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/c59f37661ede4f9ae1af893e08f9c214bc25e..." 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/c59f37661ede4f9ae1af893e08f9c214bc25e... (from https://pypi.python.org/simple/netcdf4/) Updating cache with response from "https://pypi.python.org/packages/c0/06/c59f37661ede4f9ae1af893e08f9c214bc25e..." 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