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标题: 运行gmx时如何指定GPU [打印本页]

作者
Author: xpyp 时间: 2018-4-4 15:04
标题: 运行gmx时如何指定GPU
一台服务器里装了两块GPU,　跑gmx时能否指定用其中的一块GPU ?

作者
Author: laoman 时间: 2018-4-4 19:01
以下是gmx_mpi mdrun -h的部分输出：
OPTIONS

Options to specify input and output files:

-s    [<.tpr/.tpb/...>] (topol.tpr) (Input) Run input file: tpr tpb tpa
-o    [<.trr/.cpt/...>] (traj.trr) (Output)
   Full precision trajectory: trr cpt trj tng
-x    [<.xtc/.tng>] (traj_comp.xtc) (Output, Opt.)
   Compressed trajectory (tng format or portable xdr format)
-cpi [<.cpt>] (state.cpt) (Input, Opt.) Checkpoint file
-cpo [<.cpt>] (state.cpt) (Output, Opt.) Checkpoint file
-c    [<.gro/.g96/...>] (confout.gro) (Output)
   Structure file: gro g96 pdb brk ent esp
-e    [<.edr>] (ener.edr) (Output) Energy file
-g    [<.log>] (md.log) (Output) Log file
-dhdl  [<.xvg>] (dhdl.xvg) (Output, Opt.) xvgr/xmgr file
-field [<.xvg>] (field.xvg) (Output, Opt.) xvgr/xmgr file
-table [<.xvg>] (table.xvg) (Input, Opt.) xvgr/xmgr file
-tabletf [<.xvg>] (tabletf.xvg) (Input, Opt.) xvgr/xmgr file
-tablep [<.xvg>] (tablep.xvg) (Input, Opt.) xvgr/xmgr file
-tableb [<.xvg>] (table.xvg) (Input, Opt.) xvgr/xmgr file
-rerun [<.xtc/.trr/...>] (rerun.xtc) (Input, Opt.)
   Trajectory: xtc trr cpt trj gro g96 pdb tng
-tpi [<.xvg>] (tpi.xvg) (Output, Opt.) xvgr/xmgr file
-tpid  [<.xvg>] (tpidist.xvg) (Output, Opt.) xvgr/xmgr file
-ei [<.edi>] (sam.edi) (Input, Opt.) ED sampling input
-eo [<.xvg>] (edsam.xvg) (Output, Opt.) xvgr/xmgr file
-devout [<.xvg>] (deviatie.xvg) (Output, Opt.) xvgr/xmgr file
-runav [<.xvg>] (runaver.xvg) (Output, Opt.) xvgr/xmgr file
-px [<.xvg>] (pullx.xvg) (Output, Opt.) xvgr/xmgr file
-pf [<.xvg>] (pullf.xvg) (Output, Opt.) xvgr/xmgr file
-ro [<.xvg>] (rotation.xvg) (Output, Opt.) xvgr/xmgr file
-ra [<.log>] (rotangles.log) (Output, Opt.) Log file
-rs [<.log>] (rotslabs.log) (Output, Opt.) Log file
-rt [<.log>] (rottorque.log) (Output, Opt.) Log file
-mtx [<.mtx>] (nm.mtx) (Output, Opt.) Hessian matrix
-dn [<.ndx>] (dipole.ndx) (Output, Opt.) Index file
-multidir [<dir> [...]] (rundir) (Input, Opt.) Run directory
-membed [<.dat>] (membed.dat) (Input, Opt.) Generic data file
-mp [<.top>] (membed.top) (Input, Opt.) Topology file
-mn [<.ndx>] (membed.ndx) (Input, Opt.) Index file
-if [<.xvg>] (imdforces.xvg) (Output, Opt.) xvgr/xmgr file
-swap  [<.xvg>] (swapions.xvg) (Output, Opt.) xvgr/xmgr file

Other options:

-nice  <int> (0)       Set the nicelevel
-deffnm <string>          Set the default filename for all file options
-xvg <enum> (xmgrace)  xvg plot formatting: xmgrace, xmgr, none
-dd <vector> (0 0 0) Domain decomposition grid, 0 is optimize
-ddorder <enum> (interleave) DD rank order: interleave, pp_pme, cartesian
-npme  <int> (-1)
   Number of separate ranks to be used for PME, -1 is guess
-nt <int> (0)       Total number of threads to start (0 is guess)
-ntmpi <int> (0)       Number of thread-MPI threads to start (0 is guess)
-ntomp <int> (0)
   Number of OpenMP threads per MPI rank to start (0 is guess)
-ntomp_pme <int> (0)
   Number of OpenMP threads per MPI rank to start (0 is -ntomp)
-pin <enum> (auto)    Set thread affinities: auto, on, off
-pinoffset <int> (0)
   The starting logical core number for pinning to cores; used to avoid
   pinning threads from different mdrun instances to the same core
-pinstride <int> (0)
   Pinning distance in logical cores for threads, use 0 to minimize the
   number of threads per physical core
-gpu_id <string>
   List of GPU device id-s to use, specifies the per-node PP rank to GPU
   mapping
-[no]ddcheck (yes)    Check for all bonded interactions with DD
-rdd <real> (0)
   The maximum distance for bonded interactions with DD (nm), 0 is determine
   from initial coordinates
-rcon  <real> (0)       Maximum distance for P-LINCS (nm), 0 is estimate
-dlb <enum> (auto)    Dynamic load balancing (with DD): auto, no, yes
-dds <real> (0.8)
   Fraction in (0,1) by whose reciprocal the initial DD cell size will be
   increased in order to provide a margin in which dynamic load balancing
   can act while preserving the minimum cell size.
-gcom  <int> (-1)    Global communication frequency
-nb <enum> (auto)
   Calculate non-bonded interactions on: auto, cpu, gpu, gpu_cpu
-nstlist <int>  (0)
   Set nstlist when using a Verlet buffer tolerance (0 is guess)
-[no]tunepme (yes)    Optimize PME load between PP/PME ranks or GPU/CPU
-[no]testverlet (no)    Test the Verlet non-bonded scheme
-[no]v       (no)    Be loud and noisy
-[no]compact (yes)    Write a compact log file
-[no]seppot    (no)
   Write separate V and dVdl terms for each interaction type and rank to the
   log file(s)
-pforce <real>  (-1)    Print all forces larger than this (kJ/mol nm)
-[no]reprod    (no)
   Try to avoid optimizations that affect binary reproducibility
-cpt <real> (15)    Checkpoint interval (minutes)
-[no]cpnum    (no)    Keep and number checkpoint files
-[no]append    (yes)
   Append to previous output files when continuing from checkpoint instead
   of adding the simulation part number to all file names
-nsteps <int> (-2)
   Run this number of steps, overrides .mdp file option
-maxh  <real> (-1)    Terminate after 0.99 times this time (hours)
-multi <int> (0)       Do multiple simulations in parallel
-replex <int> (0)
   Attempt replica exchange periodically with this period (steps)
-nex <int> (0)
   Number of random exchanges to carry out each exchange interval (N^3 is
   one suggestion).  -nex zero or not specified gives neighbor replica
   exchange.
-reseed <int> (-1)    Seed for replica exchange, -1 is generate a seed

加 -gpu_id参数，显卡的编号从0开始

作者
Author: tomwong4253 时间: 2018-4-10 21:26
-gpu_id <string>
List of GPU device id-s to use, specifies the per-node PP rank to GPU

这么明显的提示都没看到啊

作者
Author: lonemen 时间: 2018-5-31 09:33
那请问能够不是用gpu吗？应该如何使用命令控制？谢谢！

作者
Author: syjohn 时间: 2018-5-31 17:41

lonemen 发表于 2018-5-31 09:33
那请问能够不是用gpu吗？应该如何使用命令控制？谢谢！

你的意思是不使用GPU？
如果是这样的话命令后面加 -nb cpu

作者
Author: sobereva 时间: 2018-5-31 17:43

lonemen 发表于 2018-5-31 09:33
那请问能够不是用gpu吗？应该如何使用命令控制？谢谢！

编译一个非GPU版，不用GPU就调用那个就完了

作者
Author: lonemen 时间: 2018-6-5 08:43

sobereva 发表于 2018-5-31 17:43
编译一个非GPU版，不用GPU就调用那个就完了

谢谢sob！本来想偷懒来着，看来还是再编译一个才妥当。

作者
Author: lonemen 时间: 2018-6-5 08:55

syjohn 发表于 2018-5-31 17:41
你的意思是不使用GPU？
如果是这样的话命令后面加 -nb cpu

好的，谢谢指点!我去试试看。

作者
Author: user0203 时间: 2024-7-30 09:40

tomwong4253 发表于 2018-4-10 21:26
-gpu_id
List of GPU device id-s to use, specifies the per-node PP rank to GPU

你好，请问你用这个指令能成功指定节点吗？我按照该指令提交会报以下错误C:\Users\10343\Desktop\方向调研\报错记录.png

作者
Author: Santz 时间: 2024-7-30 10:53

user0203 发表于 2024-7-30 09:40
你好，请问你用这个指令能成功指定节点吗？我按照该指令提交会报以下错误

你这个命令简直写得一塌糊涂。看命令的用法啊，-nb 后接个参数，还有-gpu_5 这是什么写法？

gmx mdrun -deffnm md_0_1 -nb gpu -gpu_id 0

复制代码

作者
Author: user0203 时间: 2024-7-30 14:33

Santz 发表于 2024-7-30 10:53
你这个命令简直写得一塌糊涂。看命令的用法啊，-nb 后接个参数，还有-gpu_5 这是什么写法？

是，开始上手还有很多不会，刚用你的指令已经成功交上去啦。谢谢！

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