So the first important error message I can see in the log is:
-----------------------------------------------------------------------------------------------------
checking for library 'lmpe' ...
/gpfs/ts0/shared/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=native -fPIC -fPIC -c _configtest.c -o _configtest.o
/gpfs/ts0/shared/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/bin/mpicc _configtest.o -llmpe -o _configtest
/gpfs/ts0/shared/software/binutils/2.25-GCCcore-4.9.3/bin/ld.gold: error: cannot find -llmpe
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'mpe' dylib library
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/src
creating build/temp.linux-x86_64-3.5/src/lib-pmpi
/gpfs/ts0/shared/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O3 -march=native -fPIC -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-3.5/src/lib-pmpi/mpe.o
creating build/lib.linux-x86_64-3.5/mpi4py/lib-pmpi
...
-----------------------------------------------------------------------------------------------------
- To me it looks like the installer managed to work around the error but I am not certain.....?
Then further down the log there are a number of syntax-type errors. Here are the fist few:
-----------------------------------------------------------------------------------------------------
Removing source in /tmp/pip-build-b2dkectq/wrapt
*** Error compiling '/tmp/pip-build-b2dkectq/astroid/astroid/tests/testdata/python2/data/all.py'...
File "/tmp/pip-build-b2dkectq/astroid/astroid/tests/testdata/python2/data/all.py", line 7
def func(): print 'yo'
^
SyntaxError: invalid syntax
*** Error compiling '/tmp/pip-build-b2dkectq/astroid/astroid/tests/testdata/python2/data/invalid_encoding.py'...
File "/tmp/pip-build-b2dkectq/astroid/astroid/tests/testdata/python2/data/invalid_encoding.py", line 0
SyntaxError: unknown encoding: lala
*** Error compiling '/tmp/pip-build-b2dkectq/astroid/astroid/tests/testdata/python2/data/module.py'...
File "/tmp/pip-build-b2dkectq/astroid/astroid/tests/testdata/python2/data/module.py", line 32
except ValueError, ex:
^
SyntaxError: invalid syntax
*** Error compiling '/tmp/pip-build-b2dkectq/astroid/astroid/tests/testdata/python2/data/module2.py'...
File "/tmp/pip-build-b2dkectq/astroid/astroid/tests/testdata/python2/data/module2.py", line 78
exec 'c = 3'
^
SyntaxError: Missing parentheses in call to 'exec'
-----------------------------------------------------------------------------------------------------
P
Previously I did search the firedrake-install.log file for pattern 'netcdf4'...this is the last occurrence:
Looking up "https://pypi.python.org/packages/c0/06/c59f37661ede4f9ae1af893e08f9c214bc25edb3a144af71f88a2dfcb69a/netCDF4-1.3.0-cp35-cp35m-manylinux1_x86_64.whl" in
the cache
No cache entry available
"GET /packages/c0/06/c59f37661ede4f9ae1af893e08f9c214bc25edb3a144af71f88a2dfcb69a/netCDF4-1.3.0-cp35-cp35m-manylinux1_x86_64.whl HTTP/1.1" 200 6163771
Downloading netCDF4-1.3.0-cp35-cp35m-manylinux1_x86_64.whl (6.2MB)
Downloading from URL https://pypi.python.org/packages/c0/06/c59f37661ede4f9ae1af893e08f9c214bc25edb3a144af71f88a2dfcb69a/netCDF4-1.3.0-cp35-cp35m-manylinux1_x86_64.whl#md5=d4660a6dea3062578fc9cfec6b243949
(from https://pypi.python.org/simple/netcdf4/)
Updating cache with response from "https://pypi.python.org/packages/c0/06/c59f37661ede4f9ae1af893e08f9c214bc25edb3a144af71f88a2dfcb69a/netCDF4-1.3.0-cp35-cp35m-manylinux1_x86_64.whl"
Caching due to etag
Requirement already satisfied: numpy>=1.7 in /gpfs/ts0/home/pb412/firedrake-20171026/lib/python3.5/site-packages (from netCDF4->-r gusto/requirements.txt (line 1))
Installing collected packages: netCDF4
It looks like it struggled to find a compatible version of netcdf4 but in the end was successful and installed this version of netcdf4:
netCDF4-1.3.0-cp35-cp35m-manylinux1_x86_6
I will have another look at the install log and search for errors. See attached the install log - I am not an expert in this stuff.
P
From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Shipton, Jemma <j.shipton@imperial.ac.uk>
Sent: 26 October 2017 18:06:25
To: firedrake
Subject: Re: [firedrake] Firedrake installation on cluster
OK, great.
A quick google of the import error suggests this could be either a cython issue or a python version issue.
I wonder if it would be better to start from the errors that the usual firedrake install log gives?
[I'm at the end of my expertise on such matters now, by the way! What do others think?]
Jemma
From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Burns, Paul <P.Burns2@exeter.ac.uk>
Sent: 26 October 2017 17:55:20
To: firedrake
Subject: Re: [firedrake] Firedrake installation on cluster
By passing the flag '--install gusto' to the installer...
P
From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Shipton, Jemma <j.shipton@imperial.ac.uk>
Sent: 26 October 2017 15:14:50
To: firedrake
Subject: Re: [firedrake] Firedrake installation on cluster
Hi Paul,
How did you install Gusto?
Jemma
From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Burns, Paul <P.Burns2@exeter.ac.uk>
Sent: 26 October 2017 15:10:14
To: firedrake
Subject: [firedrake] Firedrake installation on cluster
Dear Sir/Madam,
I am trying to get Firedrake up and running on the Isca cluster at Exeter. The standard install method (i.e., executing 'python3 firedrake-install') does not work, however, we have managed to install Firedrake by developing an install script that loads modules
manually, that sets a number of petsc options, and that passes a number of extra options to firedrake-install.
However, when I try and run a simulation on Gusto I get the following error:
Traceback (most recent call last):
File "./examples/boussinesq_2d_lab.py", line 1, in <module>
from gusto import *
File "/gpfs/ts0/home/pb412/firedrake-20171026/src/gusto/gusto/__init__.py", line 11, in <module>
from gusto.state import * # noqa
File "/gpfs/ts0/home/pb412/firedrake-20171026/src/gusto/gusto/state.py", line 3, in <module>
from netCDF4 import Dataset
File "/gpfs/ts0/home/pb412/firedrake-20171026/lib/python3.5/site-packages/netCDF4/__init__.py", line 3, in <module>
from ._netCDF4 import *
ImportError: /gpfs/ts0/home/pb412/firedrake-20171026/lib/python3.5/site-packages/netCDF4/_netCDF4.cpython-35m-x86_64-linux-gnu.so: undefined symbol: _PyThreadState_UncheckedGet
So it looks like there is some problem with the netCDF4 library.
Please advise.
Regards,
Paul