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acelab:namd [2015/09/01 15:38]
mcawood created
acelab:namd [2015/09/02 12:05] (current)
mcawood
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-==General Info==+===General Info===
  
-NAMD is a parallel, object-oriented ​molecular dynamics code designed for high-performance simulation of large biomolecular systems.+NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. ​Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling. [[http://​www.ks.uiuc.edu/​Research/​namd/​|source]]
  
-==Useful Links==+===Useful Links===
  
-Developers Site [http://​www.ks.uiuc.edu/​Research/​namd/​]+Developers Site [[http://​www.ks.uiuc.edu/​Research/​namd/​]]
  
-==Installation Guide==+===Installation Guide===
  
   cd ~   cd ~
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 The code is shipped as a compiled binary, which has proven sufficient for testing. ​ There are two versions available below; for x86 processors, as well as for CUDA enabled GPUs. The code is shipped as a compiled binary, which has proven sufficient for testing. ​ There are two versions available below; for x86 processors, as well as for CUDA enabled GPUs.
-x86 version: ​[[FileNAMD_2.10_Linux-x86_64-ibverbs-smp.tar.gz]] <br> + 
-CUDA version: ​[[FileNAMD_2.10_Linux-x86_64-ibverbs-smp-CUDA.tar.gz]]+x86 version: ​{{http://wiki.chpc.ac.za/​_media/​acelab:​namd_2.10_linux-x86_64-ibverbs-smp.tar.gz|namd_2.10_linux-x86_64-ibverbs-smp.tar.gz}} \\ 
 +CUDA version: ​{{http://wiki.chpc.ac.za/​_media/​acelab:​namd_2.10_linux-x86_64-ibverbs-smp-cuda.tar.gz|namd_2.10_linux-x86_64-ibverbs-smp-cuda.tar.gz}}
  
 Download the two tars into the current directory. Download the two tars into the current directory.
  
-  tar -xf NAMD_2.10_Linux-x86_64-ibverbs-smp.tar.gz ​<br>+  tar -xf NAMD_2.10_Linux-x86_64-ibverbs-smp.tar.gz ​
   tar -xf NAMD_2.10_Linux-x86_64-ibverbs-smp-CUDA.tar.gz   tar -xf NAMD_2.10_Linux-x86_64-ibverbs-smp-CUDA.tar.gz
  
   cd ../bench   cd ../bench
  
-==Benchmark==+===Benchmark===
  
 Before beginning the benchmark, ensure that the correct version of the code is sourced, Before beginning the benchmark, ensure that the correct version of the code is sourced,
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 There are two benchmarks setup for NAMD, which will work with both the CUDA and x86 versions. There are two benchmarks setup for NAMD, which will work with both the CUDA and x86 versions.
-The smaller test case is the apoa1 benchmark, with 2500 timesteps and 250 step output frequency: ​[[FileApoa1.tar.gz]] <br> +The smaller test case is the apoa1 benchmark, with 2500 timesteps and 250 step output frequency: ​{{http://​wiki.chpc.ac.za/​_media/​acelab:​apoa1.tar.gz|apoa1.tar.gz}} \\ 
-The larger test case is the STMV benchmark, with 1500 timesteps and 500 step output frequency: ​[[FileStmv.tar.gz]]+The larger test case is the STMV benchmark, with 1500 timesteps and 500 step output frequency: ​{{http://​wiki.chpc.ac.za/​_media/​acelab:​stmv.tar.gz|stmv.tar.gz}}
  
 NOTE: the benchmark calculates a once off FFT based on the number of cores used, so each test should be run twice to avoid this overhead. NOTE: the benchmark calculates a once off FFT based on the number of cores used, so each test should be run twice to avoid this overhead.
  
-===CPU Benchmark===+==CPU Benchmark==
  
 To run the benchmark for x86 CPUs, use the following command: To run the benchmark for x86 CPUs, use the following command:
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 A Dell C4130 with 24 Haswell cores completed the apoa1 test in 124 seconds, and the STMV test in 794 seconds. A Dell C4130 with 24 Haswell cores completed the apoa1 test in 124 seconds, and the STMV test in 794 seconds.
  
-===GPU Benchmark===+==GPU Benchmark==
  
 To run the benchmark for CUDA GPUs, use the following command: To run the benchmark for CUDA GPUs, use the following command:
/var/www/wiki/data/attic/acelab/namd.1441114692.txt.gz · Last modified: 2015/09/01 15:38 by mcawood