The subprocess module does not work well on all HPC platforms. Please try one of the other system call methods by setting the INSTANT_SYSTEM_CALL_METHOD environment variable (see README for Instant <https://bitbucket.org/fenics-project/instant/>).
Johannes On Thu, Oct 15, 2015 at 6:44 PM Anirban Jana <[email protected]> wrote: > Hi, > I installed all components of Fenics from source on a Linux > cluster. The installation completed but on trying to run > demo_poisson.py, I get an unexplained error. Please advise. Below is > detailed information. I can provide further information as requested. > > Thanks a lot in advance > Anirban > > ***************** System info ********************* > -bash-4.2$ uname -a > Linux greenfield.psc.xsede.org 3.10.0-229.7.2.el7.x86_64 #1 SMP Tue Jun > 23 22:06:11 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > > ***************** Software environment ************ > > -bash-4.2$ module list > Currently Loaded Modulefiles: > 1) torque/5.1.1-1 4) globus/6.0.3 7) psc_path/1.0 > 10) scipy/0.15.1-mkl 13) boost/1.58.0 > 2) zlib/1.2.8 5) impi/5.1.1.109 8) xdusage/1.1-2 > 11) python/2.7.10-mkl 14) gcc/4.9.2 > 3) openssl/1.0.2d 6) icc/15.0.1 9) numpy/1.9.2-mkl > 12) swig/3.0.7 15) cmake/3.3.0 > > Note: Could it be because I built Fenics with Python 2.7.10? Thats the > optimized Python build on this cluster as of now. I read that the > recommended Python version for Fenics is 2.7.5 but I would rather not > rebuild Python ( and numpy), unless absolutely necessary. > > ***************** The error ************************* > -bash-4.2$ source > /home/anirban/fenics/1.6.0/pythonPkgs/share/dolfin/dolfin.conf > -bash-4.2$ python demo_poisson.py > 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/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/dolfin/functions/functionspace.py", > line 468, in __init__ > FunctionSpaceBase.__init__(self, mesh, element, constrained_domain) > File > > "/home/anirban/fenics/1.6.0/pythonPkgs/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/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", > line 64, in mpi_jit > return local_jit(*args, **kwargs) > File > > "/home/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", > line 128, in jit > return form_compiler.jit(form, parameters=p) > File > > "/home/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/ffc/jitcompiler.py", > line 72, in jit > return jit_element(ufl_object, parameters) > File > > "/home/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/ffc/jitcompiler.py", > line 180, in jit_element > compiled_form, module, prefix = jit_form(form, parameters) > File > > "/home/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/ffc/jitcompiler.py", > line 148, in jit_form > cache_dir = cache_dir) > File > > "/home/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/ffc/backends/ufc/build.py", > line 73, in build_ufc_module > **kwargs) > File > > "/home/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/instant/build.py", > line 563, in build_module > recompile(modulename, module_path, new_compilation_checksum, > build_system) > File > > "/home/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/instant/build.py", > line 144, in recompile > ret, output = get_status_output(cmd) > File > > "/home/anirban/fenics/1.6.0/pythonPkgs/lib/python2.7/site-packages/instant/output.py", > line 120, in get_status_output > pipe = Popen(cmd, shell=False, cwd=cwd, env=env, stdout=PIPE, > stderr=STDOUT) > File "/usr/local/packages/python/2.7.10/lib/python2.7/subprocess.py", > line 710, in __init__ > errread, errwrite) > File "/usr/local/packages/python/2.7.10/lib/python2.7/subprocess.py", > line 1335, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory > > -- > Anirban Jana, PhD > Senior Computational Scientist > (CFD, Computational Mechanics, Dynamics) > Pittsburgh Supercomputing Center, 300 S Craig Rm 371B, > Mechanical Engineering, Carnegie Mellon U, Scaife Hall Rm 326, > Pittsburgh PA 15213 > [email protected] (preferred mode of contact) > 412-268-2876 > > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support >
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