Dear all, I tried to install Firedrake on Ubuntu 18.04 but I have problem on installation. Here are the errors I get: Running firedrake-install Checking for presence of package build-essential... installed. Checking for presence of package autoconf... installed. Checking for presence of package automake... installed. Checking for presence of package cmake... installed. Checking for presence of package gfortran... installed. Checking for presence of package git-core... missing. Checking for presence of package libblas-dev... installed. Checking for presence of package liblapack-dev... installed. Checking for presence of package libopenmpi-dev... installed. Checking for presence of package libtool... installed. Checking for presence of package mercurial... installed. Checking for presence of package openmpi-bin... installed. Checking for presence of package python3-dev... installed. Checking for presence of package python3-pip... installed. Checking for presence of package python3-tk... installed. Checking for presence of package python3-venv... installed. Checking for presence of package zlib1g-dev... installed. Installing missing packages: git-core. [sudo] password for amireh: Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'git' instead of 'git-core' git is already the newest version (1:2.17.0-1ubuntu1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Creating firedrake venv in '/home/amireh/firedrake'. Cloning firedrake Failed to clone firedrake using ssh, falling back to https. Successfully cloned repository firedrake. Checking out branch master Successfully checked out branch master Cloning the dependencies of firedrake Cloning ufl Failed to clone ufl using ssh, falling back to https. Successfully cloned repository ufl. Checking out branch master Successfully checked out branch master Cloning fiat Failed to clone fiat using ssh, falling back to https. Successfully cloned repository fiat. Checking out branch master Successfully checked out branch master Cloning FInAT Failed to clone FInAT using ssh, falling back to https. Successfully cloned repository FInAT. Checking out branch master Successfully checked out branch master Cloning tsfc Failed to clone tsfc using ssh, falling back to https. Successfully cloned repository tsfc. Checking out branch master Successfully checked out branch master Cloning PyOP2 Failed to clone PyOP2 using ssh, falling back to https. Successfully cloned repository PyOP2. Checking out branch master Successfully checked out branch master Cloning the dependencies of PyOP2 Cloning petsc Failed to clone petsc using ssh, falling back to https. Successfully cloned repository petsc. Checking out branch firedrake Successfully checked out branch firedrake Cloning petsc4py Failed to clone petsc4py using ssh, falling back to https. Successfully cloned repository petsc4py. Checking out branch firedrake Successfully checked out branch firedrake Cloning COFFEE Failed to clone COFFEE using ssh, falling back to https. Successfully cloned repository COFFEE. Checking out branch master Successfully checked out branch master Installing petsc/ Downloading Eigen from 'https://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz' to 'eigen-3.3.3.tgz' Checking Eigen tarball integrity Eigen tarball hash valid Building PETSc. Depending on your platform, may take between a few minutes and an hour or more to build! Traceback (most recent call last): File "firedrake-install", line 1074, in <module> install("petsc/") File "firedrake-install", line 554, in install build_and_install_petsc() File "firedrake-install", line 660, in build_and_install_petsc run_pip_install(["--ignore-installed", "petsc/"]) File "firedrake-install", line 529, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 366, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/usr/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/usr/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/home/amireh/firedrake/bin/python', '-m', 'pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '--ignore-installed', 'petsc/']' returned non-zero exit status 1. Install log saved in firedrake-install.log Please guide me to install. Best regards, Amireh
Hi Amireh, PETSc failed to install. In order to see why that happened, we need to look at your firedrake-install.log could you post that please? Regards David Sent from my iPhone On 30 May 2018, at 13:22, Amireh Mousavi <amireh.mousavi@math.iut.ac.ir<mailto:amireh.mousavi@math.iut.ac.ir>> wrote: Dear all, I tried to install Firedrake on Ubuntu 18.04 but I have problem on installation. Here are the errors I get: Running firedrake-install Checking for presence of package build-essential... installed. Checking for presence of package autoconf... installed. Checking for presence of package automake... installed. Checking for presence of package cmake... installed. Checking for presence of package gfortran... installed. Checking for presence of package git-core... missing. Checking for presence of package libblas-dev... installed. Checking for presence of package liblapack-dev... installed. Checking for presence of package libopenmpi-dev... installed. Checking for presence of package libtool... installed. Checking for presence of package mercurial... installed. Checking for presence of package openmpi-bin... installed. Checking for presence of package python3-dev... installed. Checking for presence of package python3-pip... installed. Checking for presence of package python3-tk... installed. Checking for presence of package python3-venv... installed. Checking for presence of package zlib1g-dev... installed. Installing missing packages: git-core. [sudo] password for amireh: Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'git' instead of 'git-core' git is already the newest version (1:2.17.0-1ubuntu1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Creating firedrake venv in '/home/amireh/firedrake'. Cloning firedrake Failed to clone firedrake using ssh, falling back to https. Successfully cloned repository firedrake. Checking out branch master Successfully checked out branch master Cloning the dependencies of firedrake Cloning ufl Failed to clone ufl using ssh, falling back to https. Successfully cloned repository ufl. Checking out branch master Successfully checked out branch master Cloning fiat Failed to clone fiat using ssh, falling back to https. Successfully cloned repository fiat. Checking out branch master Successfully checked out branch master Cloning FInAT Failed to clone FInAT using ssh, falling back to https. Successfully cloned repository FInAT. Checking out branch master Successfully checked out branch master Cloning tsfc Failed to clone tsfc using ssh, falling back to https. Successfully cloned repository tsfc. Checking out branch master Successfully checked out branch master Cloning PyOP2 Failed to clone PyOP2 using ssh, falling back to https. Successfully cloned repository PyOP2. Checking out branch master Successfully checked out branch master Cloning the dependencies of PyOP2 Cloning petsc Failed to clone petsc using ssh, falling back to https. Successfully cloned repository petsc. Checking out branch firedrake Successfully checked out branch firedrake Cloning petsc4py Failed to clone petsc4py using ssh, falling back to https. Successfully cloned repository petsc4py. Checking out branch firedrake Successfully checked out branch firedrake Cloning COFFEE Failed to clone COFFEE using ssh, falling back to https. Successfully cloned repository COFFEE. Checking out branch master Successfully checked out branch master Installing petsc/ Downloading Eigen from 'https://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz' to 'eigen-3.3.3.tgz' Checking Eigen tarball integrity Eigen tarball hash valid Building PETSc. Depending on your platform, may take between a few minutes and an hour or more to build! Traceback (most recent call last): File "firedrake-install", line 1074, in <module> install("petsc/") File "firedrake-install", line 554, in install build_and_install_petsc() File "firedrake-install", line 660, in build_and_install_petsc run_pip_install(["--ignore-installed", "petsc/"]) File "firedrake-install", line 529, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 366, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/usr/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/usr/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/home/amireh/firedrake/bin/python', '-m', 'pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '--ignore-installed', 'petsc/']' returned non-zero exit status 1. Install log saved in firedrake-install.log Please guide me to install. Best regards, Amireh _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Yes of course. The firedrake-install.log has been attached. -----Original Message----- From: "Ham, David A" <david.ham@imperial.ac.uk> To: firedrake <firedrake@imperial.ac.uk> Date: 09/03/97 13:11 Subject: Re: [firedrake] Error on Installation Hi Amireh, PETSc failed to install. In order to see why that happened, we need to look at your firedrake-install.log could you post that please? Regards David Sent from my iPhone On 30 May 2018, at 13:22, Amireh Mousavi <amireh.mousavi@math.iut.ac.ir> wrote: Dear all, I tried to install Firedrake on Ubuntu 18.04 but I have problem on installation. Here are the errors I get: Running firedrake-install Checking for presence of package build-essential... installed. Checking for presence of package autoconf... installed. Checking for presence of package automake... installed. Checking for presence of package cmake... installed. Checking for presence of package gfortran... installed. Checking for presence of package git-core... missing. Checking for presence of package libblas-dev... installed. Checking for presence of package liblapack-dev... installed. Checking for presence of package libopenmpi-dev... installed. Checking for presence of package libtool... installed. Checking for presence of package mercurial... installed. Checking for presence of package openmpi-bin... installed. Checking for presence of package python3-dev... installed. Checking for presence of package python3-pip... installed. Checking for presence of package python3-tk... installed. Checking for presence of package python3-venv... installed. Checking for presence of package zlib1g-dev... installed. Installing missing packages: git-core. [sudo] password for amireh: Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'git' instead of 'git-core' git is already the newest version (1:2.17.0-1ubuntu1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Creating firedrake venv in '/home/amireh/firedrake'. Cloning firedrake Failed to clone firedrake using ssh, falling back to https. Successfully cloned repository firedrake. Checking out branch master Successfully checked out branch master Cloning the dependencies of firedrake Cloning ufl Failed to clone ufl using ssh, falling back to https. Successfully cloned repository ufl. Checking out branch master Successfully checked out branch master Cloning fiat Failed to clone fiat using ssh, falling back to https. Successfully cloned repository fiat. Checking out branch master Successfully checked out branch master Cloning FInAT Failed to clone FInAT using ssh, falling back to https. Successfully cloned repository FInAT. Checking out branch master Successfully checked out branch master Cloning tsfc Failed to clone tsfc using ssh, falling back to https. Successfully cloned repository tsfc. Checking out branch master Successfully checked out branch master Cloning PyOP2 Failed to clone PyOP2 using ssh, falling back to https. Successfully cloned repository PyOP2. Checking out branch master Successfully checked out branch master Cloning the dependencies of PyOP2 Cloning petsc Failed to clone petsc using ssh, falling back to https. Successfully cloned repository petsc. Checking out branch firedrake Successfully checked out branch firedrake Cloning petsc4py Failed to clone petsc4py using ssh, falling back to https. Successfully cloned repository petsc4py. Checking out branch firedrake Successfully checked out branch firedrake Cloning COFFEE Failed to clone COFFEE using ssh, falling back to https. Successfully cloned repository COFFEE. Checking out branch master Successfully checked out branch master Installing petsc/ Downloading Eigen from 'https://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz' to 'eigen-3.3.3.tgz' Checking Eigen tarball integrity Eigen tarball hash valid Building PETSc. Depending on your platform, may take between a few minutes and an hour or more to build! Traceback (most recent call last): File "firedrake-install", line 1074, in <module> install("petsc/") File "firedrake-install", line 554, in install build_and_install_petsc() File "firedrake-install", line 660, in build_and_install_petsc run_pip_install(["--ignore-installed", "petsc/"]) File "firedrake-install", line 529, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 366, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/usr/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/usr/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/home/amireh/firedrake/bin/python', '-m', 'pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '--ignore-installed', 'petsc/']' returned non-zero exit status 1. Install log saved in firedrake-install.log Please guide me to install. Best regards, Amireh _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Ah. This log file isn’t from the install attempt you posted earlier. This log file is from a subsequent attempt which failed because the firedrake directory already existed from the previous attempt. Please rm -rf firedrake and then run the installer again. Please post the log file from this new attempt. Regards, David Dr David Ham Department of Mathematics Imperial College London On 30 May 2018, at 14:23, Amireh Mousavi <amireh.mousavi@math.iut.ac.ir<mailto:amireh.mousavi@math.iut.ac.ir>> wrote: Yes of course. The firedrake-install.log has been attached. ________________________________ -----Original Message----- From: "Ham, David A" <david.ham@imperial.ac.uk<mailto:david.ham@imperial.ac.uk>> To: firedrake <firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk>> Date: 09/03/97 13:11 Subject: Re: [firedrake] Error on Installation Hi Amireh, PETSc failed to install. In order to see why that happened, we need to look at your firedrake-install.log could you post that please? Regards David Sent from my iPhone On 30 May 2018, at 13:22, Amireh Mousavi <amireh.mousavi@math.iut.ac.ir<mailto:amireh.mousavi@math.iut.ac.ir>> wrote: Dear all, I tried to install Firedrake on Ubuntu 18.04 but I have problem on installation. Here are the errors I get: Running firedrake-install Checking for presence of package build-essential... installed. Checking for presence of package autoconf... installed. Checking for presence of package automake... installed. Checking for presence of package cmake... installed. Checking for presence of package gfortran... installed. Checking for presence of package git-core... missing. Checking for presence of package libblas-dev... installed. Checking for presence of package liblapack-dev... installed. Checking for presence of package libopenmpi-dev... installed. Checking for presence of package libtool... installed. Checking for presence of package mercurial... installed. Checking for presence of package openmpi-bin... installed. Checking for presence of package python3-dev... installed. Checking for presence of package python3-pip... installed. Checking for presence of package python3-tk... installed. Checking for presence of package python3-venv... installed. Checking for presence of package zlib1g-dev... installed. Installing missing packages: git-core. [sudo] password for amireh: Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'git' instead of 'git-core' git is already the newest version (1:2.17.0-1ubuntu1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Creating firedrake venv in '/home/amireh/firedrake'. Cloning firedrake Failed to clone firedrake using ssh, falling back to https. Successfully cloned repository firedrake. Checking out branch master Successfully checked out branch master Cloning the dependencies of firedrake Cloning ufl Failed to clone ufl using ssh, falling back to https. Successfully cloned repository ufl. Checking out branch master Successfully checked out branch master Cloning fiat Failed to clone fiat using ssh, falling back to https. Successfully cloned repository fiat. Checking out branch master Successfully checked out branch master Cloning FInAT Failed to clone FInAT using ssh, falling back to https. Successfully cloned repository FInAT. Checking out branch master Successfully checked out branch master Cloning tsfc Failed to clone tsfc using ssh, falling back to https. Successfully cloned repository tsfc. Checking out branch master Successfully checked out branch master Cloning PyOP2 Failed to clone PyOP2 using ssh, falling back to https. Successfully cloned repository PyOP2. Checking out branch master Successfully checked out branch master Cloning the dependencies of PyOP2 Cloning petsc Failed to clone petsc using ssh, falling back to https. Successfully cloned repository petsc. Checking out branch firedrake Successfully checked out branch firedrake Cloning petsc4py Failed to clone petsc4py using ssh, falling back to https. Successfully cloned repository petsc4py. Checking out branch firedrake Successfully checked out branch firedrake Cloning COFFEE Failed to clone COFFEE using ssh, falling back to https. Successfully cloned repository COFFEE. Checking out branch master Successfully checked out branch master Installing petsc/ Downloading Eigen from 'https://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz' to 'eigen-3.3.3.tgz' Checking Eigen tarball integrity Eigen tarball hash valid Building PETSc. Depending on your platform, may take between a few minutes and an hour or more to build! Traceback (most recent call last): File "firedrake-install", line 1074, in <module> install("petsc/") File "firedrake-install", line 554, in install build_and_install_petsc() File "firedrake-install", line 660, in build_and_install_petsc run_pip_install(["--ignore-installed", "petsc/"]) File "firedrake-install", line 529, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 366, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/usr/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/usr/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/home/amireh/firedrake/bin/python', '-m', 'pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '--ignore-installed', 'petsc/']' returned non-zero exit status 1. Install log saved in firedrake-install.log Please guide me to install. Best regards, Amireh _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake ________________________________ _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake <firedrake-install.log> _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
The attachment is the new log file. -----Original Message----- From: "Ham, David A" <david.ham@imperial.ac.uk> To: firedrake <firedrake@imperial.ac.uk> Date: 09/03/97 13:58 Subject: Re: [firedrake] Error on Installation Ah. This log file isn't from the install attempt you posted earlier. This log file is from a subsequent attempt which failed because the firedrake directory already existed from the previous attempt. Please rm -rf firedrake and then run the installer again. Please post the log file from this new attempt. Regards, David Dr David Ham Department of Mathematics Imperial College London On 30 May 2018, at 14:23, Amireh Mousavi <amireh.mousavi@math.iut.ac.ir> wrote: Yes of course. The firedrake-install.log has been attached. -----Original Message----- From: "Ham, David A" <david.ham@imperial.ac.uk> To: firedrake <firedrake@imperial.ac.uk> Date: 09/03/97 13:11 Subject: Re: [firedrake] Error on Installation Hi Amireh, PETSc failed to install. In order to see why that happened, we need to look at your firedrake-install.log could you post that please? Regards David Sent from my iPhone On 30 May 2018, at 13:22, Amireh Mousavi <amireh.mousavi@math.iut.ac.ir> wrote: Dear all, I tried to install Firedrake on Ubuntu 18.04 but I have problem on installation. Here are the errors I get: Running firedrake-install Checking for presence of package build-essential... installed. Checking for presence of package autoconf... installed. Checking for presence of package automake... installed. Checking for presence of package cmake... installed. Checking for presence of package gfortran... installed. Checking for presence of package git-core... missing. Checking for presence of package libblas-dev... installed. Checking for presence of package liblapack-dev... installed. Checking for presence of package libopenmpi-dev... installed. Checking for presence of package libtool... installed. Checking for presence of package mercurial... installed. Checking for presence of package openmpi-bin... installed. Checking for presence of package python3-dev... installed. Checking for presence of package python3-pip... installed. Checking for presence of package python3-tk... installed. Checking for presence of package python3-venv... installed. Checking for presence of package zlib1g-dev... installed. Installing missing packages: git-core. [sudo] password for amireh: Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'git' instead of 'git-core' git is already the newest version (1:2.17.0-1ubuntu1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Creating firedrake venv in '/home/amireh/firedrake'. Cloning firedrake Failed to clone firedrake using ssh, falling back to https. Successfully cloned repository firedrake. Checking out branch master Successfully checked out branch master Cloning the dependencies of firedrake Cloning ufl Failed to clone ufl using ssh, falling back to https. Successfully cloned repository ufl. Checking out branch master Successfully checked out branch master Cloning fiat Failed to clone fiat using ssh, falling back to https. Successfully cloned repository fiat. Checking out branch master Successfully checked out branch master Cloning FInAT Failed to clone FInAT using ssh, falling back to https. Successfully cloned repository FInAT. Checking out branch master Successfully checked out branch master Cloning tsfc Failed to clone tsfc using ssh, falling back to https. Successfully cloned repository tsfc. Checking out branch master Successfully checked out branch master Cloning PyOP2 Failed to clone PyOP2 using ssh, falling back to https. Successfully cloned repository PyOP2. Checking out branch master Successfully checked out branch master Cloning the dependencies of PyOP2 Cloning petsc Failed to clone petsc using ssh, falling back to https. Successfully cloned repository petsc. Checking out branch firedrake Successfully checked out branch firedrake Cloning petsc4py Failed to clone petsc4py using ssh, falling back to https. Successfully cloned repository petsc4py. Checking out branch firedrake Successfully checked out branch firedrake Cloning COFFEE Failed to clone COFFEE using ssh, falling back to https. Successfully cloned repository COFFEE. Checking out branch master Successfully checked out branch master Installing petsc/ Downloading Eigen from 'https://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz' to 'eigen-3.3.3.tgz' Checking Eigen tarball integrity Eigen tarball hash valid Building PETSc. Depending on your platform, may take between a few minutes and an hour or more to build! Traceback (most recent call last): File "firedrake-install", line 1074, in <module> install("petsc/") File "firedrake-install", line 554, in install build_and_install_petsc() File "firedrake-install", line 660, in build_and_install_petsc run_pip_install(["--ignore-installed", "petsc/"]) File "firedrake-install", line 529, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 366, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/usr/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/usr/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/home/amireh/firedrake/bin/python', '-m', 'pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '--ignore-installed', 'petsc/']' returned non-zero exit status 1. Install log saved in firedrake-install.log Please guide me to install. Best regards, Amireh _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake <firedrake-install.log> _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (2)
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Amireh Mousavi
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Ham, David A