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gpu_isac [2020/06/18 12:05] fschoenfeld |
gpu_isac [2020/08/03 15:25] fschoenfeld |
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===== Overview ===== | ===== Overview ===== | ||
- | **ISAC** (Iterative Stable Alignment and Clustering) is a 2D classification algorithm | + | **ISAC** (//Iterative Stable Alignment and Clustering//) is a **2D classification algorithm**. It sorts a given stack of cryo-EM particles into different |
- | alternating equal size k-means clustering and repeated 2D alignment routines. | + | |
< | < | ||
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</ | </ | ||
- | **ISAC2** is an improved version of ISAC, and the default tool to produce 2D class averages in the **[[http:// | + | **ISAC2** is an improved version of ISAC and used by default tool to produce 2D class averages in the **[[http:// |
**GPU ISAC** is designed to run ISAC2 on a single workstation by outsourcing its computationally expensive calculations to any available GPUs. | **GPU ISAC** is designed to run ISAC2 on a single workstation by outsourcing its computationally expensive calculations to any available GPUs. | ||
<note important> | <note important> | ||
- | **Beta | + | **Chimera |
</ | </ | ||
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- **Extract the archive** to your chosen GPU ISAC installation folder. | - **Extract the archive** to your chosen GPU ISAC installation folder. | ||
- **Open a terminal** and navigate to your installation folder. | - **Open a terminal** and navigate to your installation folder. | ||
- | - **Untar the archive** | + | - **Untar the archive**: < |
- **Check CUDA path variables** using: | - **Check CUDA path variables** using: | ||
- | - '' | + | - < |
- | - '' | + | - < |
- | - 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: < |
- | * '' | + | export LD_LIBRARY_PATH=/ |
- | * '' | + | |
- | * Here '' | + | |
- **Compile the GPU ISAC C++/CUDA library:** | - **Compile the GPU ISAC C++/CUDA library:** | ||
- | - '' | + | - < |
- | - '' | + | - < |
- **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: | ||
- | - '' | + | - < |
- | - '' | + | - < |
- | - '' | + | - < |
- **Set the correct libraries and environment: | - **Set the correct libraries and environment: | ||
- | - '' | + | - < |
- | - '' | + | - < |
- | - '' | + | - < |
- | - '' | + | - < |
+ | - **Bugfix for the Chimera beta:** | ||
+ | - < | ||