Hi All,
I have never managed to install FEniCS under RedHat Linux.
Running
curl -s http://fenicsproject.org/fenics-install.sh | bash
and selecting stable version quickly fails:
Downloading http://releases.nixos.org/patchelf/patchelf-0.8/patchelf-0.8.tar.bz2...
[=========================] 100.0% (0.1MB of 0.1MB) 3.612MB/s ETA 0s
[patchelf] Building patchelf/k3rloj265ogt, follow log with:
[patchelf] tail -f /home1/sivy1/.hashdist/tmp/patchelf-k3rloj265ogt/build.log
Downloading https://github.com/xianyi/OpenBLAS/archive/v0.2.13.tar.gz...
[=========================] 100.0% (9.4MB of 9.4MB) 32.741MB/s ETA 0s
[blas] Building blas/bq7qrgo73lhs, follow log with:
[blas] tail -f /home1/sivy1/.hashdist/tmp/blas-bq7qrgo73lhs/build.log
[CRITICAL] Uncaught exception:
[CRITICAL] Traceback (most recent call last):
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/cli/main.py", line 202, in help_on_exceptions
[CRITICAL] return func(*args, **kw)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/cli/main.py", line 174, in command_line_entry_point
[CRITICAL] retcode = args.subcommand_handler(ctx, args)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/cli/frontend_cli.py", line 51, in run
[CRITICAL] self.profile_builder_action()
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/cli/frontend_cli.py", line 108, in profile_builder_action
[CRITICAL] self.args.k, self.args.debug)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/spec/builder.py", line 150, in build
[CRITICAL] keep_build=keep_build, debug=debug)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/build_store.py", line 379, in ensure_present
[CRITICAL] artifact_dir = builder.build(config, keep_build)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/build_store.py", line 554, in build
[CRITICAL] self.build_to(artifact_dir, config, keep_build)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/build_store.py", line 573, in build_to
[CRITICAL] self.run_build_commands(build_dir, artifact_dir, env, config)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/build_store.py", line 631, in run_build_commands
[CRITICAL] temp_dir=job_tmp_dir, debug=self.debug)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/run_job.py", line 342, in run_job
[CRITICAL] executor.run_command_list(assembled_commands, env, ())
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/run_job.py", line 615, in run_command_list
[CRITICAL] self.run_node(command_node, env, pos)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/run_job.py", line 501, in run_node
[CRITICAL] getattr(self, 'handle_%s' % type)(node, env, node_pos)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/run_job.py", line 541, in handle_cmd
[CRITICAL] self.handle_command_nodes(node, env, node_pos)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/run_job.py", line 602, in handle_command_nodes
[CRITICAL] func(args, node_env)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/run_job.py", line 624, in run_cmd
[CRITICAL] self.logged_check_call(args, env, stdout_to)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/run_job.py", line 718, in logged_check_call
[CRITICAL] retcode = self._log_process_with_logpipes(proc, stdout_to)
[CRITICAL] File "/tmp/fenics-install.EqFV5W/hashdist/hashdist/core/run_job.py", line 843, in _log_process_with_logpipes
[CRITICAL] events = poller.poll(50)
[CRITICAL] BuildFailedError: error: (4, 'Interrupted system call')
[CRITICAL] This exception has not been translated to a human-friendly error message,
[CRITICAL] please file an issue at https://github.com/hashdist/hashdist/issues pasting
[CRITICAL] this stack trace.
=========
Considering that FEniCS is using some highly exotic installation method instead of standard ./configure or cmake or make, I do not know where to start debugging it. Why yet another software installation method? What's wrong with the standard ones?
Do I understand correctly that FEniCS comes with all the dependencies and would not use the installed versions of BLAS, PETCS, etc?
I am using LMOD to load various software packages (we have several versions of the same packages installed in non standard locations; when you do, for example, 'module load gcc/4.9.2' the environmental variables are modified to make the corresponding package visible). What version of gcc do I need? What version of python? Does FEniCS look at PATH and LD_LIBRARY_PATH to find necessary software, or does it use hardcoded paths to, for example, /usr/bin, /usr/lib64, etc.? I got an impression that it ignores the environment.
I was not successful with using conda either: things get installed without complaints but do not work.
Do I understand correctly that with conda one can only install Python API to FEniCS?
Or does it also install C++ API? I noticed that Anaconda during the installation loads mkl. Does one need license to use Anaconda after FEniCS is installed since it looks like commercial accelerated plugin is loaded?
Thank you,
Igor
