CN103714006B - Performance test method of Gromacs software - Google Patents
Performance test method of Gromacs software Download PDFInfo
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- CN103714006B CN103714006B CN201410006794.2A CN201410006794A CN103714006B CN 103714006 B CN103714006 B CN 103714006B CN 201410006794 A CN201410006794 A CN 201410006794A CN 103714006 B CN103714006 B CN 103714006B
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- 238000000034 method Methods 0.000 title claims abstract description 16
- 238000011056 performance test Methods 0.000 title claims abstract description 8
- 238000004088 simulation Methods 0.000 claims abstract description 4
- 238000002536 laser-induced breakdown spectroscopy Methods 0.000 claims description 4
- 238000005457 optimization Methods 0.000 abstract description 6
- 238000000329 molecular dynamics simulation Methods 0.000 description 4
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Abstract
The invention provides a performance test method of Gromacs software. Different compilers, a math library and compiler parameters are used for compiling the Gromacs software. Simulation test is carried out on the Gromacs software after compiling, compiling performance data are collected, compiling performance comparison is executed, the compiler with the best compiling performance, the math library and compiling parameters are selected, nPME parameters are adjusted again, and subsequent optimization is carried out on the Gromacs software. The performance test method can improve operation efficiency of the Gromacs software.
Description
Technical field
The present invention relates to field of computer technology, and in particular to a kind of performance test methods of Gromacs softwares.
Background technology
GROMACS softwares are a general program bags of increasing income for being mainly used to carry out molecular dynamics simulation, can be simulated
Hundreds of to the millions of Newton's equation groups of scale particIe system motion.It is mainly used to as simulated albumin matter and lipid
Biomolecule, it is also possible to for studying the biomolecule system such as polymer.GROMACS software supports are common at present several
All molecular dynamics algorithms, including various heating baths, pressure bath and electrostatic interaction calculating etc..GROMACS softwares should
With widely, but with the continuous increase of computer size, calculating platform is constantly updated and simulated system constantly increases,
Everybody attention further to computational efficiency, but the optimization there is presently no people to gromacs proposes the comprehensive scheme of system.
The content of the invention
The present invention proposes a kind of performance test methods of Gromacs softwares, to improve software operation efficiency, methods described bag
Include：
Step 1：Configuration hardware platform, compiler, math library and compiling parameter；
Step 2：Gromacs softwares are compiled using the different compilers of configuration, math library and compiling parameter, it is right
Gromacs softwares after compiling perform simulation test and collect compilation performance data；
Step 3：Perform compilation performance contrast, the optimal compiler of selection compilation performance, math library and compiling parameter setting；
Step 4：Adjustment nPME parameters, carry out the follow-up optimization of Gromacs softwares.
The beneficial effects of the invention are as follows raising Gromacs software operation efficiencies.
Brief description of the drawings
Fig. 1 is a kind of flow chart of the performance test methods of Gromacs softwares proposed by the present invention.
Fig. 2 is method proposed by the present invention to nPME parameter optimization schematic diagrams.
Specific embodiment
Reference picture 1, Fig. 1 shows the flow chart of method proposed by the present invention, and methods described comprises the following steps：
Step 1：Configuration hardware platform, compiler, math library and compiling parameter.
Step 2：Gromacs softwares are compiled using different compilers and compiling parameter configuration.Can be with this step
Gromacs softwares are compiled using different compilers and compiling parameter, such as first by GNU compilers, fft math libraries
Gromacs softwares are compiled, compiling parameter uses default value；Compiling is completed, and carries out molecular dynamics simulation；Collect compiling
Performance data；Then INTEL compilers are reused, MKL math libraries carry out the compiling of Gromacs softwares, and compiling parameter is as follows：
-DCMAKE_C_COMPILER=mpiicc
-DCMAKE_CXX_COMPILER=mpiicpc
-DGMX_MPI=ON
-DGMX_GPU=OFF
-DGMX_DOUBLE=ON
-DBUILD_SHARED_LIBS=OFF
-DGMX_PREFER_STATIC_LIBS=ON
-DCMAKE_C_FLAGS="-ip xAVX-funroll-all-loops-static-O3"
-DCMAKE_EXE_LINKER_FLAGS="-L/opt/intel/composer_xe_2013.1.117/mkl/
lib/intel64/-lmkl_intel_lp64-lmkl_intel_thread-lmkl_core；
After the completion of compiling, molecular dynamics simulation is carried out；Collect compilation performance data.
Step 3：Perform compilation performance contrast, the optimal compiler of selection compilation performance, math library and compiling parameter setting.
For example by contrasting the compilation performance difference of GNU/INTEL compilers, the GROMACS performances that GNU is compiled out are compared with intel compilers
It is low by 10% or so, then carry out follow-up operation parameter optimization test using INTEL compilers, MKL math libraries and corresponding compiling parameter.
Step 4：Adjustment nPME parameters, carry out the follow-up optimization of Gromacs softwares.Usually using PME in GROMACS
（Particle-mesh Ewald）, P3M（Particle-Particle-Particle Mesh）, the treatment of the method such as Worf is global
Interact, during the long range interaction processed using Ewald plus with method, gromacs softwares can be by nPME parameters
To specify the number dedicated for carrying out PME calculate nodes, remaining node to carry out PP（particle-particle）Treatment, this
The calculate node for participating in calculating will be divided into two parts by sample, therefore the setting of nPME parameters influences larger to operational efficiency.
Gromacs softwares operationally can default allocation nPME, we test when with reference to default value its left and right float, by a large amount of
The selective rules of nPME are summarized in test, and Fig. 2 shows this process.
Certainly, the present invention can also have other various embodiments, ripe in the case of without departing substantially from spirit of the invention and its essence
Know those skilled in the art and work as and various corresponding changes and deformation, but these corresponding changes and change can be made according to the present invention
Shape should all belong to scope of the claims of the invention.
Claims (1)
1. a kind of performance test methods of Gromacs softwares, it is characterised in that methods described includes：
Step 1：Configuration hardware platform, compiler, math library and compiling parameter；
Step 2：Gromacs softwares are compiled using GUN compilers, FFT math libraries first, compiling parameter uses default value；
After the completion of compiling, simulation test is performed to the Gromacs softwares after compiling and compilation performance data are collected；Then reuse
INTEL compilers, MKL math libraries carry out the compiling of Gromacs softwares, after the completion of compiling, the Gromacs softwares after compiling are held
Row simulation test simultaneously collects compilation performance data；Wherein, Gromacs softwares are carried out using INTEL compilers, MKL math libraries
The compiling parameter of compiling is as follows：
- DCMAKE_C_COMPILER=mpiicc
- DCMAKE_CXX_COMPILER=mpiicpc
- DGMX_MPI=ON
- DGMX_GPU=OFF
- DGMX_DOUBLE=ON
- DBUILD_SHARED_LIBS=OFF
- DGMX_PREFER_STATIC_LIBS=ON
- DCMAKE_C_FLAGS="-ip xAVX-funroll-all-loops-static-O3 "
- DCMAKE_EXE_LINKER_FLAGS="-L/opt/intel/composer_xe_2013.1.117/mkl/lib/
intel64/-lmkl_intel_lp64-lmkl_intel_thread-lmkl_core；
Step 3：Perform compilation performance contrast, the optimal compiler of selection compilation performance, math library and compiling parameter setting；
Step 4：Selection nPME parameters, it is optimal with the operational efficiency for ensureing Gromacs softwares.
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| CN201410006794.2A CN103714006B (en) | 2014-01-07 | 2014-01-07 | Performance test method of Gromacs software |
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| WO2019134322A1 (en) * | 2018-05-10 | 2019-07-11 | 深圳晶泰科技有限公司 | Gromacs cloud computing process control method |
| CN108664729B (en) * | 2018-05-10 | 2021-11-23 | 深圳晶泰科技有限公司 | GROMACS cloud computing flow control method |
Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1983209A (en) * | 2005-12-14 | 2007-06-20 | 中兴通讯股份有限公司 | System and method for automatically testing software unit |
| CN103309715A (en) * | 2013-06-26 | 2013-09-18 | 曙光信息产业(北京)有限公司 | Method for installing molecular dynamics application program in high-performance trunking system |
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| Publication number | Priority date | Publication date | Assignee | Title |
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| US20050273310A1 (en) * | 2004-06-03 | 2005-12-08 | Newburn Chris J | Enhancements to performance monitoring architecture for critical path-based analysis |
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Patent Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1983209A (en) * | 2005-12-14 | 2007-06-20 | 中兴通讯股份有限公司 | System and method for automatically testing software unit |
| CN103309715A (en) * | 2013-06-26 | 2013-09-18 | 曙光信息产业(北京)有限公司 | Method for installing molecular dynamics application program in high-performance trunking system |
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