
 +mpirun -np 6 /path/to/sxisac2_gpu.py 
 +bdb:path/to/stack out_dir 
 +--CTF  
 +-–radius=160 
 +--target_radius=29 
 +--target_nx=76 
 +--img_per_grp=100 
 +--minimum_grp_size=60 
 +--thld_err=0.7
 --center_method=0 --center_method=0
---gpu_devices=0,1'' +--gpu_devices=0,1 
-''--''+</code> 
 **[ ! ] - Mandatory** parameters in the GPU ISAC call: **[ ! ] - Mandatory** parameters in the GPU ISAC call:
  
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   * Replace ''path/to/stack'' with the path to your **input .bdb stack**. If you are using an **.hdf** stack, you need to remove the ''bdb:'' prefix.   * Replace ''path/to/stack'' with the path to your **input .bdb stack**. If you are using an **.hdf** stack, you need to remove the ''bdb:'' prefix.
   * Replace ''out_dir'' with the path to your preferred **output directory**.   * Replace ''out_dir'' with the path to your preferred **output directory**.
-  * Adjust the number in ''--radius=160'' to the **radius of your particle** (in pixels).+  * Adjust the number in ''<nowiki>--</nowiki>radius=160'' to the **radius of your particle** (in pixels).
  
 **[?] - Optional** parameters in the GPU ISAC call: **[?] - Optional** parameters in the GPU ISAC call:
  
   * In ''mpirun –np 6'' the number can be set to the number of your **CPU processors** (e.g., if you have a quad core CPU, you would use 4 here).    * In ''mpirun –np 6'' the number can be set to the number of your **CPU processors** (e.g., if you have a quad core CPU, you would use 4 here). 
-  * In ''--gpu_devices=0,1'' you can set **what GPUs to use**. This example uses two GPUs with id values 0 and 1, respectively. You can check the id values of your available GPUs by executing ''nvidia-smi'' in your terminal (GPUs are sorted by capability, with 0 being your strongest GPU). +  * Using ''<nowiki>--</nowiki>gpu_devices'' you can set **what GPUs to use**. This example uses two GPUs with id values 0 and 1, respectively. You can check the id values of your available GPUs by executing ''nvidia-smi'' in your terminal (GPUs are sorted by capability, with 0 being your strongest GPU). 
-  * You can also use ''--img_per_grp'' to limit the **maximum size of individual classes**. Empirically, a class size of 100-200 (30-50 for negative stain) particles has been proven successful when dealing with around 100,000 particles. +  * You can also use ''<nowiki>--</nowiki>img_per_grp'' to limit the **maximum size of individual classes**. Empirically, a class size of 100-200 (30-50 for negative stain) particles has been proven successful when dealing with around 100,000 particles. 
-  * Similarly, you can also use ''--minimum_grp_size'' to limit the **minimum size of individual classes**. In general, this value should be around 50-60% of your maximum class size.+  * Similarly, you can also use ''<nowiki>--</nowiki>minimum_grp_size'' to limit the **minimum size of individual classes**. In general, this value should be around 50-60% of your maximum class size.
  
 <note> <note>
gpu_isac.txt · Last modified: 2021/05/08 00:41 by shaikh

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