Present installation issues with PETSc build
Dear firedrakers, some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen). This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so. As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so: $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional. A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed. I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us. Thanks, and apologies for any problems this might be causing, Lawrence
This issue should now be "fixed". On 10/04/17 10:47, Lawrence Mitchell wrote:
Dear firedrakers,
some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen).
This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so.
As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so:
$ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update
This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional.
A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed.
I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us.
Thanks, and apologies for any problems this might be causing,
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Hi Miklos, The install script still fails at the eigen step for me. Regards Will =============================================================================== Trying to download hg://https://bitbucket.org/eigen/eigen/ for EIGEN =============================================================================== ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error during download/extract/detection of EIGEN: Unable to download eigen Could not execute "hg clone https://bitbucket.org/eigen/eigen/ /tmp/pip-QhWszv-build/arch-python-linux-x86_64/externalpackages/hg.eigen": Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site Unable to download package EIGEN from: hg://https://bitbucket.org/eigen/eigen/ * If URL specified manually - perhaps there is a typo? * If your network is disconnected - please reconnect and rerun ./configure * Or perhaps you have a firewall blocking the download * You can run with --with-packages-dir=/adirectory and ./configure will instruct you what packages to download manually * or you can download the above URL manually, to /yourselectedlocation and use the configure option: --download-eigen=/yourselectedlocation ******************************************************************************* Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-QhWszv-build/setup.py", line 302, in <module> **metadata) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip-QhWszv-build/setup.py", line 218, in run config(prefix, self.dry_run) File "/tmp/pip-QhWszv-build/setup.py", line 148, in config if status != 0: raise RuntimeError(status) RuntimeError: 256 ---------------------------------------- Command "/localhome/scwb/firedrake/2017-04-20/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-QhWszv-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-yQIUun-record/install-record.txt --single-version-externally-managed --compile --install-headers /localhome/scwb/firedrake/2017-04-20/firedrake/include/site/python2.7/petsc" failed with error code 1 in /tmp/pip-QhWszv-build/ Traceback (most recent call last): File "firedrake-install", line 1310, in <module> install("petsc/") File "firedrake-install", line 754, in install run_pip_install(["--ignore-installed", package]) File "firedrake-install", line 624, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 369, in check_call subprocess.check_call(arguments, env=env) File "/opt/modules/python/2.7.9/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/localhome/scwb/firedrake/2017-04-20/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero exit status 1 ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Miklós Homolya <m.homolya14@imperial.ac.uk> Sent: 20 April 2017 10:37:29 To: firedrake@imperial.ac.uk Subject: Re: [firedrake] Present installation issues with PETSc build This issue should now be "fixed". On 10/04/17 10:47, Lawrence Mitchell wrote:
Dear firedrakers,
some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen).
This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so.
As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so:
$ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update
This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional.
A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed.
I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us.
Thanks, and apologies for any problems this might be causing,
Lawrence _______________________________________________ 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
This looks like that earlier problem that Eigen sometimes fails to download. Can you just try again? Also make sure that you re-download the install script so that you run the latest version. On 20/04/17 10:47, William Booker wrote:
Hi Miklos,
The install script still fails at the eigen step for me.
Regards Will
=============================================================================== Trying to download hg://https://bitbucket.org/eigen/eigen/ for EIGEN =============================================================================== ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error during download/extract/detection of EIGEN: Unable to download eigen Could not execute "hg clone https://bitbucket.org/eigen/eigen/ /tmp/pip-QhWszv-build/arch-python-linux-x86_64/externalpackages/hg.eigen": Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site Unable to download package EIGEN from: hg://https://bitbucket.org/eigen/eigen/ * If URL specified manually - perhaps there is a typo? * If your network is disconnected - please reconnect and rerun ./configure * Or perhaps you have a firewall blocking the download * You can run with --with-packages-dir=/adirectory and ./configure will instruct you what packages to download manually * or you can download the above URL manually, to /yourselectedlocation and use the configure option: --download-eigen=/yourselectedlocation ******************************************************************************* Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-QhWszv-build/setup.py", line 302, in <module> **metadata) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip-QhWszv-build/setup.py", line 218, in run config(prefix, self.dry_run) File "/tmp/pip-QhWszv-build/setup.py", line 148, in config if status != 0: raise RuntimeError(status) RuntimeError: 256 ---------------------------------------- Command "/localhome/scwb/firedrake/2017-04-20/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-QhWszv-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-yQIUun-record/install-record.txt --single-version-externally-managed --compile --install-headers /localhome/scwb/firedrake/2017-04-20/firedrake/include/site/python2.7/petsc" failed with error code 1 in /tmp/pip-QhWszv-build/ Traceback (most recent call last): File "firedrake-install", line 1310, in <module> install("petsc/") File "firedrake-install", line 754, in install run_pip_install(["--ignore-installed", package]) File "firedrake-install", line 624, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 369, in check_call subprocess.check_call(arguments, env=env) File "/opt/modules/python/2.7.9/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/localhome/scwb/firedrake/2017-04-20/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero exit status 1
------------------------------------------------------------------------ *From:* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Miklós Homolya <m.homolya14@imperial.ac.uk> *Sent:* 20 April 2017 10:37:29 *To:* firedrake@imperial.ac.uk *Subject:* Re: [firedrake] Present installation issues with PETSc build This issue should now be "fixed".
On 10/04/17 10:47, Lawrence Mitchell wrote:
Dear firedrakers,
some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen).
This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so.
As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so:
$ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update
This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional.
A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed.
I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us.
Thanks, and apologies for any problems this might be causing,
Lawrence _______________________________________________ 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 mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Hi Miklos, Reran again to make sure, still fails at the eigen step. Curl should mean I've got the latest install script unless the location has changed. Thanks Will ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Miklós Homolya <m.homolya14@imperial.ac.uk> Sent: 20 April 2017 11:51:22 To: firedrake@imperial.ac.uk Subject: Re: [firedrake] Present installation issues with PETSc build This looks like that earlier problem that Eigen sometimes fails to download. Can you just try again? Also make sure that you re-download the install script so that you run the latest version. On 20/04/17 10:47, William Booker wrote: Hi Miklos, The install script still fails at the eigen step for me. Regards Will =============================================================================== Trying to download hg://https://bitbucket.org/eigen/eigen/ for EIGEN =============================================================================== ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error during download/extract/detection of EIGEN: Unable to download eigen Could not execute "hg clone https://bitbucket.org/eigen/eigen/ /tmp/pip-QhWszv-build/arch-python-linux-x86_64/externalpackages/hg.eigen": Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site Unable to download package EIGEN from: hg://https://bitbucket.org/eigen/eigen/ * If URL specified manually - perhaps there is a typo? * If your network is disconnected - please reconnect and rerun ./configure * Or perhaps you have a firewall blocking the download * You can run with --with-packages-dir=/adirectory and ./configure will instruct you what packages to download manually * or you can download the above URL manually, to /yourselectedlocation and use the configure option: --download-eigen=/yourselectedlocation ******************************************************************************* Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-QhWszv-build/setup.py", line 302, in <module> **metadata) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip-QhWszv-build/setup.py", line 218, in run config(prefix, self.dry_run) File "/tmp/pip-QhWszv-build/setup.py", line 148, in config if status != 0: raise RuntimeError(status) RuntimeError: 256 ---------------------------------------- Command "/localhome/scwb/firedrake/2017-04-20/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-QhWszv-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-yQIUun-record/install-record.txt --single-version-externally-managed --compile --install-headers /localhome/scwb/firedrake/2017-04-20/firedrake/include/site/python2.7/petsc" failed with error code 1 in /tmp/pip-QhWszv-build/ Traceback (most recent call last): File "firedrake-install", line 1310, in <module> install("petsc/") File "firedrake-install", line 754, in install run_pip_install(["--ignore-installed", package]) File "firedrake-install", line 624, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 369, in check_call subprocess.check_call(arguments, env=env) File "/opt/modules/python/2.7.9/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/localhome/scwb/firedrake/2017-04-20/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero exit status 1 ________________________________ From: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk><mailto:firedrake-bounces@imperial.ac.uk> on behalf of Miklós Homolya <m.homolya14@imperial.ac.uk><mailto:m.homolya14@imperial.ac.uk> Sent: 20 April 2017 10:37:29 To: firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> Subject: Re: [firedrake] Present installation issues with PETSc build This issue should now be "fixed". On 10/04/17 10:47, Lawrence Mitchell wrote:
Dear firedrakers,
some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen).
This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so.
As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so:
$ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update
This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional.
A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed.
I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us.
Thanks, and apologies for any problems this might be causing,
Lawrence _______________________________________________ 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 mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
I cannot reproduce your problem. Does the following work for you? $ hg clone https://bitbucket.org/eigen/eigen On 20/04/17 12:45, William Booker wrote:
Hi Miklos,
Reran again to make sure, still fails at the eigen step. Curl should mean I've got the latest install script unless the location has changed.
Thanks Will
------------------------------------------------------------------------ *From:* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Miklós Homolya <m.homolya14@imperial.ac.uk> *Sent:* 20 April 2017 11:51:22 *To:* firedrake@imperial.ac.uk *Subject:* Re: [firedrake] Present installation issues with PETSc build
This looks like that earlier problem that Eigen sometimes fails to download. Can you just try again?
Also make sure that you re-download the install script so that you run the latest version.
On 20/04/17 10:47, William Booker wrote:
Hi Miklos,
The install script still fails at the eigen step for me.
Regards Will
=============================================================================== Trying to download hg://https://bitbucket.org/eigen/eigen/ for EIGEN =============================================================================== ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error during download/extract/detection of EIGEN: Unable to download eigen Could not execute "hg clone https://bitbucket.org/eigen/eigen/ /tmp/pip-QhWszv-build/arch-python-linux-x86_64/externalpackages/hg.eigen": Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site Unable to download package EIGEN from: hg://https://bitbucket.org/eigen/eigen/ * If URL specified manually - perhaps there is a typo? * If your network is disconnected - please reconnect and rerun ./configure * Or perhaps you have a firewall blocking the download * You can run with --with-packages-dir=/adirectory and ./configure will instruct you what packages to download manually * or you can download the above URL manually, to /yourselectedlocation and use the configure option: --download-eigen=/yourselectedlocation ******************************************************************************* Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-QhWszv-build/setup.py", line 302, in <module> **metadata) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip-QhWszv-build/setup.py", line 218, in run config(prefix, self.dry_run) File "/tmp/pip-QhWszv-build/setup.py", line 148, in config if status != 0: raise RuntimeError(status) RuntimeError: 256 ---------------------------------------- Command "/localhome/scwb/firedrake/2017-04-20/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-QhWszv-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-yQIUun-record/install-record.txt --single-version-externally-managed --compile --install-headers /localhome/scwb/firedrake/2017-04-20/firedrake/include/site/python2.7/petsc" failed with error code 1 in /tmp/pip-QhWszv-build/ Traceback (most recent call last): File "firedrake-install", line 1310, in <module> install("petsc/") File "firedrake-install", line 754, in install run_pip_install(["--ignore-installed", package]) File "firedrake-install", line 624, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 369, in check_call subprocess.check_call(arguments, env=env) File "/opt/modules/python/2.7.9/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/localhome/scwb/firedrake/2017-04-20/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero exit status 1
------------------------------------------------------------------------ *From:* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Miklós Homolya <m.homolya14@imperial.ac.uk> *Sent:* 20 April 2017 10:37:29 *To:* firedrake@imperial.ac.uk *Subject:* Re: [firedrake] Present installation issues with PETSc build This issue should now be "fixed".
On 10/04/17 10:47, Lawrence Mitchell wrote:
Dear firedrakers,
some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen).
This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so.
As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so:
$ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update
This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional.
A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed.
I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us.
Thanks, and apologies for any problems this might be causing,
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake <https://mailman.ic.ac.uk/mailman/listinfo/firedrake>
_______________________________________________ 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 mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
The eigen clone worked. Will ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Miklós Homolya <m.homolya14@imperial.ac.uk> Sent: 20 April 2017 13:22:32 To: firedrake@imperial.ac.uk Subject: Re: [firedrake] Present installation issues with PETSc build I cannot reproduce your problem. Does the following work for you? $ hg clone https://bitbucket.org/eigen/eigen On 20/04/17 12:45, William Booker wrote: Hi Miklos, Reran again to make sure, still fails at the eigen step. Curl should mean I've got the latest install script unless the location has changed. Thanks Will ________________________________ From: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk><mailto:firedrake-bounces@imperial.ac.uk> on behalf of Miklós Homolya <m.homolya14@imperial.ac.uk><mailto:m.homolya14@imperial.ac.uk> Sent: 20 April 2017 11:51:22 To: firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> Subject: Re: [firedrake] Present installation issues with PETSc build This looks like that earlier problem that Eigen sometimes fails to download. Can you just try again? Also make sure that you re-download the install script so that you run the latest version. On 20/04/17 10:47, William Booker wrote: Hi Miklos, The install script still fails at the eigen step for me. Regards Will =============================================================================== Trying to download hg://https://bitbucket.org/eigen/eigen/ for EIGEN =============================================================================== ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error during download/extract/detection of EIGEN: Unable to download eigen Could not execute "hg clone https://bitbucket.org/eigen/eigen/ /tmp/pip-QhWszv-build/arch-python-linux-x86_64/externalpackages/hg.eigen": Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site Unable to download package EIGEN from: hg://https://bitbucket.org/eigen/eigen/ * If URL specified manually - perhaps there is a typo? * If your network is disconnected - please reconnect and rerun ./configure * Or perhaps you have a firewall blocking the download * You can run with --with-packages-dir=/adirectory and ./configure will instruct you what packages to download manually * or you can download the above URL manually, to /yourselectedlocation and use the configure option: --download-eigen=/yourselectedlocation ******************************************************************************* Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-QhWszv-build/setup.py", line 302, in <module> **metadata) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/opt/modules/python/2.7.9/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip-QhWszv-build/setup.py", line 218, in run config(prefix, self.dry_run) File "/tmp/pip-QhWszv-build/setup.py", line 148, in config if status != 0: raise RuntimeError(status) RuntimeError: 256 ---------------------------------------- Command "/localhome/scwb/firedrake/2017-04-20/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-QhWszv-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-yQIUun-record/install-record.txt --single-version-externally-managed --compile --install-headers /localhome/scwb/firedrake/2017-04-20/firedrake/include/site/python2.7/petsc" failed with error code 1 in /tmp/pip-QhWszv-build/ Traceback (most recent call last): File "firedrake-install", line 1310, in <module> install("petsc/") File "firedrake-install", line 754, in install run_pip_install(["--ignore-installed", package]) File "firedrake-install", line 624, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 369, in check_call subprocess.check_call(arguments, env=env) File "/opt/modules/python/2.7.9/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/localhome/scwb/firedrake/2017-04-20/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero exit status 1 ________________________________ From: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk><mailto:firedrake-bounces@imperial.ac.uk> on behalf of Miklós Homolya <m.homolya14@imperial.ac.uk><mailto:m.homolya14@imperial.ac.uk> Sent: 20 April 2017 10:37:29 To: firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> Subject: Re: [firedrake] Present installation issues with PETSc build This issue should now be "fixed". On 10/04/17 10:47, Lawrence Mitchell wrote:
Dear firedrakers,
some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen).
This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so.
As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so:
$ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update
This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional.
A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed.
I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us.
Thanks, and apologies for any problems this might be causing,
Lawrence _______________________________________________ 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 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
Dear all, we finally fixed (we hope!) these problems with the download and install of Eigen. At the same time, we've tried to make the installation a little more robust. If you download the firedrake-install script anew, you will no longer need to provide --download-eigen=0 to the install or update step. Do get in touch if there are any problems. Cheers, Lawrence On 10/04/17 10:47, Lawrence Mitchell wrote:
Dear firedrakers,
some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen).
This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so.
As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so:
$ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update
This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional.
A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed.
I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us.
Thanks, and apologies for any problems this might be causing,
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Hello Lawrence, Thanks for working on fixing this. I just tried doing an update an received the following, which I think means that there was an error. Is there an example that we can use to test eigen, to see if it was properly installed? Cheers, Francis Checking Eigen tarball integrity Eigen tarball hash valid Traceback (most recent call last): File "../bin/firedrake-update", line 1206, in <module> install("petsc/") File "../bin/firedrake-update", line 623, in install build_and_install_petsc() File "../bin/firedrake-update", line 691, in build_and_install_petsc run_pip_install(["--ignore-installed", "petsc/"]) File "../bin/firedrake-update", line 597, in run_pip_install check_call(pipinstall + pipargs) File "../bin/firedrake-update", line 357, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env)) File "/usr/lib/python2.7/subprocess.py", line 574, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command '['/home/fpoulin/software/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '--ignore-installed', 'petsc/']' returned non-zero exit status 1 Update log saved in firedrake-update.log ------------------ Francis Poulin Associate Professor Department of Applied Mathematics University of Waterloo email: fpoulin@uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 ________________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Lawrence Mitchell [lawrence.mitchell@imperial.ac.uk] Sent: Thursday, May 11, 2017 10:17 AM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] Present installation issues with PETSc build Dear all, we finally fixed (we hope!) these problems with the download and install of Eigen. At the same time, we've tried to make the installation a little more robust. If you download the firedrake-install script anew, you will no longer need to provide --download-eigen=0 to the install or update step. Do get in touch if there are any problems. Cheers, Lawrence On 10/04/17 10:47, Lawrence Mitchell wrote:
Dear firedrakers,
some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen).
This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so.
As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so:
$ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update
This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional.
A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed.
I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us.
Thanks, and apologies for any problems this might be causing,
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 13 May 2017, at 23:03, Francis Poulin <fpoulin@uwaterloo.ca> wrote:
Hello Lawrence,
Thanks for working on fixing this.
I just tried doing an update an received the following, which I think means that there was an error.
Is there an example that we can use to test eigen, to see if it was properly installed?
Cheers, Francis
Checking Eigen tarball integrity Eigen tarball hash valid Traceback (most recent call last): File "../bin/firedrake-update", line 1206, in <module> install("petsc/") File "../bin/firedrake-update", line 623, in install build_and_install_petsc() File "../bin/firedrake-update", line 691, in build_and_install_petsc run_pip_install(["--ignore-installed", "petsc/"]) File "../bin/firedrake-update", line 597, in run_pip_install check_call(pipinstall + pipargs) File "../bin/firedrake-update", line 357, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env)) File "/usr/lib/python2.7/subprocess.py", line 574, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command '['/home/fpoulin/software/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '--ignore-installed', 'petsc/']' returned non-zero exit status 1
Update log saved in firedrake-update.log
Can you post the contents of this log of the update? Lawrence
I decided to try it again today. For reasons I don't understand now it works. Thanks for fixing it and sorry for the bother. Cheers, Francis ------------------ Francis Poulin Associate Professor Department of Applied Mathematics University of Waterloo email: fpoulin@uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 ________________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Lawrence Mitchell [lawrence.mitchell@imperial.ac.uk] Sent: Sunday, May 14, 2017 10:55 AM To: firedrake Subject: Re: [firedrake] Present installation issues with PETSc build
On 13 May 2017, at 23:03, Francis Poulin <fpoulin@uwaterloo.ca> wrote:
Hello Lawrence,
Thanks for working on fixing this.
I just tried doing an update an received the following, which I think means that there was an error.
Is there an example that we can use to test eigen, to see if it was properly installed?
Cheers, Francis
Checking Eigen tarball integrity Eigen tarball hash valid Traceback (most recent call last): File "../bin/firedrake-update", line 1206, in <module> install("petsc/") File "../bin/firedrake-update", line 623, in install build_and_install_petsc() File "../bin/firedrake-update", line 691, in build_and_install_petsc run_pip_install(["--ignore-installed", "petsc/"]) File "../bin/firedrake-update", line 597, in run_pip_install check_call(pipinstall + pipargs) File "../bin/firedrake-update", line 357, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env)) File "/usr/lib/python2.7/subprocess.py", line 574, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command '['/home/fpoulin/software/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '--ignore-installed', 'petsc/']' returned non-zero exit status 1
Update log saved in firedrake-update.log
Can you post the contents of this log of the update? Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (4)
-
Francis Poulin
-
Lawrence Mitchell
-
Miklós Homolya
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William Booker