On Wed, May 6, 2015 at 3:34 PM, Johannes Ring <[email protected]> wrote:
> It works fine for me with a slightly modified profile (see
> attachment). However, I'm probably just lucky:
>
> $ ldd terjekv/lib/python2.7/site-packages/dolfin/cpp/_common.so | grep boost
> libboost_filesystem.so.1.55.0 =>
> /home/johannr/.hashdist/bld/boost/wkz4j5e5un6h/lib/libboost_filesystem.so.1.55.0
> (0x00007f1b98035000)
> libboost_program_options.so.1.55.0 =>
> /home/johannr/.hashdist/bld/boost/wkz4j5e5un6h/lib/libboost_program_options.so.1.55.0
> (0x00007f1b97dc0000)
> libboost_system.so.1.55.0 =>
> /home/johannr/.hashdist/bld/boost/wkz4j5e5un6h/lib/libboost_system.so.1.55.0
> (0x00007f1b97bbd000)
> libboost_thread.so.1.55.0 =>
> /home/johannr/.hashdist/bld/boost/wkz4j5e5un6h/lib/libboost_thread.so.1.55.0
> (0x00007f1b979a3000)
> libboost_iostreams.so.1.55.0 =>
> /home/johannr/.hashdist/bld/boost/wkz4j5e5un6h/lib/libboost_iostreams.so.1.55.0
> (0x00007f1b9778c000)
> libboost_timer.so.1.55.0 =>
> /home/johannr/.hashdist/bld/boost/wkz4j5e5un6h/lib/libboost_timer.so.1.55.0
> (0x00007f1b97588000)
> libboost_chrono.so.1.55.0 =>
> /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.55.0
> (0x00007f1b88583000)
>
> Notice that _common.so is linked to libboost_chrono.so.1.55.0 from the
> system, not the one built by hashdist. I guess it works for me because
> both are the same version. I am not sure yet why it is like this and
> how to fix it.
The problem is likely in the boost package in hashstack. Can you check
if the following patch for hashstack fixes the problem:
diff --git a/pkgs/boost/boost.yaml b/pkgs/boost/boost.yaml
index 64f50e8..ae613b6 100644
--- a/pkgs/boost/boost.yaml
+++ b/pkgs/boost/boost.yaml
@@ -91,7 +91,7 @@ build_stages:
after: bjam
handler: bash
bash: |
- for lib in ${ARTIFACT}/lib/*.so; do
+ for lib in ${ARTIFACT}/lib/*.so.*; do
${PATCHELF} --set-rpath
${ARTIFACT}/lib:${BZIP2_DIR}/lib:${ZLIB_DIR}/lib ${lib}
done
Johannes
> Johannes
>
> On Wed, May 6, 2015 at 7:37 AM, Terje Kvernes <[email protected]> wrote:
>> This is still the case with the development version I built last night. Any
>> ideas on why?
>>
>>
>>> On 12 Apr 2015, at 17:52 , Terje Kvernes <[email protected]> wrote:
>>>
>>> Hi,
>>>
>>> when building a recent development version, I get the following when I test
>>> the build:
>>>
>>> $ python -c "from dolfin import *; FunctionSpace(UnitIntervalMesh(10),
>>> 'CG', 1)"
>>> Traceback (most recent call last):
>>> File "<string>", line 1, in <module>
>>> File
>>> "/mn/anatu/modules/opt/FEniCS/1.5.0_2015.04.12_dev/profile/dcoztv5kbquz/lib/python2.7/site-packages/dolfin/__init__.py",
>>> line 16, in <module>
>>> from . import cpp
>>> File
>>> "/mn/anatu/modules/opt/FEniCS/1.5.0_2015.04.12_dev/profile/dcoztv5kbquz/lib/python2.7/site-packages/dolfin/cpp/__init__.py",
>>> line 42, in <module>
>>> exec("from . import %s" % module_name)
>>> File "<string>", line 1, in <module>
>>> File
>>> "/mn/anatu/modules/opt/FEniCS/1.5.0_2015.04.12_dev/profile/dcoztv5kbquz/lib/python2.7/site-packages/dolfin/cpp/common.py",
>>> line 32, in <module>
>>> _common = swig_import_helper()
>>> File
>>> "/mn/anatu/modules/opt/FEniCS/1.5.0_2015.04.12_dev/profile/dcoztv5kbquz/lib/python2.7/site-packages/dolfin/cpp/common.py",
>>> line 28, in swig_import_helper
>>> _mod = imp.load_module('_common', fp, pathname, description)
>>> ImportError: libboost_chrono.so.1.55.0: cannot open shared object file: No
>>> such file or directory
>>>
>>> It works just fine if I add the profiles lib directory
>>> (/mn/anatu/modules/opt/FEniCS/1.5.0_2015.04.12_dev/profile/dcoztv5kbquz/lib/
>>> in this case) to LD_LIBRARY_PATH, but that’s not a particularly pretty
>>> solution. The config and build process worked fine before the transition
>>> to a newer SWIG in mid-march. Is this reproducible elsewhere?
>>>
>>> My config is as follows:
>>>
>>> extends:
>>> - file: linux.yaml
>>>
>>> packages:
>>> openblas:
>>> launcher:
>>> cmake:
>>> pcre:
>>> python:
>>> link: shared
>>> mpi:
>>> use: mpich
>>> blas:
>>> use: lapack
>>> lapack:
>>> use: lapack
>>> petsc:
>>> build_with: |
>>> parmetis, scotch, suitesparse
>>> download: |
>>> hypre, mumps, scalapack, blacs, ml
>>> coptflags: -O2
>>> link: shared
>>> debug: false
>>> swig:
>>> boost:
>>> toolset: gcc
>>> address_model: 64
>>> build_with: python
>>> ipython:
>>> matplotlib:
>>> python-netcdf4:
>>> pyvtk:
>>> vtk:
>>> ffc:
>>> fiat:
>>> instant:
>>> ufl:
>>> mshr:
>>> uflacs:
>>> h5py:
>>> numpy:
>>> scipy:
>>> slepc4py:
>>> # scitools:
>>> suitesparse:
>>> trilinos:
>>> setuptools:
>>> fenicstools:
>>> dolfin:
>>> build_with: |
>>> hdf5, parmetis, petsc, petsc4py, suitesparse, scotch, slepc, vtk,
>>> zlib, trilinos, slepc4py, qt, sphinx
>>> mpi4py:
>>> cbcblock:
>>> cbcpost:
>>>
>>>
>>> --
>>> Terje Kvernes
>>> Head sysadmin
>>> Department of Mathematics
>>> University of Oslo
>>>
>>>
>>>
>>>
>>
>>
>> --
>> Terje Kvernes
>> Driftsansvarlig
>> Matematisk Institutt
>> Universitetet i Oslo
>>
>> _______________________________________________
>> fenics-support mailing list
>> [email protected]
>> http://fenicsproject.org/mailman/listinfo/fenics-support
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