Failed:　Code Aster 13.4 Parallel with PETSc on Ubuntu 16.04

いまさらですが、Code Aster　12.6のParallel版をつくろうと思い,

Ubuntu14.04上ではhttps://sites.google.com/site/codeastersalomemeca/home/code_asterno-heiretuka/code_asterno-heiretuka-12-6の方法で構築できたのですが、Ubuntu16.04では・・・失敗しました。

でもCode Aster　13.4再挑戦です（2017/09/17）。でも動作確認したら、MEDとHDF5がない！といわれて動きませんでした。とほほ（2017・09・26）

１．OpenBLAS

先のサイトの通りです。

$ cd ~/Install_Files/
$ tar xfvz OpenBLAS-0.2.18..tar.gz
$ cd OpenBLAS-0.2.18
$ make NO_AFFINITY=1 USE_OPENMP=1
$ make PREFIX=/opt/OpenBLAS install
$ echo /opt/OpenBLAS/lib | sudo tee -a /etc/ld.so.conf.d/openblas.conf
$ sudo ldconfig

２．通常のCodeAsterのインストール

、先のサイトの通りです。

$ cd ~/Install_Files
$ tar xfvz aster-full-src-12.6.0-3.noarch.tar.gz
$ cd aster-full-src-12.6.0/
$ sed -i "s:PREFER_COMPILER\ =\ 'GNU':PREFER_COMPILER\ =\'GNU_without_MATH'\nMATHLIB=\ '/opt/OpenBLAS/lib/libopenblas.a':g" setup.cfg
$ python setup.py install

$ echo "$HOSTNAME cpu=$(cat /proc/cpuinfo | grep processor | wc -l)" > /opt/aster/etc/codeaster/mpi_hostfile

３．ScaLAPACK

これも先のサイトと同じ。

$ cd ~/Install_Files
$ tar xfvz scalapack_installer.tgz
$ cd scalapack_installer_1.0.2
$ ./setup.py --lapacklib=/opt/OpenBLAS/lib/libopenblas.a --mpicc=mpicc --mpif90=mpif90 --mpiincdir=/usr/lib/openmpi/include --ldflags_c=-fopenmp --ldflags_fc=-fopenmp --prefix=/opt/scalapac

BLACS: error running BLACS test routines xCbtest というエラーが最後に表示されても、/opt/scalapack/lib/libscalapack.aのファイルが作成されていればOKなのも同じです。

ここまでは問題ありません。

４．Parmetis

$cd ~/
$tar xfvz parmetis-4.0.3.tgz 
$cd ~/parmetis-4.0.3
$make config -prefix=/opt/parmetis-4.0.3
$make all
$make install

５．SCOTCHとPTSCOTCH

$cd /opt
$ tar xfvz scotch-6.0.4.tgz
$cd /opt/scotch-6.0.4/src

そして、Makefile.incを修正します。

EXE =
LIB = .a
OBJ = .o

MAKE = make
AR = ar
ARFLAGS = -ruv
CAT = cat
CCS = gcc
CCP = mpicc
CCD = gcc -I /usr/include/mpi
CFLAGS = -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -DSCOTCH_PTHREAD -DSCOTCH_DETERMINISTIC -Drestrict=__restrict
CLIBFLAGS =
LDFLAGS = -lz -lm -lrt -lpthread
CP = cp
LEX = flex -Pscotchyy -olex.yy.c
LN = ln
MKDIR = mkdir
MV = mv
RANLIB = ranlib
YACC = bison -pscotchyy -b y

そして、

$make scotch esmumps

../esumps内に出来たlibesumps.aは..scotch-6.0.4/libにcopyしておきます。

$make ptscotch ptesmumps

６．Mumps

$ cp ~/Install_Files/aster-full-src-13.4.0/SRC/mumps-5.1.1-aster2.tar.gz /opt/
$ cd /opt
$ tar xfvz mumps-5.1.1-aster2.tar.gz
$ mv mumps-5.1.1 mumps-5.1.1_mpi2
$ cd mumps-5.1.1_mpi2/

#
# This file is part of MUMPS 4.10.0, built on Tue May 10 12:56:32 UTC 2011
# modified for Code_Aster setup (see fields like ?CC?)
#
#Begin orderings

# NOTE that PORD is distributed within MUMPS by default. If you would like to
# use other orderings, you need to obtain the corresponding package and modify
# the variables below accordingly.
# For example, to have Metis available within MUMPS:
# 1/ download Metis and compile it
# 2/ uncomment (suppress # in first column) lines
# starting with LMETISDIR, LMETIS
# 3/ add -Dmetis in line ORDERINGSF
# ORDERINGSF = -Dpord -Dmetis
# 4/ Compile and install MUMPS
# make clean; make (to clean up previous installation)
#
# Metis/ParMetis and SCOTCH/PT-SCOTCH (ver 5.1 and later) orderings are now available for MUMPS.
#

#SCOTCHDIR = ?HOME_SCOTCH?
SCOTCHDIR = /opt/scotch-6.0.4
ISCOTCH = -I$(SCOTCHDIR)/include/

# You have to choose one among the following two lines depending on
# the type of analysis you want to perform. If you want to perform only
# sequential analysis choose the first (remember to add -Dscotch in the ORDERINGSF
# variable below); for both parallel and sequential analysis choose the second 
# line (remember to add -Dptscotch in the ORDERINGSF variable below)

LSCOTCH = -L$(SCOTCHDIR)/lib -lesmumps -lscotch -lscotcherr
#LSCOTCH = -L$(SCOTCHDIR)/lib -lptesmumps -lptscotch -lptscotcherr



LPORDDIR = $(topdir)/PORD/lib/
IPORD = -I$(topdir)/PORD/include/
LPORD = -L$(LPORDDIR) -lpord

METISDIR = /opt/aster/public/metis-5.1.0
#LMETISDIR = ?HOME_METIS?/lib
LMETISDIR = $(METISDIR)/lib/

IMETIS = -I$(METISDIR)/include/

# You have to choose one among the following two lines depending on
# the type of analysis you want to perform. If you want to perform only
# sequential analysis choose the first (remember to add -Dmetis in the ORDERINGSF
# variable below); for both parallel and sequential analysis choose the second 
# line (remember to add -Dparmetis in the ORDERINGSF variable below)

LMETIS = -L$(LMETISDIR) -lmetis
#LMETIS = -L$(LMETISDIR) -lparmetis -lmetis

# The following variables will be used in the compilation process.
# Please note that -Dptscotch and -Dparmetis imply -Dscotch and -Dmetis respectively.
#ORDERINGSF = -Dscotch -Dmetis -Dpord -Dptscotch -Dparmetis
#ORDERINGSF = -Dscotch -Dmetis -Dpord -Dparmetis
#ORDERINGSF = -Dpord -Dmetis
#ORDERINGSF = -Dpord -Dparmetis -Dmetis
ORDERINGSF = -Dscotch -Dpord -Dmetis
ORDERINGSC = $(ORDERINGSF)

LORDERINGS = $(LMETIS) $(LPORD) $(LSCOTCH)
IORDERINGSF = $(ISCOTCH) $(IMETIS)
IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH)

#End orderings
########################################################################
################################################################################

PLAT =
LIBEXT = .a
OUTC = -o 
OUTF = -o 
RM = /bin/rm -f
CC = mpicc
FC = mpif90
FL = mpif90
# WARNING: AR must ends with a blank space!
AR = ar vr 
#RANLIB = ranlib
RANLIB = echo
# See point 17 in the FAQ to have more details on the compilation of mpich with gfortran
SCALAP = /opt/scalapack/lib/libscalapack.a \
 /opt/OpenBLAS/lib/libopenblas.a

INCPAR = -I/usr/include/openmpi $(IPORD)
LIBPAR = $(SCALAP) -L/usr/lib -lmpi

#LIBPAR = $(SCALAP) -L/usr/local/lib/ -llamf77mpi -lmpi -llam
#LIBPAR = $(SCALAP) -lutil -ldl -lpthread
#LIBPAR = -lmpi++ -lmpi -ltstdio -ltrillium -largs -lt
INCSEQ = -I$(topdir)/libseq
LIBSEQ = -L$(topdir)/libseq -lmpiseq
#LIBBLAS = -L/usr/lib/xmm/ -lf77blas -latlas
LIBBLAS = -L/opt/OpenBLAS/lib/ -lopenblas
LIBOTHERS = -lpthread
#Preprocessor defs for calling Fortran from C (-DAdd_ or -DAdd__ or -DUPPER)
CDEFS = -DAdd_

#Begin Optimized options
#OPTF = -O -Dintel_ -DALLOW_NON_INIT ?F90FLAGS?
#OPTL = -O ?LDFLAGS?
#OPTC = -O ?CFLAGS?
OPTF = -O -Dintel_ -DALLOW_NON_INIT -ffixed-line-length-0 -x f77-cpp-input -fPIC -fopenmp -DDETERMINISTIC_PARALLEL_GRAPH
#OPTF = -O -Dintel_ -DALLOW_NON_INIT -ffixed-line-length-0 -x f77-cpp-input -fPIC -fopenmp 
OPTL = -O -fopenmp
OPTC = -O -fno-stack-protector -fPIC -fopenmp
#End Optimized options
#INCS = $(INCSEQ)
#LIBS = $(LIBSEQ)
#LIBSEQNEEDED = libseqneeded
INCS = $(INCPAR)
LIBS = $(LIBPAR)
LIBSEQNEEDED =

そして、

$make all

です。

７．PETSC

$ cp ~/Install_Files/petsc-3.7.6.tar.gz /opt
$ cd /opt
$ tar xfvz petsc-3.7.6.tar.gz
$ cd petsc-3.7.6

そして、configureです.。

./config/configure.py --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-mpi-dir=/usr/lib/openmpi --with-blas-lapack-lib=/opt/OpenBLAS/lib/libopenblas.a --download-hypre=yes --download-ml=yes --with-debugging=0 COPTFLAGS=-O1 CXXOPTFLAGS=-O1 FOPTFLAGS=-O1 --configModules=PETSc.Configure --optionsModule=PETSc.compilerOptions --with-x=0 --with-shared-libraries=0 --download-mumps=yes --with-scalapack-dir=/opt/scalapack --with-ptscotch-dir=/opt/scotch-6.0.4 --with-parmetis-dir=/opt/parmetis-4.0.3 --with-metis-dir=/opt/aster/public/metis-5.1.0 --download-mumps-commit=v5.1.1-p1

なぜか、

--with-mumps-dir=/opt/mumps-5.1.1-mpi2

が動作しない、というエラーがでるので、download-mumpsで代用です。mumps-5.0.25.1.1がダウンロードされました。(2017/9/23訂正）

Configureが終了したら、

$ make PETSC_DIR=/opt/petsc-3.7.6 PETSC_ARCH=arch-linux2-c-opt all
$ make PETSC_DIR=/opt/petsc-3.7.6 PETSC_ARCH=arch-linux2-c-opt test

して、コンパイルと成功の確認をします。

８．CODE　ASTER再構築

bitbucketのTutorialを参考に、Code AsterのSourceをダウンロードします。

mkdir -p $HOME/dev/codeaster && cd $HOME/dev/codeaster
hg clone https://bitbucket.org/code_aster/codeaster-devtools devtools
hg clone https://bitbucket.org/code_aster/codeaster-src src

並列用設定ファイル：Ubuntu_gnu.py、

# encoding: utf-8

"""
Fichier de configuration WAF pour version séquentielle sur Ubuntu 12.04 :
- Compilateur : GNU
- BLAS : OpenBLAS
"""
import os

def configure(self):
 opts = self.options

# opts.with_prog_metis = True

# official_programs.configure(self)

self.env.append_unique('LINKFLAGS', ['-Wl,--allow-multiple-definition'])
# self.env.append_value('CXXFLAGS', ['-D_GLIBCXX_USE_CXX11_ABI=0'])
 self.env['ADDMEM'] = 350

self.env.append_value('LIBPATH', [
 '/opt/aster/public/hdf5-1.8.14/lib',
 '/opt/aster/public/med-3.2.1/lib',
 '/opt/aster/public/metis-5.1.0/lib',
 '/opt/aster/public/mfront-3.0.0/lib',
 '/opt/scotch-6.0.4/lib',
 '/opt/OpenBLAS/lib',])

self.env.append_value('INCLUDES', [
 '/opt/aster/public/hdf5-1.8.14/include',
 '/opt/aster/public/med-3.2.1/include',
 '/opt/aster/public/metis-5.1.0/include',
 '/opt/aster/public/mfront-3.0.0/include',
 '/opt/mumps-5.1.1-mpi2/include',
 '/opt/mumps-5.1.1-mpi2/include_seq',
 '/opt/scotch-6.0.4/include',
 '/opt/OpenBLAS/include'])

opts.maths_libs = 'openblas'
 opts.embed_math = True

opts.enable_med = True
 opts.hdf5_libs = 'hdf5 z'
 opts.embed_hdf5 = True
# opts.med_libs = 'med stdc++'
 opts.embed_med = True

# opts.enable_petsc = True

opts.enable_mfront = False

opts.enable_scotch = True
 opts.embed_scotch = True

opts.embed_aster = True
 opts.embed_fermetur = True

もう１つのUbuntu_gnu_mpi.py：

# encoding: utf-8

"""
Fichier de configuration WAF pour version parallèle sur Ubuntu 12.04 :
- Compilateur : GNU
- MPI : système (OpenMPI, Ubuntu 12.04)
- BLAS : OpenBLAS
- Scalapack : système (Ubuntu 12.04)
- PETSc : 
"""
import Ubuntu_gnu

def configure(self):
 opts = self.options
 Ubuntu_gnu.configure(self)

self.env.prepend_value('LIBPATH', [
 '/opt/parmetis-4.0.3/lib',
 '/opt/mumps-5.1.1-mpi2/lib',
 '/opt/petsc-3.7.6/arch-linux2-c-opt/lib',
 '/opt/scalapack/lib',])

self.env.prepend_value('INCLUDES', [
 '/opt/parmetis-4.0.3/include',
 '/opt/mumps-5.1.1-mpi2/include',
 '/opt/petsc-3.7.6/arch-linux2-c-opt/include',
 '/opt/petsc-3.7.6/include',])

self.env.append_value('LIB', ('X11',))

opts.parallel = True

opts.enable_mumps = True
 opts.mumps_version = '5.1.1'
 opts.mumps_libs = 'dmumps zmumps smumps cmumps mumps_common pord metis scalapack openblas esmumps scotch scotcherr'

opts.enable_petsc = True
 self.env.append_value('LIB_METIS', ('parmetis'))
 self.env.append_value('LIB_SCOTCH', ('ptscotch','ptscotcherr','ptscotcherrexit','ptesmumps'))

opts.petsc_libs='petsc HYPRE ml'
# opts.embed_petsc = True

そして、../codeaster/srcに移動して、

$ export ASTER_ROOT=/opt/aster
$ ./waf configure --use-config-dir=$ASTER_ROOT/13.4/share/aster --use-config=Ubuntu_gnu_mpi --prefix=$ASTER_ROOT/PAR13.4-petsc

ここで、ｂｌａｐａｃがない、とエラーが出たら、

Code_Aster installation » Parallel installation of aster-13.2: blacs not found

を参考に、対応しました。

$./waf build -p

途中Warningが大量にでましたが、buildは完了しました。

$./waf install

動作確認は、MEDとHDF5がない！といわれて動きませんでした。とほほ（2017・09・26）