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--- gpu_isac [2020/05/29 18:50]
fschoenfeld
+++ gpu_isac [2020/06/18 12:35]
fschoenfeld
@@ Line 38: / Line 38: @@
   - **Extract the archive** to your chosen GPU ISAC installation folder.
   - **Open a terminal** and navigate to your installation folder.
-  - **Untar the archive** using ''tar -xf GPU_ISAC_CHIMERA.tar''.
+  - **Untar the archive**: <code>tar -xf GPU_ISAC_CHIMERA.tar</code>
   - **Check CUDA path variables** using:
-    - ''echo $PATH'' Does it contain the path to your **cuda/bin** folder?
+    - <code>echo $PATH</code> Confirm your ''PATH'' variable contains the path to your **cuda/bin** folder.
-    - ''echo $LD_LIBRARY_PATH'' Does it contain the path to your **cuda/lib64** folder?
+    - <code>echo $LD_LIBRARY_PATH</code> Confirm your ''LD_LIBRARY_PATH'' variable contain the path to your **cuda/lib64** folder.
-    - If the path variables do **not** contain these path variables, you can add them like so:
+    - If the path variables do **not** contain these path variables, you can add them like so: <code>export PATH=/path/to/cuda/bin:${PATH}
-      * ''export PATH=/path/to/cuda/bin:${PATH}'' and
+export LD_LIBRARY_PATH=/path/to/cuda/lib64:${LD_LIBRARY_PATH}</code> Where ''path/to/cuda/bin'' and ''path/to/cuda/lib64'' need to be replaced with the real paths to the respective folders. If you do not know where to find them, by default they should be located in ''/usr/local/cuda''.
-      * ''export LD_LIBRARY_PATH=/path/to/cuda/lib64:${LD_LIBRARY_PATH}''
-      * Here ''path/to/cuda/bin'' and ''path/to/cuda/lib64'' need to be replaced with the real paths to the respective folders. If you do not know where to find them, by default they should be located in ''/usr/local/cuda''.
   - **Compile the GPU ISAC C++/CUDA library:**
-    - ''cd cuda'' (note that this assumes you entered your installation folder in your terminal)
+    - <code>cd vChimera/cuda</code>//Note: This assumes you did not change directories after unpacking the .tar archive.//
-    - ''nvcc gpu_aln_common.cu gpu_aln_noref.cu -o gpu_aln_pack.so -shared -Xcompiler -fPIC -lcufft -std=c++11''
+    - <code>nvcc gpu_aln_common.cu gpu_aln_noref.cu -o gpu_aln_pack.so -shared -Xcompiler -fPIC -lcufft -std=c++11</code>
   - **Adjust sparx libraries** to work with the C++/CUDA library we just compiled:
-    - ''cd ../eman2/sparx/libpy''
+    - <code>cd ../eman2/sparx/libpy</code>
-    - ''sed -i.bkp "s|/home/schoenf/work/code/cuISAC/cuda|$(realpath ../../../cuda)|g" applications.py''
+    - <code>sed -i.bkp "s|/home/schoenf/work/code/cuISAC/cuda|$(realpath ../../../cuda)|g" applications.py</code>
-    - ''sed -i.bkp2 's|statistics.sum_oe( data, "a", CTF, EMData(), myid=myid|statistics.sum_oe( data, "a", CTF, EMData()|g' applications.py ''
+    - <code>sed -i.bkp2 's|statistics.sum_oe( data, "a", CTF, EMData(), myid=myid|statistics.sum_oe( data, "a", CTF, EMData()|g' applications.py</code>
   - **Set the correct libraries and environment:**
-    - ''cd ../bin'' (we are now in the **/eman2/sparx/bin** folder of your GPU ISAC installation folder)
+    - <code>cd ../bin</code> //Note: We are now in the **/eman2/sparx/bin** folder of your GPU ISAC installation folder.//
-    - ''ln -rs ../libpy/* .'' (don't forget the dot at the end)
+    - <code>ln -rs ../libpy/* .</code> //Note: Don't forget the dot at the end!//
-    - ''sed -i.bkp "s|/home/schoenf/applications/sphire/v1.1/envs/sphire_1.3/bin|$(dirname $(which sphire))|g" sxisac2_gpu.py''
+    - <code>sed -i.bkp "s|/home/schoenf/applications/sphire/v1.1/envs/sphire_1.3/bin|$(dirname $(which sphire))|g" sxisac2_gpu.py</code>
-    - ''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''
+    - <code>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</code>
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