Hi, I’m still attempting to get a stable version of firedrake installed on my MacBook, I have encountered an issue with PETSc. It first hit an issue with the file 'eigen-3.3.3.tgz’, so I downloaded this separately and modified the installation file to point it towards this. The installation seemingly got over this issue, but returned the following error on the command line. I’ve also attached the install log. Any help would be much appreciated! Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake-install", line 1650, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake-install", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake-install", line 1019, in build_and_install_petsc check_call(["make", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch), "all"]) File "/Users/os3918/Documents/firedrake-install", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['make', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', 'all']' returned non-zero exit status 2. Install log saved in /Users/os3918/Documents/firedrake-install.log
Hi Oliver, It seems that your eigen is at "/Users/os3918/Documents/eigen-3.3.3.tgz", but Firedrake still tells PETSc that eigen is at "/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz"; this path is hard-coded here https://github.com/firedrakeproject/firedrake/blob/master/scripts/firedrake-.... I think the easiest solution is, using your failed installation, to move eigen-3.3.3.tgz to "/Users/os3918/Documents/firedrake/src", activate firedrake venv, and run `firedrake-update --rebuild` (using unmodified install script). Thanks, Koki ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Ollie Street <olliestreet@outlook.com> Sent: Thursday, November 25, 2021 11:13 AM To: firedrake <firedrake@imperial.ac.uk> Subject: [firedrake] Installation issue Hi, I’m still attempting to get a stable version of firedrake installed on my MacBook, I have encountered an issue with PETSc. It first hit an issue with the file 'eigen-3.3.3.tgz’, so I downloaded this separately and modified the installation file to point it towards this. The installation seemingly got over this issue, but returned the following error on the command line. I’ve also attached the install log. Any help would be much appreciated! Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake-install", line 1650, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake-install", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake-install", line 1019, in build_and_install_petsc check_call(["make", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch), "all"]) File "/Users/os3918/Documents/firedrake-install", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['make', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', 'all']' returned non-zero exit status 2. Install log saved in /Users/os3918/Documents/firedrake-install.log
Hi Koki, Thanks for your reply and your suggestion. I implemented those steps and it’s given me another error seemingly related to C compilers - it’s also given me an update log. Any ideas? Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1766, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1017, in build_and_install_petsc check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch)] + petsc_options) File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Users/os3918/Documents/firedrake/bin/python', './configure', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', '--download-hwloc', '--download-superlu_dist', '--download-hdf5', '--download-mpich', '--download-mpich-configure-arguments=--disable-opencl', '--with-fortran-bindings=0', '--with-x=0', '--download-chaco', '--download-pastix', '--with-cxx-dialect=C++11', '--CFLAGS=-I/usr/local/opt/openblas/include -Wno-implicit-function-declaration', '--with-zlib', '--download-metis', '--download-eigen=/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz ', '--LDFLAGS=-Wl,-rpath,/usr/local/opt/openblas/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gcc/lib/gcc/8', '--download-hypre', '--with-debugging=0', '--download-hwloc-configure-arguments=--disable-opencl', '--download-netcdf', '--download-scalapack', '--with-c2html=0', '--download-ptscotch', '--with-shared-libraries=1', '--download-mumps', '--download-pnetcdf', '--download-suitesparse', '--with-blaslapack-dir=/usr/local/opt/openblas', '--download-ml']' returned non-zero exit status 1. Update log saved in /Users/os3918/Documents/firedrake/firedrake-update.log On 26 Nov 2021, at 00:29, Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>> wrote: Hi Oliver, It seems that your eigen is at "/Users/os3918/Documents/eigen-3.3.3.tgz", but Firedrake still tells PETSc that eigen is at "/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz"; this path is hard-coded here https://github.com/firedrakeproject/firedrake/blob/master/scripts/firedrake-.... I think the easiest solution is, using your failed installation, to move eigen-3.3.3.tgz to "/Users/os3918/Documents/firedrake/src", activate firedrake venv, and run `firedrake-update --rebuild` (using unmodified install script). Thanks, Koki ________________________________ 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 Ollie Street <olliestreet@outlook.com<mailto:olliestreet@outlook.com>> Sent: Thursday, November 25, 2021 11:13 AM To: firedrake <firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk>> Subject: [firedrake] Installation issue Hi, I’m still attempting to get a stable version of firedrake installed on my MacBook, I have encountered an issue with PETSc. It first hit an issue with the file 'eigen-3.3.3.tgz’, so I downloaded this separately and modified the installation file to point it towards this. The installation seemingly got over this issue, but returned the following error on the command line. I’ve also attached the install log. Any help would be much appreciated! Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake-install", line 1650, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake-install", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake-install", line 1019, in build_and_install_petsc check_call(["make", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch), "all"]) File "/Users/os3918/Documents/firedrake-install", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['make', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', 'all']' returned non-zero exit status 2. Install log saved in /Users/os3918/Documents/firedrake-install.log
Hi Oliver, I'm not sure. Could you also post "/Users/os3918/Documents/firedrake/src/petsc/configure.log"? Thanks, Koki ________________________________ From: Street, Oliver <o.street18@imperial.ac.uk> Sent: Friday, November 26, 2021 11:50 AM To: Sagiyama, Koki <k.sagiyama@imperial.ac.uk>; firedrake <firedrake@imperial.ac.uk> Subject: Re: Installation issue Hi Koki, Thanks for your reply and your suggestion. I implemented those steps and it’s given me another error seemingly related to C compilers - it’s also given me an update log. Any ideas? Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1766, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1017, in build_and_install_petsc check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch)] + petsc_options) File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Users/os3918/Documents/firedrake/bin/python', './configure', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', '--download-hwloc', '--download-superlu_dist', '--download-hdf5', '--download-mpich', '--download-mpich-configure-arguments=--disable-opencl', '--with-fortran-bindings=0', '--with-x=0', '--download-chaco', '--download-pastix', '--with-cxx-dialect=C++11', '--CFLAGS=-I/usr/local/opt/openblas/include -Wno-implicit-function-declaration', '--with-zlib', '--download-metis', '--download-eigen=/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz ', '--LDFLAGS=-Wl,-rpath,/usr/local/opt/openblas/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gcc/lib/gcc/8', '--download-hypre', '--with-debugging=0', '--download-hwloc-configure-arguments=--disable-opencl', '--download-netcdf', '--download-scalapack', '--with-c2html=0', '--download-ptscotch', '--with-shared-libraries=1', '--download-mumps', '--download-pnetcdf', '--download-suitesparse', '--with-blaslapack-dir=/usr/local/opt/openblas', '--download-ml']' returned non-zero exit status 1. Update log saved in /Users/os3918/Documents/firedrake/firedrake-update.log On 26 Nov 2021, at 00:29, Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>> wrote: Hi Oliver, It seems that your eigen is at "/Users/os3918/Documents/eigen-3.3.3.tgz", but Firedrake still tells PETSc that eigen is at "/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz"; this path is hard-coded here https://github.com/firedrakeproject/firedrake/blob/master/scripts/firedrake-.... I think the easiest solution is, using your failed installation, to move eigen-3.3.3.tgz to "/Users/os3918/Documents/firedrake/src", activate firedrake venv, and run `firedrake-update --rebuild` (using unmodified install script). Thanks, Koki ________________________________ 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 Ollie Street <olliestreet@outlook.com<mailto:olliestreet@outlook.com>> Sent: Thursday, November 25, 2021 11:13 AM To: firedrake <firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk>> Subject: [firedrake] Installation issue Hi, I’m still attempting to get a stable version of firedrake installed on my MacBook, I have encountered an issue with PETSc. It first hit an issue with the file 'eigen-3.3.3.tgz’, so I downloaded this separately and modified the installation file to point it towards this. The installation seemingly got over this issue, but returned the following error on the command line. I’ve also attached the install log. Any help would be much appreciated! Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake-install", line 1650, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake-install", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake-install", line 1019, in build_and_install_petsc check_call(["make", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch), "all"]) File "/Users/os3918/Documents/firedrake-install", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['make', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', 'all']' returned non-zero exit status 2. Install log saved in /Users/os3918/Documents/firedrake-install.log
Hi Koki, Of course, see attached. Best, Oliver On 26 Nov 2021, at 14:45, Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>> wrote: Hi Oliver, I'm not sure. Could you also post "/Users/os3918/Documents/firedrake/src/petsc/configure.log"? Thanks, Koki ________________________________ From: Street, Oliver <o.street18@imperial.ac.uk<mailto:o.street18@imperial.ac.uk>> Sent: Friday, November 26, 2021 11:50 AM To: Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>>; firedrake <firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk>> Subject: Re: Installation issue Hi Koki, Thanks for your reply and your suggestion. I implemented those steps and it’s given me another error seemingly related to C compilers - it’s also given me an update log. Any ideas? Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1766, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1017, in build_and_install_petsc check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch)] + petsc_options) File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Users/os3918/Documents/firedrake/bin/python', './configure', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', '--download-hwloc', '--download-superlu_dist', '--download-hdf5', '--download-mpich', '--download-mpich-configure-arguments=--disable-opencl', '--with-fortran-bindings=0', '--with-x=0', '--download-chaco', '--download-pastix', '--with-cxx-dialect=C++11', '--CFLAGS=-I/usr/local/opt/openblas/include -Wno-implicit-function-declaration', '--with-zlib', '--download-metis', '--download-eigen=/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz ', '--LDFLAGS=-Wl,-rpath,/usr/local/opt/openblas/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gcc/lib/gcc/8', '--download-hypre', '--with-debugging=0', '--download-hwloc-configure-arguments=--disable-opencl', '--download-netcdf', '--download-scalapack', '--with-c2html=0', '--download-ptscotch', '--with-shared-libraries=1', '--download-mumps', '--download-pnetcdf', '--download-suitesparse', '--with-blaslapack-dir=/usr/local/opt/openblas', '--download-ml']' returned non-zero exit status 1. Update log saved in /Users/os3918/Documents/firedrake/firedrake-update.log On 26 Nov 2021, at 00:29, Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>> wrote: Hi Oliver, It seems that your eigen is at "/Users/os3918/Documents/eigen-3.3.3.tgz", but Firedrake still tells PETSc that eigen is at "/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz"; this path is hard-coded here https://github.com/firedrakeproject/firedrake/blob/master/scripts/firedrake-.... I think the easiest solution is, using your failed installation, to move eigen-3.3.3.tgz to "/Users/os3918/Documents/firedrake/src", activate firedrake venv, and run `firedrake-update --rebuild` (using unmodified install script). Thanks, Koki ________________________________ 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 Ollie Street <olliestreet@outlook.com<mailto:olliestreet@outlook.com>> Sent: Thursday, November 25, 2021 11:13 AM To: firedrake <firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk>> Subject: [firedrake] Installation issue Hi, I’m still attempting to get a stable version of firedrake installed on my MacBook, I have encountered an issue with PETSc. It first hit an issue with the file 'eigen-3.3.3.tgz’, so I downloaded this separately and modified the installation file to point it towards this. The installation seemingly got over this issue, but returned the following error on the command line. I’ve also attached the install log. Any help would be much appreciated! Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake-install", line 1650, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake-install", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake-install", line 1019, in build_and_install_petsc check_call(["make", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch), "all"]) File "/Users/os3918/Documents/firedrake-install", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['make', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', 'all']' returned non-zero exit status 2. Install log saved in /Users/os3918/Documents/firedrake-install.log
On Sat, Nov 27, 2021 at 5:41 AM Street, Oliver <o.street18@imperial.ac.uk> wrote:
Hi Koki,
Of course, see attached.
You have this configure argument --LDFLAGS="-Wl,-rpath,/usr/local/opt/openblas/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gcc/lib/gcc/8" but the directory /usr/local/opt/gcc/lib/gcc/8 does not exist. I am guessing that something is screwed up in the environment and Firedrake is not catching it. Thanks, Matt Best,
Oliver
On 26 Nov 2021, at 14:45, Sagiyama, Koki <k.sagiyama@imperial.ac.uk> wrote:
Hi Oliver,
I'm not sure. Could you also post "/Users/os3918/Documents/firedrake/src/petsc/configure.log"?
Thanks, Koki ------------------------------ *From:* Street, Oliver <o.street18@imperial.ac.uk> *Sent:* Friday, November 26, 2021 11:50 AM *To:* Sagiyama, Koki <k.sagiyama@imperial.ac.uk>; firedrake < firedrake@imperial.ac.uk> *Subject:* Re: Installation issue
Hi Koki, Thanks for your reply and your suggestion. I implemented those steps and it’s given me another error seemingly related to C compilers - it’s also given me an update log. Any ideas? Best, Oliver
Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1766, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1017, in build_and_install_petsc check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch)] + petsc_options) File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Users/os3918/Documents/firedrake/bin/python', './configure', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', '--download-hwloc', '--download-superlu_dist', '--download-hdf5', '--download-mpich', '--download-mpich-configure-arguments=--disable-opencl', '--with-fortran-bindings=0', '--with-x=0', '--download-chaco', '--download-pastix', '--with-cxx-dialect=C++11', '--CFLAGS=-I/usr/local/opt/openblas/include -Wno-implicit-function-declaration', '--with-zlib', '--download-metis', '--download-eigen=/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz ', '--LDFLAGS=-Wl,-rpath,/usr/local/opt/openblas/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gcc/lib/gcc/8', '--download-hypre', '--with-debugging=0', '--download-hwloc-configure-arguments=--disable-opencl', '--download-netcdf', '--download-scalapack', '--with-c2html=0', '--download-ptscotch', '--with-shared-libraries=1', '--download-mumps', '--download-pnetcdf', '--download-suitesparse', '--with-blaslapack-dir=/usr/local/opt/openblas', '--download-ml']' returned non-zero exit status 1.
Update log saved in /Users/os3918/Documents/firedrake/firedrake-update.log
On 26 Nov 2021, at 00:29, Sagiyama, Koki <k.sagiyama@imperial.ac.uk> wrote:
Hi Oliver,
It seems that your eigen is at "/Users/os3918/Documents/eigen-3.3.3.tgz", but Firedrake still tells PETSc that eigen is at "/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz"; this path is hard-coded here https://github.com/firedrakeproject/firedrake/blob/master/scripts/firedrake-... .
I think the easiest solution is, using your failed installation, to move eigen-3.3.3.tgz to "/Users/os3918/Documents/firedrake/src", activate firedrake venv, and run `firedrake-update --rebuild` (using unmodified install script).
Thanks, Koki
------------------------------
*From:* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Ollie Street <olliestreet@outlook.com> *Sent:* Thursday, November 25, 2021 11:13 AM *To:* firedrake <firedrake@imperial.ac.uk> *Subject:* [firedrake] Installation issue
Hi, I’m still attempting to get a stable version of firedrake installed on my MacBook, I have encountered an issue with PETSc. It first hit an issue with the file 'eigen-3.3.3.tgz’, so I downloaded this separately and modified the installation file to point it towards this. The installation seemingly got over this issue, but returned the following error on the command line. I’ve also attached the install log. Any help would be much appreciated! Best, Oliver
Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake-install", line 1650, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake-install", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake-install", line 1019, in build_and_install_petsc check_call(["make", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch), "all"]) File "/Users/os3918/Documents/firedrake-install", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['make', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', 'all']' returned non-zero exit status 2.
Install log saved in /Users/os3918/Documents/firedrake-install.log
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
Thanks for spotting this, I suppose Firedrake can’t find a C compiler. Can anyone advise me how to rectify this? Best, Oliver On 27 Nov 2021, at 12:59, Matthew Knepley <knepley@gmail.com<mailto:knepley@gmail.com>> wrote: This email from knepley@gmail.com<mailto:knepley@gmail.com> originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. On Sat, Nov 27, 2021 at 5:41 AM Street, Oliver <o.street18@imperial.ac.uk<mailto:o.street18@imperial.ac.uk>> wrote: Hi Koki, Of course, see attached. You have this configure argument --LDFLAGS="-Wl,-rpath,/usr/local/opt/openblas/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gcc/lib/gcc/8" but the directory /usr/local/opt/gcc/lib/gcc/8 does not exist. I am guessing that something is screwed up in the environment and Firedrake is not catching it. Thanks, Matt Best, Oliver On 26 Nov 2021, at 14:45, Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>> wrote: Hi Oliver, I'm not sure. Could you also post "/Users/os3918/Documents/firedrake/src/petsc/configure.log"? Thanks, Koki ________________________________ From: Street, Oliver <o.street18@imperial.ac.uk<mailto:o.street18@imperial.ac.uk>> Sent: Friday, November 26, 2021 11:50 AM To: Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>>; firedrake <firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk>> Subject: Re: Installation issue Hi Koki, Thanks for your reply and your suggestion. I implemented those steps and it’s given me another error seemingly related to C compilers - it’s also given me an update log. Any ideas? Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1766, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 1017, in build_and_install_petsc check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch)] + petsc_options) File "/Users/os3918/Documents/firedrake/src/../bin/firedrake-update", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Users/os3918/Documents/firedrake/bin/python', './configure', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', '--download-hwloc', '--download-superlu_dist', '--download-hdf5', '--download-mpich', '--download-mpich-configure-arguments=--disable-opencl', '--with-fortran-bindings=0', '--with-x=0', '--download-chaco', '--download-pastix', '--with-cxx-dialect=C++11', '--CFLAGS=-I/usr/local/opt/openblas/include -Wno-implicit-function-declaration', '--with-zlib', '--download-metis', '--download-eigen=/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz ', '--LDFLAGS=-Wl,-rpath,/usr/local/opt/openblas/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gcc/lib/gcc/8', '--download-hypre', '--with-debugging=0', '--download-hwloc-configure-arguments=--disable-opencl', '--download-netcdf', '--download-scalapack', '--with-c2html=0', '--download-ptscotch', '--with-shared-libraries=1', '--download-mumps', '--download-pnetcdf', '--download-suitesparse', '--with-blaslapack-dir=/usr/local/opt/openblas', '--download-ml']' returned non-zero exit status 1. Update log saved in /Users/os3918/Documents/firedrake/firedrake-update.log On 26 Nov 2021, at 00:29, Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>> wrote: Hi Oliver, It seems that your eigen is at "/Users/os3918/Documents/eigen-3.3.3.tgz", but Firedrake still tells PETSc that eigen is at "/Users/os3918/Documents/firedrake/src/eigen-3.3.3.tgz"; this path is hard-coded here https://github.com/firedrakeproject/firedrake/blob/master/scripts/firedrake-.... I think the easiest solution is, using your failed installation, to move eigen-3.3.3.tgz to "/Users/os3918/Documents/firedrake/src", activate firedrake venv, and run `firedrake-update --rebuild` (using unmodified install script). Thanks, Koki ________________________________ 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 Ollie Street <olliestreet@outlook.com<mailto:olliestreet@outlook.com>> Sent: Thursday, November 25, 2021 11:13 AM To: firedrake <firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk>> Subject: [firedrake] Installation issue Hi, I’m still attempting to get a stable version of firedrake installed on my MacBook, I have encountered an issue with PETSc. It first hit an issue with the file 'eigen-3.3.3.tgz’, so I downloaded this separately and modified the installation file to point it towards this. The installation seemingly got over this issue, but returned the following error on the command line. I’ve also attached the install log. Any help would be much appreciated! Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake-install", line 1650, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake-install", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake-install", line 1019, in build_and_install_petsc check_call(["make", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch), "all"]) File "/Users/os3918/Documents/firedrake-install", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['make', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', 'all']' returned non-zero exit status 2. Install log saved in /Users/os3918/Documents/firedrake-install.log _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knepley/>
participants (4)
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Matthew Knepley
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Ollie Street
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Sagiyama, Koki
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Street, Oliver