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--- gpu_isac [2020/05/29 17:46]
fschoenfeld
+++ gpu_isac [2020/05/29 18:48]
fschoenfeld
@@ Line 63: / Line 63: @@
 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
---gpu_devices=0,1''
+--gpu_devices=0,1
+</code>
 **[ ! ] - Mandatory** parameters in the GPU ISAC call:
@@ Line 73: / Line 88: @@
   * 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**.
-  * Adjust the number in ''--radius=160'' to the **radius of your particle** (in pixels).
+  * Adjust the number in ''radius=160'' to the **radius of your particle** (in pixels).
 **[?] - 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 ''--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>

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