yade-mpi team mailing list archive

[Bruno Chareyre <bruno.chareyre@xxxxxxxxxxxxxxx>]

Hi there,
I wanted to let you know that yade-mpi is now running on froggy cluster 
(Grenoble) based on the NIX package by William (thanks!).
An alternative method without using NIX has been also found by Deepak. 
It may be more transparent than NIX in terms of compilation, so also 
good to have (Deepak, could you please forward your explanations here?).

Here is a quick walkthrough (one-liner at the end), please try it and 
let us know if you find problems, so we can update it before moving it 
to ciment's wiki.
Cheers
Bruno
___________

// Connect to froggy
/ssh yourlogin@xxxxxxxxxxxxxxxxxxxxxxxx////ssh froggy.ujf-grenoble.fr/

// Activate NIX and create/switch to user profile
/source /applis/site/nix.sh /
/nix-env --switch-profile $NIX_USER_PROFILE_DIR/yade_mpi_profile/

// set python2.7 environment (copy-paste the 3 lines at once), or jump directly to the one-liner at the end of this message
/printf "with import <nixpkgs> {};\npython.buildEnv.override {\n \////extraLibs = with pkgs.python27Packages;[ pip virtualenv ipython numpy \////scipy matplotlib];\n ignoreCollisions = true;\n}\n" > python27-env.nix; 
nix-env -if python27-env.nix /
// checkout yade-nix package and unzip, update sources, compile, install
/wget https://github.com/bchareyre/nix-yade/archive/master.zip; unzip master/
/cd nix-yade-master/mpi/
/python update-daily.py /    <----- to re-compile after changes upstream start here again
/nix-build daily.nix /   <----- will compile (~10min)
/nix-env -if //daily.nix /   <----- load package, yadempi-daily is now available in path
/cd ~/

// go run something in interactive mode
//// 1) download test script from github/yade-mpi (part of the sources we just compiled but they are well hidden)
/wget 
https://github.com/bchareyre/yade-mpi/raw/master/examples/mpi/testMPI_2D.py 
--no-check-certificate/


// 2) start interactive job
/oarsub -I -l /nodes=1/core=10,walltime=00:30:00 -t devel --project 
pr-hackathon2018/

// 3) submit in single thread, then multithread, for 90k spheres (100x100x(10-1))
/time yadempi-daily -n -x ///testMPI_2D/.py 100 100 10////Total force on floor= -12300237.8629 real 2m19.895s user 2m18.320s //time mpiexec -np 10 yadempi-daily -n -x ////testMPI_2D/.py/ 100 100 master:Total force on floor=-12286573.8994 
real 0m59.425s user 9m35.380s /


One-liner for yade install (copy paste as a whole):

/printf "with import <nixpkgs> {};\npython.buildEnv.override {\n \////extraLibs = with pkgs.python27Packages;[ pip virtualenv ipython numpy \////scipy matplotlib];\n ignoreCollisions = true;\n}\n" > python27-env.nix; 
nix-env -if python27-env.nix //wget https://github.com/bchareyre/nix-yade/archive/master.zip; unzip master/
/cd nix-yade-master/mpi; //python update-daily.py; //nix-build daily.nix; //nix-env -if //daily.nix; //cd ~/
/wget 
https://github.com/bchareyre/yade-mpi/raw/master/examples/mpi/testMPI_2D.py 
--no-check-certificate/






--
_______________
Bruno Chareyre
Associate Professor
ENSE³ - Grenoble INP
Lab. 3SR
BP 53
38041 Grenoble cedex 9
Tél : +33 4 56 52 86 21
Fax : +33 4 76 82 70 43
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