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

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'

-----------------------------------------------------------------------------------------------------

From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Burns, Paul <P.Burns2@exeter.ac.uk>
Sent: 27 October 2017 10:39:31
To: firedrake
Subject: Re: [firedrake] Firedrake installation on cluster

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.

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...

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