johannesring

johannr@login-0-1:tmp$ gdb python
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johannesring

[johannr:~/Downloads/test_louvain] [cyto] 15s $ python test_louvain.py ~/dev/simula/cyto/models/MYC_signaling_v1_r404929.sbml
Clustering with 94 elements and 9 clusters
[0] 4, 5, 6, 8, 9, 10, 15, 41, 42, 44, 46, 47, 55, 82
[1] 18, 19, 20, 22, 23, 27, 30, 53, 68, 71, 72, 73, 78, 79
[2] 7, 14, 35, 36, 40, 58, 59, 64, 65, 90, 91, 92, 93
[3] 1, 11, 12, 32, 33, 39, 48, 49, 50, 83, 84, 85, 86
[4] 0, 28, 29, 31, 38, 56, 57, 75, 76, 77, 81, 87
[5] 16, 17, 21, 24, 25, 52, 54, 67, 69, 70, 74, 80
[6] 13, 34, 62, 63, 88, 89
[7] 3, 37, 60, 61, 66

johannesring

$ cat test.py
from dolfin import *

mesh = UnitSquareMesh(10, 10)
W = VectorFunctionSpace(mesh, 'Lagrange', 1)
u = TrialFunction(W)
v = TestFunction(W)
sol = Function(W)
solve(
    inner(u, v)*dx == inner(Constant((3.14, 2.71)), v) * dx, sol,

johannesring

diff --git a/ChangeLog b/ChangeLog
index 57796e1..ec9c6c1 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,4 @@
+2016.2.0 [2016-11-30]
  - Jit compiler now compiles elements separately from forms to avoid duplicate work
  - Add parameter max_signature_length to optionally shorten signatures in the jit cache
  - Move uflacs module into ffc.uflacs
diff --git a/ffc/__init__.py b/ffc/__init__.py

johannesring

# The following debian packages should be installed when using this
# profile:
# 
# git curl python-dev time build-essential gfortran freeglut3-dev

# This profile file controls your <#> (HashDist) build environment.

# In the future, we'll provide better incorporation of
# automatic environment detection.  For now, have a look
# at the YAML files in the top-level directory and choose

johannesring

johannr@debian-t420s:test (master)$ ./runtests.sh 
Running tests in serial:
================================================================================================ test session starts ================================================================================================
platform linux2 -- Python 2.7.11+, pytest-2.8.7, py-1.4.31, pluggy-0.3.1 -- /usr/bin/python
cachedir: .cache
rootdir: /home/johannr/dev/fenics/src/dijitso/test, inifile: pytest.ini
plugins: cov-2.2.1
collected 8 items 

test_mpi_dijitso.py::test_mpi_jit_strategies[root] root 0

johannesring

CMake Error at googletest-stamp/download-googletest.cmake:22 (message):
  error: downloading
  'https://github.com/google/googletest/archive/release-1.7.0.tar.gz' failed

    status_code: 28
    status_string: "Timeout was reached"
    log: Hostname was NOT found in DNS cache
    Trying 192.30.252.128...

  Connected to github.com (192.30.252.128) port 443 (#0)

johannesring

(2008, 4, 30, 14, 12, 50) la-vector-access-cpp 15.8298 "Accessing vector of size 10000000 (100 repetitions)"
(2008, 4, 30, 14, 13, 9) la-vector-assignment-cpp 18.8627 "Assigning to vector of size 10000000 (100 repetitions)"
(2008, 4, 30, 14, 13, 16) fem-jit-python 0.555803 "JIT compilation (in memory cache)"
(2008, 4, 30, 14, 13, 28) fem-convergence-cpp 11.4321 "Solving Poisson's equation in 2D for q = 1, n = 2."
(2008, 4, 30, 14, 13, 34) mesh-unitcube-cpp 6.08171 "Creating unit cube of size 128 x 128 x 128 (10 repetitions)"
(2008, 4, 30, 14, 14, 50) mesh-refinement-cpp 75.8 "Uniform refinement of unit cube of size 4 x 4 x 4 (5 refinements)"
(2008, 4, 30, 14, 15, 5) mesh-iteration-cpp 14.4 "Iteration over entities of unit cube of size 128 x 128 x 128 (100 repetitions)"
(2008, 4, 30, 14, 38, 58) common-progress-cpp 526.775 "Creating progress bar with 500000000 steps (5 repetitions)"
(2008, 6, 23, 14, 18, 43) la-vector-access-cpp 15.0198 "Accessing vector of size 10000000 (100 repetitions)"
(2008, 6, 23, 14, 19

johannesring

2015/06/18 13:49:56 - INFO: [package:run_job] running [u'/bin/bash', '_hashdist/build.sh']
2015/06/18 13:49:56 - INFO: [package:run_job] environment:
2015/06/18 13:49:56 - INFO: [package:run_job]   {'ARTIFACT': u'/home/david/.hashdist/bld/boost/alwhg2upzmto',
2015/06/18 13:49:56 - INFO: [package:run_job]    'BASH': u'/bin/bash',
2015/06/18 13:49:56 - INFO: [package:run_job]    'BUILD': u'/home/david/.hashdist/tmp/boost-alwhg2upzmto',
2015/06/18 13:49:56 - INFO: [package:run_job]    u'BZIP2_DIR': u'/home/david/.hashdist/bld/bzip2/yhn7t7sdxdfd',
2015/06/18 13:49:56 - INFO: [package:run_job]    u'BZIP2_ID': u'bzip2/yhn7t7sdxdfdkhyie6hg36hqvgccj7rj',
2015/06/18 13:49:56 - INFO: [package:run_job]    'HASHDIST_CPU_COUNT': '4',
2015/06/18 13:49:56 - INFO: [package:run_job]    'HDIST_CONFIG': '{"gc_roots":"/home/david/.hashdist/gcroots","build_stores":[{"dir":"/home/david/.hashdist/bld"}],"source_caches":[{"dir":"/home/david/.hashdist/src"}],"cache":"/home/david/.hashdist/cache","build_temp":"/home/david/.hashdist/tm

johannesring

2015/05/26 09:10:25 - INFO: [package:run_job] running [u'/bin/bash', '_hashdist/build.sh']
2015/05/26 09:10:25 - INFO: [package:run_job] environment:
2015/05/26 09:10:25 - INFO: [package:run_job]   {'ARTIFACT': u'/home/johannr/.hashdist/bld/armadillo/octesp5d4icv',
2015/05/26 09:10:25 - INFO: [package:run_job]    'BASH': u'/bin/bash',
2015/05/26 09:10:25 - INFO: [package:run_job]    'BUILD': u'/home/johannr/.hashdist/tmp/armadillo-octesp5d4icv',
2015/05/26 09:10:25 - INFO: [package:run_job]    'CMAKE': u'/home/johannr/.hashdist/bld/cmake/adha2ex3su3d/bin/cmake',
2015/05/26 09:10:25 - INFO: [package:run_job]    u'CMAKE_DIR': u'/home/johannr/.hashdist/bld/cmake/adha2ex3su3d',
2015/05/26 09:10:25 - INFO: [package:run_job]    u'CMAKE_ID': u'cmake/adha2ex3su3dwskcdtr5cyslb4sihgci',
2015/05/26 09:10:25 - INFO: [package:run_job]    'HASHDIST_CPU_COUNT': '1',
2015/05/26 09:10:25 - INFO: [package:run_job]    'HDIST_CONFIG': '{"gc_roots":"/home/johannr/.hashdist/gcroots","build_stores":[{"dir":"/home/johannr/.hashdist/