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namd [2017/09/18 11:38]
meesters
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-===== High-performance simulation of large bimolecular systems - NAMD ===== 
  
-<WRAP center round todo 90%> 
-''This page is outdated. We hope to provide more information, soon.'' 
-</WRAP> 
- 
-NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. 
-Documentation and source code on the web page of "[[http://www.ks.uiuc.edu/Research/namd/|Theoretical and computational biophysics group]]" 
- 
-There are few possibilities to start NAMD simulation on the MOGON cluster. 
- 
-//<PATH TO NAMD INSTALLATION>/namd2 <input configuration file>// 
- 
-This starts one threaded simulation direkt on the login host. Input configuration file describes simulation. Complete description of the input file format is available in the [[http://www.ks.uiuc.edu/Research/namd/2.9/ug/node9.html|NAMD Documentation]]. 
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-=== Threaded jobs === 
- 
-Using threaded start allows to achieve performance increasing: 
- 
-//bsub -R "affinity[core(<number of cores>)]" <PATH TO NAMD INSTALLATION>/namd2 +p<number of threads> <input configuration file>// 
- 
-where <number of threads> is normally equal to <number of cores>. 
-For example 
- 
-//bsub -R "affinity[core(16)]" <PATH TO NAMD INSTALLATION>/namd2 +p 16 <input configuration file>// 
- 
-starts NAMD simulation with 16 threads using 16 cores of a node. 
- 
-Mogon cluster contains different nodes with up to 64 cores. 
- 
-On machines with more than 32 cores it may be necessary to add a communication thread and run on one fewer core than the machine has.  For example on a 64-core machine this would be run as 
- 
-//bsub -R "affinity[core(64)]" <PATH TO NAMD INSTALLATION>/namd2 +p 63 +commthread <input configuration file>// 
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-=== Memory Usage === 
- 
-NAMD has traditionally used less than 100MB of memory even for systems 
-of 100,000 atoms.  With the reintroduction of pairlists in NAMD 2.5, however, memory usage for a 100,000 atom system with a 12A cutoff can approach 300MB, and will grow with the cube of the cutoff.  This extra memory is distributed across processors during a parallel run, but a single workstation may run out of physical memory with a large system. 
-Appropriate method for memory reservation is using of application profile, for example: 
-start 1 NAMD process with 64 calculation threads in 15G memory pool 
- 
-//bsub -app Reserve15G -R "affinity[core(64)]" <PATH TO NAMD INSTALLATION>/namd2 +p 64 <input configuration file>// 
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-or with reservation 5000000 Kb of memory for this 1 process 
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-//bsub -M 5000000 -R "affinity[core(64)]" <PATH TO NAMD INSTALLATION>/namd2 +p 64 <input configuration file>// 
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-=== non threaded MPI jobs === 
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-//bsub -n <number of processes> -M 1000000 mpirun <PATH TO NAMD INSTALLATION>/namd2 <input configuration file>// 
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-=== Using of affinity and core mapping === 
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-There are two possibility to set process to core mapping. 
- 
-//bsub -n <number of processes> -M 1000000 -R "affinity[core(1)*2]" mpirun <PATH TO NAMD INSTALLATION>/namd2 <input configuration file>// 
- 
-...under construction ... 
  • namd.1505727492.txt.gz
  • Last modified: 2017/09/18 11:38
  • by meesters