Hi All, I've just tried to install firedrake on my laptop and it's failing with errors in libsupermesh: Failed to clone libsupermesh using ssh, falling back to https. Successfully cloned repository libsupermesh. Checking out branch master Successfully checked out branch master Traceback (most recent call last): File "firedrake-install", line 1173, in <module> build_and_install_libsupermesh() File "firedrake-install", line 823, in build_and_install_libsupermesh check_call(["make"]) File "firedrake-install", line 438, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/usr/local/Cellar/python/3.6.5_1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/usr/local/Cellar/python/3.6.5_1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['make']' returned non-zero exit status 2. I've attached the log file. Any suggestions much appreciated! Jemma
On 6 Mar 2019, at 22:00, Shipton, Jemma <j.shipton@imperial.ac.uk> wrote:
Failed to clone libsupermesh using ssh, falling back to https. Successfully cloned repository libsupermesh. Checking out branch master Successfully checked out branch master Traceback (most recent call last): File "firedrake-install", line 1173, in <module> build_and_install_libsupermesh() File "firedrake-install", line 823, in build_and_install_libsupermesh check_call(["make"]) File "firedrake-install", line 438, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/usr/local/Cellar/python/3.6.5_1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/usr/local/Cellar/python/3.6.5_1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['make']' returned non-zero exit status 2.
It looks like libsupermesh (a new dependency) has some tests which use the c++ api to MPI. But that is deprecated for a long time and seemingly removed by openmpi 4 which you have? Lawrence
On 06/03/2019 23:06, Lawrence Mitchell wrote:
It looks like libsupermesh (a new dependency) has some tests which use the c++ api to MPI. But that is deprecated for a long time and seemingly removed by openmpi 4 which you have?
This should be fixed in libsupermesh PR #2: https://bitbucket.org/libsupermesh/libsupermesh/pull-requests/2/remove-depre... Patrick
Note that the HDF5 in PETSc currently also has OpenMPI 4.0.0 issues. See: https://github.com/firedrakeproject/firedrake/issues/1380 The workaround is probably to use MPICH (which is better for other reasons too). On 07/03/2019, 08:44, "firedrake-bounces@imperial.ac.uk on behalf of Patrick Farrell" <firedrake-bounces@imperial.ac.uk on behalf of patrick.farrell@maths.ox.ac.uk> wrote: On 06/03/2019 23:06, Lawrence Mitchell wrote: > It looks like libsupermesh (a new dependency) has some tests which use the c++ api to MPI. But that is deprecated for a long time and seemingly removed by openmpi 4 which you have? This should be fixed in libsupermesh PR #2: https://bitbucket.org/libsupermesh/libsupermesh/pull-requests/2/remove-depre... Patrick _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
We fixed that. I think its in 3.10.4, if not we release at the end of the month. Matt On Thu, Mar 7, 2019 at 4:08 AM Ham, David A <david.ham@imperial.ac.uk> wrote:
Note that the HDF5 in PETSc currently also has OpenMPI 4.0.0 issues. See: https://github.com/firedrakeproject/firedrake/issues/1380
The workaround is probably to use MPICH (which is better for other reasons too).
On 07/03/2019, 08:44, "firedrake-bounces@imperial.ac.uk on behalf of Patrick Farrell" <firedrake-bounces@imperial.ac.uk on behalf of patrick.farrell@maths.ox.ac.uk> wrote:
On 06/03/2019 23:06, Lawrence Mitchell wrote: > It looks like libsupermesh (a new dependency) has some tests which use the c++ api to MPI. But that is deprecated for a long time and seemingly removed by openmpi 4 which you have?
This should be fixed in libsupermesh PR #2:
https://bitbucket.org/libsupermesh/libsupermesh/pull-requests/2/remove-depre...
Patrick
_______________________________________________ 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
-- 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/>
OK. We probably need to move our PETSc pointer. From: Matthew Knepley <knepley@gmail.com> Date: Thursday, 7 March 2019 at 10:47 To: "Ham, David A" <david.ham@imperial.ac.uk> Cc: Patrick Farrell <patrick.farrell@maths.ox.ac.uk>, firedrake <firedrake@imperial.ac.uk> Subject: Re: [firedrake] firedrake install not working We fixed that. I think its in 3.10.4, if not we release at the end of the month. Matt On Thu, Mar 7, 2019 at 4:08 AM Ham, David A <david.ham@imperial.ac.uk<mailto:david.ham@imperial.ac.uk>> wrote: Note that the HDF5 in PETSc currently also has OpenMPI 4.0.0 issues. See: https://github.com/firedrakeproject/firedrake/issues/1380 The workaround is probably to use MPICH (which is better for other reasons too). On 07/03/2019, 08:44, "firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> on behalf of Patrick Farrell" <firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> on behalf of patrick.farrell@maths.ox.ac.uk<mailto:patrick.farrell@maths.ox.ac.uk>> wrote: On 06/03/2019 23:06, Lawrence Mitchell wrote: > It looks like libsupermesh (a new dependency) has some tests which use the c++ api to MPI. But that is deprecated for a long time and seemingly removed by openmpi 4 which you have? This should be fixed in libsupermesh PR #2: https://bitbucket.org/libsupermesh/libsupermesh/pull-requests/2/remove-depre... Patrick _______________________________________________ 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 -- 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 (6)
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Ham, David A
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Lawrence Mitchell
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Lawrence Mitchell
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Matthew Knepley
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Patrick Farrell
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Shipton, Jemma