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gpu_isac [2020/06/18 12:35]
fschoenfeld 		gpu_isac [2020/07/27 12:39]
fschoenfeld
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 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}</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''.
   - **Compile the GPU ISAC C++/CUDA library:**   - **Compile the GPU ISAC C++/CUDA library:**
-    - <code>cd vChimera/cuda</code>//Note: This assumes you did not change directories after unpacking the .tar archive.//+    - <code>cd vChimera/cuda</code>//**Note:** This assumes you did not change directories after unpacking the .tar archive.//
     - <code>nvcc gpu_aln_common.cu gpu_aln_noref.cu -o gpu_aln_pack.so -shared -Xcompiler -fPIC -lcufft -std=c++11</code>     - <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:   - **Adjust sparx libraries** to work with the C++/CUDA library we just compiled:
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     - <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>     - <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:**   - **Set the correct libraries and environment:**
-    - <code>cd ../bin</code> //Note: 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.// 
-    - <code>ln -rs ../libpy/* .</code> //Note: Don't forget the dot at the end!//+    - <code>ln -rs ../libpy/* .</code> //**Note:** Don't forget the dot at the end!//
     - <code>sed -i.bkp "s|/home/schoenf/applications/sphire/v1.1/envs/sphire_1.3/bin|$(dirname $(which sphire))|g" sxisac2_gpu.py</code>     - <code>sed -i.bkp "s|/home/schoenf/applications/sphire/v1.1/envs/sphire_1.3/bin|$(dirname $(which sphire))|g" sxisac2_gpu.py</code>
-    - <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>+    - <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> 
 +  - **Bugfix for the Chimera beta:** 
 +    - <code>sed -i.bkp3 "s/output_text = \"\n/output_text = \"/g" sxisac2_gpu.py</code>
  
  
gpu_isac.txt · Last modified: 2021/05/08 00:41 by shaikh

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