本家様 https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Main_Page

MATLABが必要です.
ですが、ダウンロードしたファイルに MATLAB のRuntime版(コンパイル済みのMATLABファイルを実行できる)が入ってますので
それを使えばMATLAB(フル機能版)は不要です.

ここではダウンロードしたファイルに付属の MATLAB Runtime版でDynamoを動かす.

アプリ取得†

https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/DownloadsからLinux向けのtarファイルを取得します。

ファイル名： dynamo-v-1.1.532_MCR-9.9.0_GLNXA64_withMCR.tar (6.9GB)

↑

下拵え†

開発環境と openmpi-devel を組み込んでおきます

[root@rockylinux ~]# dnf groupinstall "Development Tools"
[root@rockylinux ~]# dnf install openmpi-devel environment-modules

「environment-modules」を有効にさせるために、一度再ログインします

↑

インストール†

まずは展開します. 展開したら 7.3 GB 消費してました

[root@rockylinux ~]# mkdir -p /apps/dynamo/
[root@rockylinux ~]# cd /apps/dynamo/
[root@rockylinux dynamo]# 
 
[root@rockylinux dynamo]# tar xf ~/dynamo-v-1.1.532_MCR-9.9.0_GLNXA64_withMCR.tar
[root@rockylinux dynamo]# du -hs .
7.3G    .
 
[root@rockylinux dynamo]# ls -CF
C/       dynamo_activate_linux.sh*              dynamo_setup_cluster.sh*  matlab/    README_dynamo_installation.txt*
cuda/    dynamo_activate_linux_shipped_MCR.sh*  dynamo_setup_linux.sh*    MCRLinux/
ddemos/  dynamo_activate.m*                     examples/                 mex/
doc/     dynamo_compile_mpi.sh*                 licenses/                 mpi/
 
[root@rockylinux dynamo]#

次に OpenMP(OMP)プログラムをコンパイルします. いわゆる threads アプリです.

[root@rockylinux dynamo]# source dynamo_activate_linux_shipped_MCR.sh
MCR for linux has been  found in location: /apps/dynamo/MCRLinux
Activating Dynamo as standalone
-------------------------------------------------------------
 
              Dynamo Setup for standalone Linux
 
-------------------------------------------------------------
 
 
1- Adding execution paths
   ----------------------
 
    Identifying directories of Dynamo distribution hanging from the specified Dynamo root directory:
     /apps/dynamo
 
    [OK] Done updating Linux paths.
 
2- Testing OpenMP
   --------------
 
ls: cannot access '/apps/dynamo/mpi/dynamo_iteration_assemble_omp': No such file or directory     <-- 無視して構わない
 
  Binaries for OpenMP not ready: executables not found
 
  ------------------------------------
  compiling  OpenMP Wrappers
  ------------------------------------
 
  Setting up executables of Dynamo installation on root location:  /apps/dynamo
  Trying to recompile the OpenMP wrappers on your system
    iteration_setup  compiled under OpenMP
    iteration_compute  compiled under OpenMP
    iteration_assemble  compiled under OpenMP
    iteration_check  compiled under OpenMP
    ccmatrix_compute  compiled under OpenMP
    ccmatrix_assemble  compiled under OpenMP
  All OpenMP wrappers compiled successfully
    checking functionality of OpenMP wrappers....
 
    [OK] OpenMP tools seem functional
 
3- Testing MCR libraries
   ---------------------
 
    [OK] MCR library seems active
 
 
------------------------------------
Dynamo is ready for standalone use in your Linux system
 
 
[root@rockylinux dynamo]# 
 
(確認)
 
[root@rockylinux dynamo]# ls -l mpi/*omp
-rwxr-xr-x. 1 root 13449 18480 Oct 30 18:16 mpi/dynamo_ccmatrix_assemble_omp
-rwxr-xr-x. 1 root 13449 23040 Oct 30 18:16 mpi/dynamo_ccmatrix_compute_omp
-rwxr-xr-x. 1 root 13449 18480 Oct 30 18:16 mpi/dynamo_iteration_assemble_omp
-rwxr-xr-x. 1 root 13449 18480 Oct 30 18:16 mpi/dynamo_iteration_check_omp
-rwxr-xr-x. 1 root 13449 24968 Oct 30 18:16 mpi/dynamo_iteration_compute_omp
-rwxr-xr-x. 1 root 13449 18480 Oct 30 18:16 mpi/dynamo_iteration_setup_omp
[root@rockylinux dynamo]#

次に mpi プログラムをコンパイルします. 事前に mpi 実行/コンパイル環境をロードします
ドキュメントには「mpicc」が指定されているが「mpic++」でコンパイルされる.

[root@rockylinux dynamo]# module load mpi
[root@rockylinux dynamo]# which mpirun
/usr/lib64/openmpi/bin/mpirun
[root@rockylinux dynamo]#
 
[root@rockylinux dynamo]# source mpi/dynamo_compile_mpi.sh mpic++
 
Using selected compiler mpic++
trying to compile MPI wrappers for Dynamo standalone executables
/usr/lib64/openmpi/bin/mpic++
ok, mpic++ found, proceeding to compile MPI-wrappers....
 
     ./mpi/dynamo_iteration_setup_mpi.cc compiled
     ./mpi/dynamo_iteration_compute_mpi.cc compiled
     ./mpi/dynamo_iteration_assemble_mpi.cc compiled
     ./mpi/dynamo_iteration_check_mpi.cc compiled
     ./mpi/dynamo_ccmatrix_compute_mpi.cc compiled
     ./mpi/dynamo_ccmatrix_assemble_mpi.cc compiled
     ./mpi/dynamo_iteration_compute_mpi_gpu.cc compiled
Warnings are in principle ok
------------------------------------------------
MPI compilation SUCCESSFUL
------------------------------------------------
 
[root@rockylinux dynamo]#
[root@rockylinux dynamo]# ls -l mpi/*_mpi
-rwxr-xr-x. 1 root 13449 116424 Oct 30 18:25 mpi/dynamo_ccmatrix_assemble_mpi
-rwxr-xr-x. 1 root 13449 116696 Oct 30 18:25 mpi/dynamo_ccmatrix_compute_mpi
-rwxr-xr-x. 1 root 13449 116424 Oct 30 18:25 mpi/dynamo_iteration_assemble_mpi
-rwxr-xr-x. 1 root 13449 116424 Oct 30 18:25 mpi/dynamo_iteration_check_mpi
-rwxr-xr-x. 1 root 13449 121960 Oct 30 18:25 mpi/dynamo_iteration_compute_mpi
-rwxr-xr-x. 1 root 13449 116424 Oct 30 18:25 mpi/dynamo_iteration_setup_mpi
 
[root@rockylinux dynamo]#

最後に cuda アプリケーションをコンパイル
既にcuda-8.0で作られたバイナリーが提供されているが、ここでは cuda-11.8 でコンパイルし直します.

[root@rockylinux dynamo]# ls -l cuda/bin
total 284
-rwxrwxrwx. 1 4121 13449 290304 Aug 27  2021 dynamo_compute_iteration_spp
 
[root@rockylinux dynamo]# ldd cuda/bin/dynamo_compute_iteration_spp
        linux-vdso.so.1 (0x00007ffd42be1000)
        libcudart.so.8.0 => not found
        libcufft.so.8.0 => not found
        libcublas.so.8.0 => not found
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f3d8dbf4000)
        libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f3d8d85f000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f3d8d4dd000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f3d8d2c5000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f3d8cf00000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f3d8de14000)
 
[root@rockylinux dynamo]#
(退避)
 
[root@rockylinux dynamo]# mv cuda/bin/dynamo_compute_iteration_spp cuda/bin/dynamo_compute_iteration_spp.old
 
(re-compile)
 
[root@rockylinux dynamo]# cd cuda/
[root@rockylinux cuda]# export PATH=/usr/local/cuda/bin:$PATH
 
[root@rockylinux cuda]# nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2022 NVIDIA Corporation
Built on Wed_Sep_21_10:33:58_PDT_2022
Cuda compilation tools, release 11.8, V11.8.89
Build cuda_11.8.r11.8/compiler.31833905_0
 
[root@rockylinux cuda]# source config.sh
----------------------------------------------------------------
 
 Configuring makefile for the CUDA installation in your system
 
Looking for a CUDA installation in this environment:
  Found CUDA nvcc compiler at /usr/local/cuda/bin/nvcc
  CUDA installation assumed to be in  /usr/local/cuda
we will use /lib64 (standard procedure)
 
Substituting the CUDA location assignment:
  CUDA_ROOT=/usr/local/cuda-8.0
with the actual value:
  CUDA_ROOT=/usr/local/cuda
 
 [ok]
 
 you can now compile the CUDA utilities by :
 make all
 or :
 make motors
 if "make all" produces an error when trying to compile the Nvidia utility infoGPU
 
------------------------------------------------------------------
 
[root@rockylinux cuda]# make all
/usr/local/cuda/bin/nvcc   -o  bin/dynamo_compute_iteration_spp  src/dynamo_compute_iteration_spp.cu -lcudart -lcufft -lcublas -L/usr/local/cuda/lib64 -I/usr/local/cuda/include -Isrc -Isrc/classes  src/classes/gpuAngles.cpp -w
echo 'Compilation of Dynamo completed. Use make extended to include Nvidia GPU'
Compilation of Dynamo completed. Use make extended to include Nvidia GPU
 
[root@rockylinux cuda]# 
 
(確認)
 
[root@rockylinux cuda]# ldd bin/dynamo_compute_iteration_spp
        linux-vdso.so.1 (0x00007ffd273f9000)
        libcudart.so.11.0 => /usr/local/cuda/targets/x86_64-linux/lib/libcudart.so.11.0 (0x00007fe22e7a0000)
        libcufft.so.10 => /usr/local/cuda/targets/x86_64-linux/lib/libcufft.so.10 (0x00007fe21d8c5000)
        libcublas.so.11 => /usr/local/cuda/targets/x86_64-linux/lib/libcublas.so.11 (0x00007fe217c67000)
        librt.so.1 => /lib64/librt.so.1 (0x00007fe217a5f000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe21783f000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007fe21763b000)
        libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fe2172a6000)
        libm.so.6 => /lib64/libm.so.6 (0x00007fe216f24000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fe216d0c000)
        libc.so.6 => /lib64/libc.so.6 (0x00007fe216947000)
        /lib64/ld-linux-x86-64.so.2 (0x00007fe22ea47000)
        libcublasLt.so.11 => /usr/local/cuda/targets/x86_64-linux/lib/libcublasLt.so.11 (0x00007fe1f23c1000)
 
[root@rockylinux cuda]#

以上でインストールは完了となる

↑

起動†

環境設定を行います
「source /apps/Dynamo/dynamo_activate_linux_shipped_MCR.sh silent」と末尾に「silent」を入れると
メッセージの表示が抑えられる.

[illya@rockylinux ~]$ source /apps/dynamo/dynamo_activate_linux_shipped_MCR.sh silent
MCR for linux has been  found in location: /apps/dynamo/MCRLinux
Activating Dynamo as standalone
 
[illya@rockylinux ~]$ dynamo
Initializing MATLAB Runtime version 9.9
"MCR libraries starting dynamo. Starting the Dynamo console can take some time. A good choice of MCR_CACHE_ROOT might speed this up."
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Warning: MCR_CACHE_ROOT is empty.
  Initialize this variable in your shell for a quicker startup.
  To know more, type:
  dwiki MCR_CACHE_ROOT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Warning: MCR_CACHE_ROOT points to non-existing location:
  Correct this variable in your shell for a quicker startup.
  To know more, type:
  dwiki MCR_CACHE_ROOT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Launching the console....
 (use "dynamo x" for a Dynamo graphics terminal  on a independent window)
 
     Dynamo console for standalone modus
     -----------------------------------
 
 
     * Commands starting with the symbol "!" will be passed to the system
     * Commands starting with the symbol "\" will be executed as Matlab expressions
     * Strings including the symbol ":" are treated as database queries
     * Graphic output: enabled
     * Type "help" for a list of console control commands
 
 
Dynamo >

GUI画面を出してみる

Dynamo >  dcm
Passing to MATLAB...
Resize selection
Resize selection
Dynamo >

これで下記画面が表示される
2022y10m30d_183735079.png

あるいは

[illya@rockylinux ~]$ source /apps/dynamo/dynamo_activate_linux_shipped_MCR.sh silent
MCR for linux has been  found in location: /apps/dynamo/MCRLinux
Activating Dynamo as standalone
 
[illya@rockylinux ~]$ dynamo x

これで下記画面が表示されます.

2022y10m30d_184016118.png

https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Standalone

MATLABで動かすには Dynamo/MATLAB

↑

modulefiles†

「source /apps/dynamo/dynamo_activate_linux_shipped_MCR.sh」が面倒なのでmodulefilesを作ってみた

[root@rockylinux ~]# vi /apps/modulefiles/dynamo
#%Module1.0
puts         stdout               "source /apps/local/bin/dynamo-mkdir;"
set          dynamo               /apps/dynamo
setenv       DYNAMO_FOLDER        $dynamo
setenv       MCR_CACHE_ROOT       /tmp/mcr_cache_root_$env(USER)
prepend-path LD_LIBRARY_PATH      $dynamo/MCRLinux/runtime/glnxa64:$dynamo/MCRLinux/bin/glnxa64:$dynamo/MCRLinux/sys/os/glnxa64
prepend-path PATH                 $dynamo/matlab/bin:$dynamo/matlab/src:$dynamo/cuda/bin:$dynamo/mpi:$dynamo/examples:$dynamo/doc
#prepend-path LD_PRELOAD           $dynamo/MCRLinux/bin/glnxa64/glibc-2.17_shim.so
 
[root@rockylinux ~]#

あと「/apps/local/bin/dynamo-mkdir」を用意します

#!/bin/bash
if [ ! -d /tmp/mcr_cache_root_$USER ]; then
   /bin/mkdir /tmp/mcr_cache_root_$USER
fi

この「/apps/local/bin/dynamo-mkdir」には実行権(+x)を設けます[chmod +x /apps/local/bin/dynamo-mkdir]

上記をロードすれば(module load dynamo)、「source /apps/dynamo/dynamo_activate_linux_shipped_MCR.sh」の代わりになります.
事前に「module use --append /apps/modulefiles」が必要です

↑

メモ†

「/apps/dynamo/dynamo_compile_mpi.sh」と「/apps/dynamo/mpi/dynamo_compile_mpi.sh」は同じファイル

環境変数MCR_CACHE_ROOTを ssd/nvme なデバイスに指定すると早くなるそうな. ccp4のcacheと同じ思想かな

[illya@rockylinux ~]$ mkdir /scratch/dynamo
[illya@rockylinux ~]$ export MCR_CACHE_ROOT=/scratch/dynamo

version確認は、「dynamo_version」で得られる

[illya@rockylinux ~]$ module use --append /apps/modulefiles
[illya@rockylinux ~]$ module load dynamo
 
[illya@rockylinux ~]$ dynamo
Initializing MATLAB Runtime version 9.9
"MCR libraries starting dynamo. Starting the Dynamo console can take some time. A good choice of MCR_CACHE_ROOT might speed this up."
Launching the console....
 (use "dynamo x" for a Dynamo graphics terminal  on a independent window)
 
     Dynamo console for standalone modus
     -----------------------------------
 
 
     * Commands starting with the symbol "!" will be passed to the system
     * Commands starting with the symbol "\" will be executed as Matlab expressions
     * Strings including the symbol ":" are treated as database queries
     * Graphic output: enabled
     * Type "help" for a list of console control commands
 
 
Dynamo >  dynamo_version
Passing order to Matlab engine:
dynamo_version
 Dynamo version: v-1.1.532
 
ans =
 
    'v-1.1.532'
 
Dynamo >  quit
ok, bye!
 
 
Exiting Dynamo console.
Returning control to system.
 
 
 
 Note after exiting the Dynamo console:
 
       if you experience difficulties with the text display you might need to type:
       stty echo
       in your system shell to fix them.
 
[delete:pmodelpool.Manager] Deletion of model pool manager from memory.
[illya@rockylinux ~]$
↑

memo†

AMD Ryzen CPUだとmodulefilesの末尾「prepend-path LD_PRELOAD $dynamo/MCRLinux/bin/glnxa64/glibc-2.17_shim.so」は無効にする事

#prepend-path LD_PRELOAD           $dynamo/MCRLinux/bin/glnxa64/glibc-2.17_shim.so
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Last-modified: 2022-11-02 (水) 02:26:17