No rule to make target `/usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.so'

[sakhan007]

I tried $ instant-clean but it did not solve this problem.

python poisson_convergence1.py 
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
In instant.recompile: The module did not compile with command 'make VERBOSE=1', see '/home/sohail/.instant/error/dolfin_compile_code_7c28a3053842033e63e724baf19e43119eaa0567/compile.log'
Traceback (most recent call last):
File "poisson_convergence1.py", line 16, in <module>
 f = Expression("5*pi*pi*sin(pi*x[0])*sin(2*pi*x[1])")
 File "/home/sohail/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/functions/expression.py", line 602, in __new__
mpi_comm=mpi_comm)
File "/home/sohail/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 217, in compile_expressions
mpi_comm=mpi_comm)
File "/home/sohail/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 145, in compile_expression_code
mpi_comm=mpi_comm)
File "/home/sohail/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 64, in mpi_jit
return local_jit(*args, **kwargs)
File "/home/sohail/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.py", line 458, in compile_extension_module
**instant_kwargs)
 File "/home/sohail/anaconda/envs/fenics27/lib/python2.7/site-packages/instant/build.py", line 563, in build_module
 recompile(modulename, module_path, new_compilation_checksum, build_system)
 File "/home/sohail/anaconda/envs/fenics27/lib/python2.7/site-packages/instant/build.py", line 165, in recompile
instant_error(msg % (cmd, compile_log_filename_dest))
File "/home/sohail/anaconda/envs/fenics27/lib/python2.7/site-packages/instant/output.py", line 85, in instant_error
raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile with command 'make VERBOSE=1', see '/home/sohail/.instant/error/dolfin_compile_code_7c28a3053842033e63e724baf19e43119eaa0567/compile.log'

The compile.log, mentioned in the above error log is: http://pastebin.com/U7fhfEiX

 $ conda info
 Current conda install:

         platform : linux-64
    conda version : 3.16.0
   conda-build version : 1.11.0
   python version : 2.7.10.final.0
   requests version : 2.7.0
   root environment : /home/sohail/anaconda  (writable)
   default environment : /home/sohail/anaconda/envs/fenics27
   envs directories : /home/sohail/anaconda/envs
    package cache : /home/sohail/anaconda/pkgs
    channel URLs : https://repo.continuum.io/pkgs/free/linux-64/
                    https://repo.continuum.io/pkgs/free/noarch/
                    https://repo.continuum.io/pkgs/pro/linux-64/
                    https://repo.continuum.io/pkgs/pro/noarch/
      config file : /home/sohail/.condarc
    is foreign system : False

The conda list: http://pastebin.com/43KDy6K3

[astrojuanlu]

I am unable to reproduce this. Could you please paste conda info -a so we can see the environment variables too? In the meanwhile, please do conda update --all in the environment.

[sakhan007]

After doing conda update --all, the conda info -a returns: http://pastebin.com/Bj38KQEh

[astrojuanlu]

I don't think this will solve the issue, but just to check: would you try this?

$ bash
$ unset LD_LIBRARY_PATH
$ python poisson_convergence1.py

In the meanwhile, more questions:

• I assume you're using Ubuntu 14.04, am I right?
• Is libgfortran installed in your system? In other words, is the file /usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.so present in your system?

If you don't have libgfortran, then you will need it. There might be a way to provide it in conda, but I would have to make sure first.

If you already have it, then I still won't know what's happening and I will request you to do the following:

$ instant-clean
$ echo 'from dolfin import *
> f = Expression("5*pi*pi*sin(pi*x[0])*sin(2*pi*x[1])")
' > test.py
$ python test.py

and upload to pastebin all the files that appear under ~/.instant/.

[astrojuanlu]

For the record: there's actually the option to install gfortran and libgfortran in conda: https://groups.google.com/a/continuum.io/d/msg/conda/HZlV2LXxWhs/UM_EgEeiYZIJ.

[sakhan007]

Here is the answer to every question I was asked: http://pastebin.com/0h7kN2NP I don't think I need to install libgfortran, correct??? ~.instant/ contained too many files, so here is the archive: https://www.sendspace.com/file/31ecqv

[astrojuanlu]

Actually, as a last step, try to remove libgfortran from conda (conda remove libgfortran). If that doesn't work, I will have to inspect your files...

[sakhan007]

conda remove libgfortran removed libgfortran as conda package.

[astrojuanlu]

Yes, I meant to try to rerun the script without the libgfortran conda package.

[sakhan007]

https://www.sendspace.com/file/molvi8

[sakhan007]

The above archive is when I run possion_convergence1.py and here is when I run test.py: https://www.sendspace.com/file/myowfl after instant-clean

[astrojuanlu]

The conflict with libgfortran dissapeared now, but apparently you mistyped the expression in the last case:

53: error: expected ‘)’ before ‘;’ token
       values[0] = 5*pi*pi*sin(pi*x[0])*sin(2*pi*x[1];

[astrojuanlu]

Holy sh*t, now I found what's happening. You have an older version of gfortran than me! The program is looking for 4.8 and you have 4.6 (https://github.com/Juanlu001/fenics-recipes/issues/31#issuecomment-138124574). Can you confirm again what is your Linux distro and version? Now everything makes sense, but I'll have to figure out how to fix it.

[sakhan007]

Thanks for being so kind.

$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 12.04.5 LTS
Release:    12.04
Codename:   precise

Updated archive after correcting the mistyping in test.py: https://www.sendspace.com/file/c9pp7i

[sakhan007]

Moreover my gcc version is 4.8.1 and gfortran is 4.6.4. I always thought that gfortran comes with gcc.

[astrojuanlu]

On 2015-09-07 01:16, sakhan007 wrote:

Moreover my gcc version is 4.8.1 and gfortran is 4.6.4. I always thought that gfortran comes with gcc.

Yeah, that looks like a strange mismatch for me too!

I assume that you cannot upgrade either gfortran or Ubuntu (FEniCS developers dropped Ubuntu 12.04 testing this year), so there are two options:

• Try FEniCS 1.4.0, which in principle is compiled for older Linux versions, or
• Wait for me to compile FEniCS 1.6.0 with the conda gfortran and libgfortran packages. Unfortunately I won't have time to do it until next week probably.

[sakhan007]

I can upgrade gfortran and Ubuntu both as I have super user right. What do you suggest?

[astrojuanlu]

Sorry, I automatically assumed you were in a shared server or something!

Well, if you find a way to install gfortran 4.8 in your Ubuntu version that would be perfect. Obviously upgrading to a newer version of Ubuntu also would work but I understand that this can be a total mess.

Anyway, if you are not in a hurry and wait for the new package I would use your help to try if everything works :)

[sakhan007]

Ok I will wait.

[astrojuanlu]

I'm getting some errors while trying to build instant with anaconda gcc and gfortran:

https://groups.google.com/a/continuum.io/d/msg/anaconda/lmJatGVqklU/QVIfYFkWCAAJ

[astrojuanlu]

There are some suggestions to improve portability here:

https://github.com/conda/conda-recipes/pull/279#issuecomment-98254389

I would need to see how to fit them into instant. I might need to submit an upstream patch, but definitely I will need to look at it with some care. @sakhan007 You should probably update gfortran because I will need some weeks to get this right.

[sakhan007]

Does just updating gfortran would do the trick? or I have to build the whole fenics afterwards??

[astrojuanlu]

In principle updating gfortran should be enough. On Sep 14, 2015 10:16 AM, "sakhan007" notifications@github.com wrote:

Does just updating gfortran would do the trick? or I have to build the whole fenics afterwards??

— Reply to this email directly or view it on GitHub https://github.com/Juanlu001/fenics-recipes/issues/31#issuecomment-139993717 .

[stuarteberg]

Hey guys, I didn't read the above thread too closely, but I noticed you referenced conda/conda-recipes#279.

Just FYI, for best results, you should use the latest version of the gcc package, which is only available via the asmeurer channel: conda install -c asmeurer gcc=4.8.5. That version also includes some important fixes from conda/conda-recipes#401.

(BTW, the gcc package includes gfortran, and the libgcc package includes libgfortran.)

Theoretically, the conda guys will eventually push that gcc package over to the main anaconda channel. Until then, you'll need to specifically reference the asmeuer channel (or copy that package to your own channel, of course.) Just to repeat: Don't use the gcc 4.8.2 package that conda provides by default. It has portability problems.

[astrojuanlu]

Hi @stuarteberg, do you know if the Anaconda guys already pushed the latest fixes to the main channel? I'm waiting for that to fix my own packages. Thanks!

[stuarteberg]

do you know if the Anaconda guys already pushed the latest fixes to the main channel?

It looks like they finally did: https://anaconda.org/anaconda/gcc/files

$ conda search gcc
Fetching package metadata: ....
gcc                       .  4.8.2                         5  defaults        
                          .  4.8.5                         3  defaults        
libgcc                    .  4.8.4                         1  defaults        
                          .  4.8.5                         1  defaults

[astrojuanlu]

Thanks a lot for your answer, I will try to fix our issues now.

[astrojuanlu]

I pushed some changes that should fix these issues, but now I'm getting build errors related to PETSc. This is the neverending story :)

[astrojuanlu]

New packages uploaded. @e-aranda @sakhan007 Could you try updating DOLFIN to see if the errors are gone already? In principle the packages should be much more portable now.

[e-aranda]

Juan Luis,

thanks for your effort, but... I installed gcc-4.8 in my system and everything was fine. In order to try the new packages, I uninstalled gcc-4.8 and update dolfin from your channel. Then, running demo_poisson.py gives the following:

$ python demo_poisson.py 
Vendor:  Continuum Analytics, Inc. 
Package: mkl
Message: trial mode expires in 30 days
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Solving linear variational problem.
libGL error: unable to load driver: nouveau_dri.so
libGL error: driver pointer missing
libGL error: failed to load driver: nouveau
libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
X Error of failed request:  BadValue (integer parameter out of range for operation)
  Major opcode of failed request:  156 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
 Value in failed request:  0x0
 Serial number of failed request:  58
 Current serial number in output stream:  59
(fenics27)$

How can I undo the changes I made?

Ernesto

[astrojuanlu]

Hello @e-aranda, sorry for the inconvenience! Apparently I introduced some problem with the graphics which I have yet to understand. I will open a new issue, in the meanwhile you can manually install the previous build and run $ conda install /tmp/linux-64_dolfin-1.6.0-py27_2.tar.bz2.