This page is a note of the work to build parallel version. But a procedure regarding to PETSc is old. Latest article is here.
The linux box is xUbuntu 18.04LTS on VMware.
Python is python 2.7.17 and Python3 is python 3.6.9.
０．preparation
Preparation is same as the case of CodeAster 14.4.
Some packages are installed as follows.
$sudo apt-get install gfortran g++ python-dev python-numpy liblapack-dev libblas-dev tcl tk zlib1g-dev bison flex checkinstall openmpi-bin libx11-dev cmake grace gettext libboost-all-dev swig
And install superlu package.
$sudo apt-get install libsuperlu-dev
１．OpenBLAS
To get source code from author’s HP. Then execute following procedure.
$ tar xfvz OpenBLAS-0.2.20.tar.gz $ cd OpenBLAS-0.2.20 $ 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．Code_Aster eith OpenBLAS
$ cd aster-full-src-14.4.0 $ sed -i "s:PREFER_COMPILER\ =\ 'GNU':PREFER_COMPILER\ =\'GNU_without_MATH'\nMATHLIB=\ '/opt/OpenBLAS/lib/libopenblas.a':g" setup.cfg
And
$ python3 setup.py install
After the build complete, to make host file for parallel calculation.
$ echo "$HOSTNAME cpu=$(cat /proc/cpuinfo | grep processor | wc -l)" > /opt/aster/etc/codeaster/mpi_hostfile
３．ScaLAPACK
$ tar xfvz scalapack_installer.tgz $ cd scalapack_installer $ ./setup.py --lapacklib=/opt/OpenBLAS/lib/libopenblas.a --mpicc=mpicc --mpif90=mpif90 --mpiincdir=/usr/lib/x86_64-linux-gnu/openmpi/include --ldflags_c=-fopenmp --ldflags_fc=-fopenmp --prefix=/opt/scalapack-n
４．Parmetis
Get source code and unpack it. Integer size is 8 byte in this work.
#define IDXTYPEWIDTH 64″ and “#define REALTYPEWIDTH 32” is written in ~/parmetis-4.0.3/metis/include/metis.h. or add followings to metis.h
#ifdef INTSIZE32 #define IDXTYPEWIDTH 32 #else #define IDXTYPEWIDTH 64 #endif
then
$ tar xvf parmetis-4.0.3.tar.gz $ cd parmetis-4.0.3 $ make config prefix=/opt/parmetis-4.0.3 $ make
Next, checking.
$ cd Graphs $ mpirun -np 8 ptest rotor.graph rotor.graph.xyz
When any error is reported, go to~/parmetis-4.0.3 and execute follows:
$ make install
This part is finished.
５．Scotch and Ptscotch
Unpack scotch-6.0.4-aster5.tar.gz which is included the package of code_aster in /opt.
$ cd /opt/scotch-6.0.4/src
Makefile.inc is here
$ make scotch esmumps ptscotch ptesmumps CCD=mpicc
After building, check it.
$ make check $ make ptcheck
This part is finised.
６．MUMPS
Pick mumps-5.1.2-aster6.tar.gz from the package of code_aster out and unpack it. The name of folder is changed to mumps-5.1.2_mob.
$ cd /opt/mumps-5.1.2_mob
Makefile.inc is.here.
$ make all
Next, to go to ~/examples and check the MUMPS.
７．Petsc
petsc-3.9.4.tar.gz is downloaded from author’s HP. Then unpack it in /opt. First , a few line (line 43 to 48) is commented out metis.py in /opt/petsc-3.9.4/config/BuildSystem/config/packages.
def configureLibrary(self): config.package.Package.configureLibrary(self) oldFlags = self.compilers.CPPFLAGS self.compilers.CPPFLAGS += ' '+self.headers.toString(self.include) # if not self.checkCompile('#include "metis.h"', '#if (IDXTYPEWIDTH != '+ str(self.getDefaultIndexSize())+')\n#error incompatible IDXTYPEWIDTH\n#endif'): # if self.defaultIndexSize == 64: # msg= '--with-64-bit-indices option requires a metis build with IDXTYPEWIDTH=64.\n' # else: # msg= 'IDXTYPEWIDTH=64 metis build appears to be specified for a default 32-bit-indices build of PETSc.\n' # raise RuntimeError('Metis specified is incompatible!\n'+msg+'Suggest using --download-metis for a compatible metis')
And when openmpi is used, path to openmpi library is added to LD_LIBRARY_PATH. Next is a sample.
$ export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/openmpi/lib/:$LD_LIBRARY_PATH
Then, “configure” is done.
$./configure --with-debugging=0 COPTFLAGS=-O CXXOPTFLAGS=-O FOPTFLAGS=-O --with-shared-libraries=0 --with-scalapack-dir=/opt/scalapack-n --PETSC_ARCH=linux-metis-mumps --with-metis-dir=/opt/aster/public/metis-5.1.0 --with-parmetis-dir=/opt/parmetis-4.0.3 --with-ptscotch-dir=/opt/scotch-6.0.4 --LIBS="-lgomp" --with-mumps-dir=/opt/mumps-5.1.2_mob -with-x=0 --with-blas-lapack-lib=[/opt/OpenBLAS/lib/libopenblas.a] --download-hypre=yes --download-ml=yes
and “make”
$ make PETSC_DIR=/opt/petsc-3.9.4 PETSC_ARCH=linux-metis-mumps all
８．Parallel version Code_Aster
Go to the folder stored the source code of code_aster. And unpack aster-14.4.0.
$ cd ~/Install_Files $ cd aster-full-src-14.4.0/SRC $ tar xfvz aster-14.4.0.tgz $ cd aster-14.4.0
Next a part of ~/waftools/mathematics.py is modified to skip the checking of blacs.
# program testing a blacs call, output is 0 and 1
blacs_fragment = r"""
program test_blacs
integer iam, nprocs
# call blacs_pinfo (iam, nprocs)
# print *,iam
# print *,nprocs
end program test_blacs
"""
Then copy Ubuntu_gnu.py and Ubuntu_gnu_mpi.py to the folder. Now preparation of build is ready.
$ export ASTER_ROOT=/opt/aster $ export PYTHONPATH=/$ASTER_ROOT/lib/python3.6/site-packages/:$PYTHONPATH $ ./waf configure --use-config-dir=$ASTER_ROOT/14.4/share/aster --use-config=Ubuntu_gnu_mpi --prefix=$ASTER_ROOT/PAR14.4MUPT $ ./waf install -p --jobs=1
When build is finished. add register the parallel version to /opt/aster/etc/codeaster/aster.
# Code_Aster versions
# versions can be absolute paths or relative to ASTER_ROOT
# examples : NEW11, /usr/lib/codeaster/NEW11
# default version (overridden by --vers option)
default_vers : stable
# available versions
# DO NOT EDIT FOLLOWING LINE !
#?vers : VVV?
vers : stable:/opt/aster/14.4/share/aster
vers : 13.6MUPT:/opt/aster/PAR14.4MUPT/share/aster
Whole work is finished.
I got many information from Code_aster forum. I appreciate the form members.
コメント
Dear mr. Hitory,
I found your advice about Code-Aster with MPI reading Coda-Aster Forum.
Reading your procedure to install CA 13.6 with MPI was very interesting, and now I’m reading new suggestions up here.
Before to begin to try the compilation, I want emphasize that I’n not a programmer, but only a structural analyst, so pleas be patient with me.
My workstation is equipped with a single AMD Ryzen 1900X (8 cores, 64 GB RAM, SATA3 disks) and UBUNTUx64 18.04.04
Some question:
1) I could install openBLAS 0.2.20 using Synaptic: it is correct, or it is better to build it by sources? and what about release: 0.2.20 or last 0.38?
2) same for scaLAPACK (rel. 2.0.2-4) Scotch (6.0.4), PTScotch (6.0.4), Petsc(3.7.7), parmetis(4.0.3-5), MUMPS (5.1.2, both parallel an non-parallel): coud I simpley install all them using Synaptic?
3) could You explain why aster-full-src-14.4.0 has to be compiled just after openBLAS and BEFORE other pre-requisite sw?
Thank you very much for you willingness to help Coda-Aster community
Best greeting,
Piero
Hello Mr. Cirrottola -san,
Thank you for your comment.
About your 1st and 2nd question,
My work is based on https://sites.google.com/site/codeastersalomemeca/home/code_asterno-heiretuka/parallel-code_aster-12-6 .
By the article, It is necessary many special settings to to build Code_Aster.
Therefore, I think to build from source code is better way.
Third question, my idea are follows:
to check output step by step
to use configure data built by setup.py
Thank you again,
Hitori
Hallo Mr. Hitori-san,
thank you very much for your fast reply and for your suggestions.
I’m now reading the article You are citing.
Because of our big timing difference, I ‘m already proceeding following your instructions, and now I have a result I don’t understand: I have installed MUMPS without any error, but testing some example in mumps-5.1.2_mob/examples, I obtain this:
$ /opt/mumps-5.1.2_mob/examples/csimpletest
/opt/mumps-5.1.2_mob/examples/csimpletest: symbol lookup error: /usr/lib/x86_64-linux-gnu/liblapack.so.3: undefined symbol: gotoblas
does it means that something was wrong?
Many thanks again,
Piero
Hello Cirrottola-san,
Do you build parallel version?
If yes, please try
“mpirun -np 2 ./csimpletest < input_simpletest_cmplx"
written in README under ~/examples.
thank you,
Hitori
Hello Mr. Hitori-san,
unfortunately no, I wasn’t able to build parallel version.
I discovered (oh, my memory!) that I have active a complete OpenFOAM1906 environment, added to my .bashrc in recent past: obviously it load a special PATH containing some SCOTCH reference. I think that it was the principal reason of all my errors.
Now I’m cleaning my environment and I will try again a.s.a.p.
Thank you a lot
Piero
Hello Mr. Hitori-san
now I’ve fiished to build Code-Aster with openMPI.
Now it works and I’m testing if it is working really fine.
I found some minor problem:
1) openBLAS: I wasn’t able to understand wich release to use, among 3.7, 3.8 and the last stable 3.9; so, I decided to install through Synaptic the official Ubuntu 18.04 version: it seems to work properly;
2) Code_Aster with openBLAS: MATHLIB=’/usr/lib/x86_64-linux-gnu/libopenblas.a’ this is the right address for openBLAS lib, in all files where it is used;
3) ScalaPACK: no problem, but I received this
Running BLACS test routines…
BLACS: error running BLACS test routines xCbtest
BLACS: Command -np 4 ./xCbtest
stderr:
****************************************
/bin/sh: 1: -np: not found
****************************************
so I don’t know if it is OK, but it seams to work;
4) Parmetis, Scotch and Ptscotch and MUMPS: all OK
5) Petsc: I was pushed to install Valgrind, I did with Synaptic; but package ml was missing and I loaded it by
$ git clone https://bitbucket.org/petsc/pkg-ml.git git.ml
But it wasn’t installed and Code_Aster successive configuration (via waf) failed because ml was missing.
So, I reinstalled Petsc without ml package. Now, all OK.
6) Code_Aster Parallel: insatllation via waf was now OK and I’m testing Code_Aster Parallel
I want thank you again for your courtesy and willingness
best regards
Piero
Dear Mr. Hitori-san,
I cannot seem to get past this extremely frustrating error (I have followed your installation guide):
https://code-aster.org/forum2/viewtopic.php?pid=61323#p61323
Do you happen to have ANY idea on how to fix this segmentation error ?
I had success with reinstalling the packages used before, but I have still no clue what the actual culprit is… and now even that does not seem to work.
Hello Balogh-san,
Sorry. I don7t have any idea about your trouble.
Hey, I am getting this weird petsc issue. Any idea what might be causing it?
[4594/8114] Compiling bibfor/algorith/cuacat.F90
/program/code-aster-14.5.12/Code-aster/bibfor/petsc/aster_petsc_module.F90(23): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [PETSCSYSDEF]
use petscsysdef
—-^
/program/code-aster-14.5.12/Code-aster/bibfor/petsc/aster_petsc_module.F90(24): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [PETSCVECDEF]
use petscvecdef
—-^
Hello, I could run the whole process, however, I have a problem when I want to link the openmpi to patsc. Can you please tell me where should I apply the following code that you mentioned:
“export LD_LIBRARY_PATH =/usr/lib/x86_64-linux-gnu/openmpi/lib/:$LD_LIBRARY_PATH”.
It does not work when I copy it into my terminal inside the petsc directory.
Hello
Is your problem this ?
https://lists.mcs.anl.gov/pipermail/petsc-dev/2018-October/023619.html
Thank you,
Hitori
Thank you for your response. I checked the link you sent me but I could not still solve my problem. Actually, I do not know how should I add the openmpi library path to LD_LIBRARY_PATH. Where should I exactly apply the code that you mentioned in the tutorial (I mean this code: $ export LD_LIBRARY_PATH =/usr/lib/x86_64-linux-gnu/openmpi/lib/:$LD_LIBRARY_PATH
)?
And should I apply any changes to this command?
Hello
Please check the path to openmpi libraly on your system and apply it.
1. The command run in a terminal before building petsc.
2. This was added to .bashrc after building parallel code_aster.
And I don’t have any idea.
Thank you,
Hitori
I am getting below error Aster not getting install, what can be possible reason. kindly reply.
med install
but
Installation of : aster 14.4.0
Destination : /opt/aster
Elapsed time : 774.72 s
*** Exception None raised : None
See detailed traceback in the logfile
[FAILED]
log file attached herewith.
Waf: Leaving directory `/tmp/install_aster.11869/aster-14.4.0/build/std/release’
+ build the elements catalog elem.1 using installed aster (from /tmp/install_aster.11869/aster-14.4.0/build/std/release/catalo/cata_ele.ojb)
stdout:
stderr: Segmentation fault (core dumped)
To run manually, use:
BINDIR=”/opt/aster/14.4/bin”
LIBDIR=”/opt/aster/14.4/lib”
PYTHONDIR=”/opt/aster/14.4/lib/python3.6/site-packages”
export LD_LIBRARY_PATH=”/opt/aster/public/hdf5-1.10.3/lib:/opt/aster/public/med-4.0.0/lib:/opt/aster/public/mumps-5.1.2/lib:/opt/aster/public/metis-5.1.0/lib:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/scotch-6.0.4/lib:/opt/aster/public/hdf5-1.10.3/lib64:/opt/aster/public/med-4.0.0/lib64:/opt/aster/14.4/lib:/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/usr:/usr/lib/gcc/x86_64-linux-gnu/7:/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/tfel-3.2.1″
export PYTHONPATH=”/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/opt/aster/lib/python3.6/site-packages:/opt/aster/public/tfel-3.2.1/lib/python3.6/site-packages”
${BINDIR}/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes /tmp/install_aster.11869/aster-14.4.0/build/std/release/fort.1 -memjeveux 500 -tpmax 120
Command ‘LD_LIBRARY_PATH=”/opt/aster/public/hdf5-1.10.3/lib:/opt/aster/public/med-4.0.0/lib:/opt/aster/public/mumps-5.1.2/lib:/opt/aster/public/metis-5.1.0/lib:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/scotch-6.0.4/lib:/opt/aster/public/hdf5-1.10.3/lib64:/opt/aster/public/med-4.0.0/lib64:/opt/aster/14.4/lib:/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/usr:/usr/lib/gcc/x86_64-linux-gnu/7:/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/tfel-3.2.1″ ${BINDIR}/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes /tmp/install_aster.11869/aster-14.4.0/build/std/release/fort.1 -memjeveux 500 -tpmax 120’ returned 139
EXIT_COMMAND_11869_00000106=1
*** Exception raised : error during installation
——————————————————————————–
SUMMARY OF INSTALLATION
——————————————————————————–
Installation of : hdf5 1.10.3
Destination : /opt/aster/public/hdf5-1.10.3
Elapsed time : 309.33 s
[ OK ]
Installation of : med 4.0.0
Destination : /opt/aster/public/med-4.0.0
Elapsed time : 253.32 s
[ OK ]
Installation of : gmsh 3.0.6
Destination : /opt/aster/public/gmsh-3.0.6-Linux
Elapsed time : 1.14 s
[ OK ]
Installation of : scotch 6.0.4
Destination : /opt/aster/public/scotch-6.0.4
Elapsed time : 40.96 s
[ OK ]
Installation of : astk 2019.0
Destination : /opt/aster/lib/python3.6/site-packages
Elapsed time : 1.01 s
[ OK ]
Installation of : metis 5.1.0
Destination : /opt/aster/public/metis-5.1.0
Elapsed time : 30.50 s
[ OK ]
Installation of : tfel 3.2.1
Destination : /opt/aster/public/tfel-3.2.1
Elapsed time : 789.70 s
[ OK ]
Installation of : mumps 5.1.2
Destination : /opt/aster/public/mumps-5.1.2
Elapsed time : 149.88 s
[ OK ]
Installation of : homard 11.12
Destination : /opt/aster/public/homard-11.12
Elapsed time : 4.72 s
[ OK ]
Installation of : aster 14.4.0
Destination : /opt/aster
Elapsed time : 774.72 s
*** Exception None raised : None
See detailed traceback in the logfile
[FAILED]
Exit code : 4
Installation of : Code_Aster + 10 of its prerequisites
Destination : /opt/aster
Elapsed time : 2598.24 s
[ OK ]
Hello Sameer-san,
What is your linux system? xUbuntu 18.0.4?
And please check your python and python3 version.
Thank you,
HITORI