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[SageMathCloud] Update: Fwd: [FEniCS-support] slepc | ERROR - build.log
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William Stein, Jul 16, 14:09
Hi André,
Could you open a github ticket here about FEniCS in SMC?
https://github.com/sagemathinc/smc/issues
If you have trouble doing so, let me know.
---
William Stein Founder and CEO
*[SageMathCloud](https://cloud.sagemath.com) Support - SageMath, Inc.*
----------------------------------------------
André Timótheo, Jul 15, 18:30
Johannes Ring,
thank you VERY much!! I follow yours hints and
I have FEniCS project [1] stable version ( has_petsc_tao() = TRUE )
inside the beutiful cloud project of Willian Stein SageMathCoud.
I ll put some post on FEniCS q&a about it in order to share it with
another python entusiastic people.
André Timótheo
----------------------------------------------------------------
The problem is that it links with the system LAPACK and BLAS instead of
OpenBLAS that HashDist has built. The quick fix will be to build PETSc without
MUMPS. Try this:
git clone https://bitbucket.org/fenics-project/fenics-developer-tools.git
cd fenics-developer-tools
cp install/profiles/fenics.Linux.yaml local.yaml
editor local.yaml
Now remove the following two lines from local.yaml:
download: |
mumps, scalapack, blacs, ml
Finally, run:
./install/fenics-install.sh local.yaml
----------------------------------------------------------------
---------- Forwarded message ---------
From: nguyen dang <[email protected]>
Date: qua, 15 de jul de 2015 às 12:31
Subject: Re: [FEniCS-support] slepc | ERROR - build.log
To: Johannes Ring <[email protected]>
Cc: André Timótheo <[email protected]>, [email protected]
<[email protected]>
Dear Johannes,
Thanks! Now, python version works well but there is error with c++ version.
cmake . - works well
make - error with the attached messages.
How to fix the error? Thanks!
Dang
Linking CXX executable demo_poisson
/usr/bin/ld: warning: libbz2.so.1.0, needed by
/home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so,
not found (try using -rpath or -rpath-link)
/home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so:
undefined reference to `BZ2_bzDecompress'
/home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so:
undefined reference to `BZ2_bzCompressInit'
/home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so:
undefined reference to `BZ2_bzDecompressInit'
/home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so:
undefined reference to `BZ2_bzDecompressEnd'
/home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so:
undefined reference to `BZ2_bzCompressEnd'
/home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so:
undefined reference to `BZ2_bzCompress'
collect2: error: ld returned 1 exit status
make[2]: *** [demo_poisson] Error 1
make[1]: *** [CMakeFiles/demo_poisson.dir/all] Error 2
make: *** [all] Error 2
On 7/15/15, Johannes Ring <[email protected]> wrote:
> The files in $HOME/.hashdist/bld are write protected, so if you copy from
> there you will have to change the permission on them.
>
> Johannes
>
> On Wed, Jul 15, 2015, 17:10 nguyen dang <[email protected]> wrote:
>
>> Dear Johannes,
>> The compilation comes to an end without error.
>> I run: source fenics.custom
>> then, I can clarify dolfin version 1.5.0
>> I copied the demo from
>> .hashdist/bld/dolfin/7zdpq5r4sgsm/share/dolfin/demo to /Documents.
>> There is an error when the poisson demo in
>> /demo/documented/poisson/python is tested
>> python demo_poisson.py
>> I attach error messages. Can you please show me again how to fix? Thanks!
>> Best regards,
>> Dang
>>
>> ==================================================
>> Calling FFC just-in-time (JIT) compiler, this may take some time.
>> Traceback (most recent call last):
>> File "demo_poisson.py", line 41, in <module>
>> V = FunctionSpace(mesh, "Lagrange", 1)
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/dolfin/functions/functionspace.py",
>> line 468, in __init__
>> FunctionSpaceBase.__init__(self, mesh, element, constrained_domain)
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/dolfin/functions/functionspace.py",
>> line 153, in __init__
>> ufc_element, ufc_dofmap = jit(self._ufl_element,
>> mpi_comm=mesh.mpi_comm())
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/dolfin/compilemodules/jit.py",
>> line 64, in mpi_jit
>> return local_jit(*args, **kwargs)
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/dolfin/compilemodules/jit.py",
>> line 128, in jit
>> return form_compiler.jit(form, parameters=p)
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/jitcompiler.py",
>> line 72, in jit
>> return jit_element(ufl_object, parameters)
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/jitcompiler.py",
>> line 177, in jit_element
>> compiled_form, module, prefix = jit_form(form, parameters)
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/jitcompiler.py",
>> line 130, in jit_form
>> parameters=parameters)
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/compiler.py",
>> line 176, in compile_form
>> format_code(code, wrapper_code, prefix, parameters)
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/formatting.py",
>> line 114, in format_code
>> _write_file(code_h, prefix, ".h", parameters)
>> File
>> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/formatting.py",
>> line 137, in _write_file
>> hfile = open(filename, "w")
>> IOError: [Errno 13] Permission denied:
>> './ffc_form_746ebe8521dc9d314e6f65075dbc60d03cfee94b.h'
>> ==================================================
>>
>>
>> On 7/15/15, Johannes Ring <[email protected]> wrote:
>> > The problem is this:
>> >
>> > c++: internal compiler error: Killed (program cc1plus)
>> >
>> > This is usually caused by a bug in the compiler or that you ran out of
>> > memory. If it is the latter case, you can try to build with only one
>> thread
>> > to save some memory:
>> >
>> > export PROCS=1
>> >
>> > Then run fenics-install.sh again.
>> >
>> > Johannes
>> >
>> > On Wed, Jul 15, 2015 at 3:45 PM nguyen dang <[email protected]>
>> wrote:
>> >
>> >> Hello,
>> >> I could fix that error by installing libXt-devel
>> >> sudo yum install libXt-devel
>> >> There is a new error with mshr
>> >> [mshr] Building mshr/7olinw2dfk5t, follow log with:
>> >> [mshr] tail -f
>> >> /home/fenics/.hashdist/tmp/mshr-7olinw2dfk5t/_hashdist/build.log
>> >> [mshr|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' returned
>> >> non-zero exit status 2
>> >> [mshr|ERROR] command failed (code=2); raising
>> >> real 3607.89
>> >> user 2537.20
>> >> sys 382.04
>> >> I attach log file.
>> >> Thanks again for your help.
>> >> Best regards,
>> >> Dang
>> >>
>> >>
>> >> On 7/15/15, Johannes Ring <[email protected]> wrote:
>> >> > Ok, this is a different error, so I assume that slepc has been built
>> >> > successfully. The problem with vtk is this:
>> >> >
>> >> > fatal error: X11/StringDefs.h: No such file or directory
>> >> >
>> >> > This file can be found in the libxt-dev package on Ubuntu, but I'm
>> >> > not
>> >> sure
>> >> > what system you are on. You can either install this file or build
>> >> > without
>> >> > vtk by removing it from local.yaml. In the latter case, you will not
>> be
>> >> > able to do any plotting with DOLFIN.
>> >> >
>> >> > Johannes
>> >> >
>> >> >
>> >> > On Wed, Jul 15, 2015 at 11:23 AM nguyen dang
>> >> > <[email protected]>
>> >> > wrote:
>> >> >
>> >> >> Dear Johannes,
>> >> >> Thanks for your quick response. I followed your instructions but I
>> >> >> still get error:
>> >> >> [vtk] Building vtk/of7hll3bl2ul, follow log with:
>> >> >> [vtk] tail -f
>> >> >> /home/fenics/.hashdist/tmp/vtk-of7hll3bl2ul-3/_hashdist/build.log
>> >> >> [vtk|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' returned
>> >> >> non-zero exit status 2
>> >> >> [vtk|ERROR] command failed (code=2); raising
>> >> >> real 1267.00
>> >> >> user 1092.49
>> >> >> sys 147.74
>> >> >> I attach build.log and local.yaml
>> >> >> Thanks for your help,
>> >> >> Best regards,
>> >> >> Dang
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> On 7/15/15, Johannes Ring <[email protected]> wrote:
>> >> >> > [Please include fenics-support in Cc]
>> >> >> >
>> >> >> > The problem is that it links with the system LAPACK and BLAS
>> instead
>> >> of
>> >> >> > OpenBLAS that HashDist has built. The quick fix will be to build
>> >> >> > PETSc
>> >> >> > without MUMPS. Try this:
>> >> >> >
>> >> >> > git clone
>> >> >> https://bitbucket.org/fenics-project/fenics-developer-tools.git
>> >> >> > cd fenics-developer-tools
>> >> >> > cp install/profiles/fenics.Linux.yaml local.yaml
>> >> >> > editor local.yaml
>> >> >> >
>> >> >> > Now remove the following two lines from local.yaml:
>> >> >> >
>> >> >> > download: |
>> >> >> > mumps, scalapack, blacs, ml
>> >> >> >
>> >> >> > Finally, run:
>> >> >> >
>> >> >> > ./install/fenics-install.sh local.yaml
>> >> >> >
>> >> >> > Johannes
>> >> >> >
>> >> >> > On Tue, Jul 14, 2015 at 7:13 PM André Timótheo
>> >> >> > <[email protected]>
>> >> >> > wrote:
>> >> >> >
>> >> >> >>
>> >> >> >>
>> >> >> >> Em ter, 14 de jul de 2015 às 09:33, Johannes Ring
>> >> >> >> <[email protected]
>> >> >
>> >> >> >> escreveu:
>> >> >> >>
>> >> >> >>> The error in the build.log is this:
>> >> >> >>>
>> >> >> >>> 2015/07/13 23:09:48 - INFO: [package:run_job] ERROR: See
>> >> >> >>> "arch-linux2-c-opt/conf/configure.log" file for
>> >> >> >>> details
>> >> >> >>>
>> >> >> >>> 2015/07/13 23:09:48 - INFO: [package:run_job] Checking
>> >> >> >>> environment...
>> >> >> >>> 2015/07/13 23:09:48 - INFO: [package:run_job] Checking PETSc
>> >> >> >>> installation...
>> >> >> >>> 2015/07/13 23:09:48 - INFO: [package:run_job] ERROR: Unable to
>> >> >> >>> link
>> >> >> with
>> >> >> >>> PETSc
>> >> >> >>>
>> >> >> >>> Please send us
>> >> >> >>>
>> >> >>
>> >>
>> /projects/d800605f-5bec-48c8-8c21-5fa60022fa9a/.hashdist/tmp/slepc-bvy3tmydxkf2-3/arch-linux2-c-opt/conf/configure.log
>> >> >> >>> as an attachment.
>> >> >> >>>
>> >> >> >>> Johannes
>> >> >> >>>
>> >> >> >>> On Tue, Jul 14, 2015 at 2:26 PM André Timótheo <
>> >> [email protected]>
>> >> >> >>> wrote:
>> >> >> >>>
>> >> >> >>>> I am trying to install FEniCS on SageMathCloud via curl -s
>> >> >> >>>> http://fenicsproject.org/fenics-install.sh | bash
>> >> >> >>>> ( the option [1] stable fenics version )
>> >> >> >>>>
>> >> >> >>>> I have some problems with slepc:
>> >> >> >>>> [slepc
>> >> >> >>>> ] tail -f
>> >> >> >>>>
>> >> >>
>> >>
>> /projects/d800605f-5bec-48c8-8c21-5fa60022fa9a/.hashdist/tmp/slepc-bvy3tmydx
>> >> >> >>>> kf2-3/_hashdist/build.log
>> >> >> >>>> [slepc|ERROR
>> >> >> >>>> ] Command '[u'/bin/bash', '_hashdist/build.sh']' returned
>> >> >> >>>> non-zero
>> >> >> exit
>> >> >> >>>> status 1
>> >> >> >>>> [slepc|ERROR] command failed (code=1); raising
>> >> >> >>>>
>> >> >> >>>> The build.log error file is attached.
>> >> >> >>>>
>> >> >> >>>> Thank you very much for any kind of *help*.
>> >> >> >>>>
>> >> >> >>>> André Timótheo
>> >> >> >>>>
>> >> >> >>> _______________________________________________
>> >> >> >>>> fenics-support mailing list
>> >> >> >>>> [email protected]
>> >> >> >>>> http://fenicsproject.org/mailman/listinfo/fenics-support
>> >> >> >>>>
>> >> >> >>>
>> >> >> >
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Nguyen Van Dang
>> >> >> Hand phone: +34 675 16 95 90
>> >> >> Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia
>> >> >> Spain
>> >> >>
>> >> >
>> >>
>> >>
>> >> --
>> >> Nguyen Van Dang
>> >> Hand phone: +34 675 16 95 90
>> >> Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia
>> >> Spain
>> >>
>> >
>>
>>
>> --
>> Nguyen Van Dang
>> Hand phone: +34 675 16 95 90
>> Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia
>> Spain
>>
>
--
Nguyen Van Dang
Hand phone: +34 675 16 95 90
Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia
Spain
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