acelab:namd
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acelab:namd [2015/09/01 15:38] mcawood created |
acelab:namd [2021/12/09 16:42] (current) |
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| - | ==General Info== | + | ===General Info=== |
| - | NAMD is a parallel, object-oriented | + | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
| - | ==Useful Links== | + | ===Useful Links=== |
| - | Developers Site [http:// | + | Developers Site [[http:// |
| - | ==Installation Guide== | + | ===Installation Guide=== |
| cd ~ | cd ~ | ||
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| The code is shipped as a compiled binary, which has proven sufficient for testing. | The code is shipped as a compiled binary, which has proven sufficient for testing. | ||
| - | x86 version: | + | |
| - | CUDA version: | + | x86 version: |
| + | CUDA version: | ||
| 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 | + | 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: | + | The smaller test case is the apoa1 benchmark, with 2500 timesteps and 250 step output frequency: |
| - | The larger test case is the STMV benchmark, with 1500 timesteps and 500 step output frequency: | + | The larger test case is the STMV benchmark, with 1500 timesteps and 500 step output frequency: |
| 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: | ||
/app/dokuwiki/data/attic/acelab/namd.1441114692.txt.gz · Last modified: 2021/12/09 16:42 (external edit)
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