Hi, Now I am getting new error like
TypeError: assemble() got an unexpected keyword argument 'reset_sparsity' Thanks On Wed, Jan 28, 2015 at 2:17 PM, <[email protected]> wrote: > Send fenics-support mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://fenicsproject.org/mailman/listinfo/fenics-support > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fenics-support digest..." > > > Today's Topics: > > 1. Re: Conda package for FEniCS (Juan Luis Cano) > 2. Using fenics-install.sh on a cluster (Laboure, Vincent M) > 3. Re: dolfin problem with Mac 10.9.5 (Johannes Ring) > 4. Getting error while running old program (Palraj J) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 27 Jan 2015 23:12:37 +0100 > From: Juan Luis Cano <[email protected]> > To: Maarten <[email protected]> > Cc: fenics-support <[email protected]> > Subject: Re: [FEniCS-support] Conda package for FEniCS > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > On 2015-01-27 11:40, Maarten wrote: > > Here you go: > > > > > ldd > > > > <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so > > | grep libbz2 > > ldd: warning: you do not have execution permission for > > > > `<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so' > > > > <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so: > > /lib64/libc.so.6: version `GLIBC_2.14' not found (required by > > > > <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/../../../../libboost_filesystem.so.1.55.0) > > > > <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so: > > /lib64/libc.so.6: version `GLIBC_2.14' not found (required by > > > > <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/../../../../libboost_program_options.so.1.55.0) > > libbz2.so.1.0 => not found > > > > > > Okay, I suspect you are installing some version cached in your system: I > say this because boost is trying to locate libc 2.14, but that was for > the package I compiled nearly a month ago in Linux Mint. I had already > recompiled it in CentOS 6.6, checked in my system and my linking > information is different than yours. > > So what I think will solve the problem is: > > 1. Remove the boost 1.55 conda package from all your environments. If > you only have one: > > (fenics27) $ conda remove boost > > 2. Clean the conda cache, both the packages and the tarballs. Important: > if you type these commands and boost is not in the list of things to > remove, you need to go to step 1 and find in which environment is boost > still installed. conda won't clean it from the cache until it's used > nowhere. > > $ conda clean --packages > $ conda clean --tarballs > > 3. Go to step 4 :) > > 4. Reinstall it: > > (fenics27) $ conda install "boost=1.55" --channel > https://conda.binstar.org/juanlu001/channel/fenics:1.4.0:centos > > 5. Repeat the ldd steps. If boost is still looking for GLIBC 2.14 then > I'm afraid you have to go back to step 1. > > 6. Our libbz2 libraries are the same, so there are good chances the next > one will be a happy email with a working FEniCS installation :) > > 7. You always have the option of removing the created environment with > all its packages, clean all the caches and start afresh: > > $ conda remove -n fenics27 --all > $ conda clean --packages > $ conda clean --tarballs > > I hope this helps! > > Regards, > > Juan Luis > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://fenicsproject.org/pipermail/fenics-support/attachments/20150127/762fce82/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Tue, 27 Jan 2015 17:31:46 -0600 > From: "Laboure, Vincent M" <[email protected]> > To: "[email protected]" > <[email protected]> > Subject: [FEniCS-support] Using fenics-install.sh on a cluster > Message-ID: > < > caco0e4yp+sevjvy2pxfppsdw_stqubp3isid-dkedxxvh-m...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > Now that I have FEniCS 1.5 working on my local machine, I am eager to > install it on a cluster to run bigger problems. > > Since I don't have the administrative privileges, I have been trying to use > fenics-install.sh typing: > > curl -s http://fenicsproject.org/fenics-install.sh | bash > > I tried on two different clusters (Red Hat Enterprise Linux Server release > 6.3 for the first one and 6.5 for the second one) from two completely > different institutions. Both returns the same error: > > > > --2015-01-27 17:07:50-- http://fenicsproject.org/fenics-install.sh > Resolving fenicsproject.org... 82.118.24.73 > Connecting to fenicsproject.org|82.118.24.73|:80... connected. > HTTP request sent, awaiting response... 200 OK > Length: 6275 (6.1K) [text/x-sh] > Saving to: ?STDOUT? > > 100%[======================================>] 6,275 --.-K/s in > 0s > > Created temporary directory /tmp/fenics-install.dlAW9R for FEniCS > installation. > > Downloading HashDist... > 2015-01-27 17:07:50 (30.9 MB/s) - written to stdout [6275/6275] > > Initialized empty Git repository in > /tmp/fenics-install.dlAW9R/hashdist/.git/ > remote: Counting objects: 4775, done. > remote: Total 4775 (delta 0), reused 0 (delta 0) > Receiving objects: 100% (4775/4775), 2.13 MiB | 1.10 MiB/s, done. > Resolving deltas: 100% (2889/2889), done. > > Downloading HashStack... > Initialized empty Git repository in > /tmp/fenics-install.dlAW9R/hashstack/.git/ > remote: Counting objects: 5852, done. > remote: Compressing objects: 100% (8/8), done. > remote: Total 5852 (delta 2), reused 0 (delta 0) > Receiving objects: 100% (5852/5852), 1.12 MiB | 963 KiB/s, done. > Resolving deltas: 100% (3460/3460), done. > > Downloading FEniCS Install... > Initialized empty Git repository in > /tmp/fenics-install.dlAW9R/fenics-developer-tools/.git/ > remote: Counting objects: 138, done. > remote: Compressing objects: 100% (133/133), done. > remote: Total 138 (delta 72), reused 0 (delta 0) > Receiving objects: 100% (138/138), 92.18 KiB, done. > Resolving deltas: 100% (72/72), done. > > patching file pkgs/petsc/petsc.py > patching file pkgs/petsc/petsc.yaml > Ready to build FEniCS. This may take about 2 hours. > > The following build types are supported: > > [0] development version of FEniCS [default] > [1] latest stable version of FEniCS, currently 1.5 > [2] only dependencies, including e.g. MPI, PETSc, Swig, Boost > > Please select build type [0, 1, 2]: 1 > Using HashStack profile fenics.Linux.yaml. > > Stable build requested. > > Starting build... > > Directory ba created. > Directory bld created. > Directory src created. > Directory db created. > Directory cache created. > Directory gcroots created. > Default configuration file /home/user1/.hashdist/config.yaml written. > Downloading > http://releases.nixos.org/patchelf/patchelf-0.8/patchelf-0.8.tar.bz2... > [=========================] 100.0% (0.1MB of 0.1MB) 0.223MB/s ETA 0s > [patchelf] Building patchelf/k3rloj265ogt, follow log with: > [patchelf] tail -f > /home/user1/.hashdist/tmp/patchelf-k3rloj265ogt/build.log > Downloading > https://sourceforge.net/projects/pcre/files/pcre/8.34/pcre-8.34.tar.bz2... > [ERROR] urllib failed to download (reason: unknown url type: https): > https://sourceforge.net/projects/pcre/files/pcre/8.34/pcre-8.34.tar.bz2 > Downloading > https://sourceforge.net/projects/pcre/files/pcre/8.34/pcre-8.34.tar.bz2... > [ERROR] urllib failed to download (reason: unknown url type: https): > https://sourceforge.net/projects/pcre/files/pcre/8.34/pcre-8.34.tar.bz2 > Downloading > https://sourceforge.net/projects/pcre/files/pcre/8.34/pcre-8.34.tar.bz2... > [ERROR] urllib failed to download (reason: unknown url type: https): > https://sourceforge.net/projects/pcre/files/pcre/8.34/pcre-8.34.tar.bz2 > [CRITICAL] You may wish to check your Internet connection or the remote > server > > > Does anybody know what the problem could be? > > Many thanks! > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://fenicsproject.org/pipermail/fenics-support/attachments/20150127/3e75226b/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Wed, 28 Jan 2015 08:26:52 +0100 > From: Johannes Ring <[email protected]> > To: Jinyong Ying <[email protected]> > Cc: "[email protected]" > <[email protected]> > Subject: Re: [FEniCS-support] dolfin problem with Mac 10.9.5 > Message-ID: > <CALjQY_E6_Xbh0z9L= > [email protected]> > Content-Type: text/plain; charset=UTF-8 > > On Tue, Jan 27, 2015 at 5:20 PM, Jinyong Ying <[email protected]> wrote: > > Hi, > > > > I used to use FEniCS 1.2 on mac 10.7. Everything was fine. Now i just > > updated to the OS 10.9.5, but i met a problem when i try to load in the > > library dolfin using the binary file provided on the website. > > > > > > After i sourced FEniCS 1.3, then i did the following in the terminal: > > > > python > >>>> from dolfin import * > > > > Then it just hangs there like forever. I check the cup time for this > > operation. It seems it took only small amount of time, but it just did > not > > finish the job. > > > > > > > > Then i turned to FEniCS 1.5 for another try, i also did the following > > > > python > >>>>from dolfin import * > >>>>mesh=UnitSquareMesh(4,4) > > > > This time loading in the library is fine, but it again hangs like forever > > when trying to generate the mesh. > > > > > > The only change to the new system was I deleted the default gcc and g++ > > compilers in /usr/bin/ and installed the GNU gcc and g++ in > /usr/local/bin. > > I am not sure this will cause the problem or not now. > > This could very well be the problem. The default gcc and g++ compilers > in /usr/bin are actually clang compilers, which were used when > compiling the binary package. Using GNU gcc and g++ with the binary > package might lead to unexpected problems. > > Johannes > > > > > Did someone know what caused this problem and how to fixed it? Any help > is > > really appreciated. Thanks a lot. > > > > > > --jying > > > > > > > > _______________________________________________ > > fenics-support mailing list > > [email protected] > > http://fenicsproject.org/mailman/listinfo/fenics-support > > > > > ------------------------------ > > Message: 4 > Date: Wed, 28 Jan 2015 14:17:30 +0530 > From: Palraj J <[email protected]> > To: [email protected] > Subject: [FEniCS-support] Getting error while running old program > Message-ID: > <CAAU9pfb19EvsPA5RH0QAt= > [email protected]> > Content-Type: text/plain; charset="utf-8" > > Lastly I update the latest version of fenics while I am running old program > I am getting the following error > > bcs=bc, reassemble_lhs=False) > File "/home/palraj/Desktop/work/cbc/pdesys/PDESubSystems.py", line 324, in > *init* > PDESubSystemBase.*init*(self, solver_namespace, sub_system, bcs, normalize, > **kwargs) > File "/home/palraj/Desktop/work/cbc/pdesys/PDESubSystems.py", line 61, in > __init__ > self.query_args(sub_system) > File "/home/palraj/Desktop/work/cbc/pdesys/PDESubSystems.py", line 99, in > query_args > self.work = self.get_work_vector() > File "/home/palraj/Desktop/work/cbc/pdesys/PDESubSystems.py", line 288, in > get_work_vector > info_green('Creating new work vector for {0:s}'.format(self.name)) > File "/home/palraj/Desktop/work/cbc/pdesys/PDESubSystems.py", line 909, in > info_green > if MPI.process_number()==0: > AttributeError: type object 'MPI' has no attribute 'process_number' > -- > *J. Palraj,* > Research Scholar, > Department of Mathematics, > PSG College of Arts & Science, > Coimbatore - 641 014, > Tamilnadu, India. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://fenicsproject.org/pipermail/fenics-support/attachments/20150128/1fc82ba2/attachment.html > > > > ------------------------------ > > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support > > > End of fenics-support Digest, Vol 21, Issue 44 > ********************************************** > -- *J. Palraj,* Research Scholar, Department of Mathematics, PSG College of Arts & Science, Coimbatore - 641 014, Tamilnadu, India.
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