FreeFEM v4.x installation

S["MPI_INCLUDE"]="-I\"/opt/intel/oneapi/..." -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker -Xlinker -rpath -Xlinker -Xlinker --enable-new-dtags "

S["MPI_INCLUDE"]="-I\"/opt/intel/oneapi/..." -Xlinker --enable-new-dtags "

# src/mpi/Makefile を修正

MPI_INCLUDE と AM_CPPFLAGS

# plugin/seq/WHERE_LIBRARY-config を修正

mpi INCLUDE -I"/opt/intel/oneapi/mpi/xxxx.x.x/include" -Xlinker --enable-new-dtags -rpath -Xlinker -Xlinker -rpath -Xlinker -Xlinker --enable-new-dtags

mpi INCLUDE -I"/opt/intel/oneapi/mpi/xxxx.x.x/include" -Xlinker --enable-new-dtags

$ make -j<nb_of_processes>

$ make check

$ sudo bash

# source /opt/intel/oneapi/setvars.sh

# make install

OneAPI を利用
- Intel oneAPI Toolkits から oneAPI Base Toolkit と oneAPI HPC Toolkit をインストール
- 下記のファイルで MPI_INCLUDE と mpi INCLUDE (src/mpi/Makefile では AM_CPPFLAGSも) での記述が誤って、reconfigure 後の make で "-rpath " がエラーとなる
  - config.status, Makefile, src/Makefile, src/mpi/Makefile, plugin/Makefile, plugin/seq/Makefile, plugin/seq/WHERE_LIBRARY-config

... -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker -Xlinker -rpath -Xlinker -Xlinker --enable-new-dtags ...

- とりあえずの対処方法：reconfigure の後で対象ファイルを手動で修正して、make を再実行

... -Xlinker --enable-new-dtags ...

アップデートまたは再インストールの場合
- 現バージョンのコンパイルディレクトリで $ sudo make uninstall
- インストール済みの PETSc を削除 $ sudo rm /usr/local/ff-petsc (make ff-petsc 実行時のコンパイルエラーの原因となる場合あり)

過去の情報：

MKL を利用
- apt から MKL をインストール

$ sudo apt install intel-mkl-full

- $ source /opt/intel/bin/compilervars.sh intel64 などが必要
[2024-09-06] 4.14 で 3rdparty/getall 時にリンクエラー ( 4.15 で解消 )
- https://github.com/FreeFem/FreeFem-sources/blob/develop/3rdparty/getall　に差し替えて実行
- [バージョンが合わないのか，取得エラーが出ます] getall中の "http://pkgs.freefem.org" -> "https://www.ljll.fr/hecht/" に変換して，実行

$ cd 3rdparty

$ sed -e "s/http\:\/\/pkgs\.freefem\.org/https\:\/\/www\.ljll\.fr\/hecht/g" < getall > getall_fixed

$ perl ./getall_fixed -a

FreeFEM 4.4.3 - 4.9 on ubuntu

FreeFEM 4.9 on ubuntu 20.04 LTS with intel MKL (2021-05-30)

FreeFEM 4.7 on ubuntu 20.04 LTS (WSL2) with intel MKL (2020-09-09)

FreeFEM 4.6 on ubuntu 18.04.3 LTS (clean) with intel MKL (2020-06-11)

FreeFEM 4.5 on ubuntu 18.04.3 LTS (clean) with intel MKL (2020-03-03)

FreeFEM 4.4.3 on ubuntu 18.04.3 LTS (clean) with intel MKL (2020-01-13)

1. Install Intel MKL
  1. - $ wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
    - $ sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
    - $ sudo sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list'
    - $ sudo apt update
    - $ sudo apt install intel-mkl-64bit-2020.0-088

1. Install FreeFEM (make install でも MKL用設定を読み込むことに注意)
  1. - $ sudo apt install autoconf build-essential unzip m4 bison flex patch cmake freeglut3-dev gfortran python2.7 gnuplot git openmpi-bin libopenmpi-dev valgrind
      - (ubuntu20.04 WSL2) $ export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
      - (ubuntu20.04 WSL2) $ sudo apt install python

$ source /opt/intel/bin/compilervars.sh intel64

$ autoreconf -i

$ ./configure --enable-download --with-mkl=$MKLROOT/lib --enable-mkl_mlt

$ ./3rdparty/getall -a

$ cd 3rdparty/ff-petsc

$ make petsc-slepc SUDO=sudo

$ cd -

$ ./reconfigure

$ make

$ make check

$ sudo bash

# source /opt/intel/bin/compilervars.sh intel64

# make install

CentOS

FreeFEM 4.7 on CentOS 7

FreeFEM 4.7 on CentOS 7 with intel compiler (2020-09-09)

SuperLU のコンパイルでエラーが出ます。

対応：

configure で --disable-superlu
3rdparty/ff-petsc/Makefile で superlu 関連を全てコメントアウト

Install

$ yum install gcc-g++ cmake valgrind-devel
$ tar zxvf v4.6.tar.gz
$ cd FreeFem-sources-4.4.3
$ source /opt/intel/bin/compilervars.sh intel64
$ export CC=icc; export CXX=icpc; export FC=ifort; export F77=ifort; export MPICC=mpiicc; export MPICXX=mpiicpc; export MPIFC=mpiifort
$ autoreconf -i
$ ./configure --enable-download --with-mpi=mpiicpc --with-mkl=$MKLROOT/lib --enable-mkl_mlt --disable-superlu | tee configure.out
$ ./3rdparty/getall -a
$ cd 3rdparty/ff-petsc/
Makefile から superlu 関連を全てコメントアウト
$ make petsc-slepc SUDO=sudo
$ cd ../..
$ MPIRUN=mpiexec ./reconfigure
$ make
$ sudo bash
# source /opt/intel/bin/compilervars.sh intel64
# export CC=icc; export CXX=icpc; export FC=ifort; export F77=ifort; export MPICC=mpiicc; export MPICXX=mpiicpc; export MPIFC=mpiifort
# make install

エラーメッセージ

===============================================================================

***** WARNING: F77 (set to ifort) found in environment variables - ignoring

use ./configure F77=$F77 if you really want to use that value ******

===============================================================================

$ less petsc-3.13.0/configure.log

*******************************************************************************

UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):

-------------------------------------------------------------------------------

Error configuring SUPERLU with cmake

*******************************************************************************

File "/home/ttks/src/c/FreeFem/FreeFem-sources-4.6/3rdparty/ff-petsc/petsc-3.13.0/config/configure.py", line 440, in petsc_configure

framework.configure(out = sys.stdout)

File "/home/ttks/src/c/FreeFem/FreeFem-sources-4.6/3rdparty/ff-petsc/petsc-3.13.0/config/BuildSystem/config/framework.py", line 1229, in configure

self.processChildren()

File "/home/ttks/src/c/FreeFem/FreeFem-sources-4.6/3rdparty/ff-petsc/petsc-3.13.0/config/BuildSystem/config/framework.py", line 1218, in processChildren

self.serialEvaluation(self.childGraph)

File "/home/ttks/src/c/FreeFem/FreeFem-sources-4.6/3rdparty/ff-petsc/petsc-3.13.0/config/BuildSystem/config/framework.py", line 1193, in serialEvaluation

child.configure()

File "/home/ttks/src/c/FreeFem/FreeFem-sources-4.6/3rdparty/ff-petsc/petsc-3.13.0/config/BuildSystem/config/package.py", line 1110, in configure

self.executeTest(self.configureLibrary)

File "/home/ttks/src/c/FreeFem/FreeFem-sources-4.6/3rdparty/ff-petsc/petsc-3.13.0/config/BuildSystem/config/base.py", line 139, in executeTest

ret = test(*args,**kargs)

File "/home/ttks/src/c/FreeFem/FreeFem-sources-4.6/3rdparty/ff-petsc/petsc-3.13.0/config/BuildSystem/config/package.py", line 875, in configureLibrary

for location, directory, lib, incl in self.generateGuesses():

File "/home/ttks/src/c/FreeFem/FreeFem-sources-4.6/3rdparty/ff-petsc/petsc-3.13.0/config/BuildSystem/config/package.py", line 453, in generateGuesses

FreeFEM 4.4.3 on CentOS 7

FreeFEM 4.4.3 on CentOS 7 with intel compiler (2019-12-19)

$ tar zxvf FreeFem-sources-4.4.3.tar.gz
$ cd FreeFem-sources-4.4.3
$ source /opt/intel/bin/compilervars.sh intel64
$ autoreconf -i
$ export CC=icc; export CXX=icpc; export FC=ifort; export F77=ifort; export MPICC=mpiicc; export MPICXX=mpiicpc; export MPIFC=mpiifort
$ ./configure --enable-download --with-optim \
--with-mpi=mpiicpc --with-mkl=$MKLROOT/lib --enable-mkl_mlt | tee configure.out
$ ./3rdparty/getall -a
$ cd 3rdparty/ff-petsc/
$ make petsc-slepc SUDO=sudo
$ cd ../..
$ MPIRUN=mpiexec ./reconfigure
$ make
$ sudo bash
# source /opt/intel/bin/compilervars.sh intel64
# export CC=icc; export CXX=icpc; export FC=ifort; export F77=ifort; export MPICC=mpiicc; export MPICXX=mpiicpc; export MPIFC=mpiifort
# make install

WSL2

PATH : WSL では PATH に Windows 関連 PATH も設定されてしまうため，ubuntu 関連のものだけに設定し直したほうが安全
- 空白の入った PATH は reconfigure の際にエラーを誘発
[動作が変わりました(調査中) 2020-09-14] X window : WSL2 では毎回 IP address が変わるので，環境変数 DISPLAY を正しく設定する必要あり
- (~/.bashrc) export DISPLAY=$(cat /etc/resolv.conf | grep nameserver | awk '{print $2}'):0
  - [動かなくなりました 2020-09-14]
- (vcXsrv option) Disable access control: ON, additional parameters "-ac"
- (Windows firewall) vcXsrv: private/public "OK"
- (MobaXterm) OK
- Ref.
  - Can't use X-Server in WSL 2 https://github.com/microsoft/WSL/issues/4106
  - WSL2のGUI設定でつまずいたところ https://qiita.com/baibai25/items/5841b0592727893d960f
  - WSL上にXサーバをインストールしてGUIを実現する（VcXsrv編） https://www.atmarkit.co.jp/ait/articles/1812/06/news040.html

[4.15 では解消] getall でのエラー

3rdparty/getall 実行時にリンクエラーが起きる

当面の解決方法　[2024-09-06]：

- https://github.com/FreeFem/FreeFem-sources/blob/develop/3rdparty/getall　に差し替えて実行

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