If I don't load the old MPI, it seems like I don't have any: "mpicc -v" gives "mpicc: command not found". Without loading MPI, the installation gives the following error: ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Did not find package MPI needed by hdf5. Enable the package using --with-mpi ******************************************************************************* Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-2fa0Ik-build/setup.py", line 302, in <module> **metadata) File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip-2fa0Ik-build/setup.py", line 218, in run config(prefix, self.dry_run) File "/tmp/pip-2fa0Ik-build/setup.py", line 148, in config if status != 0: raise RuntimeError(status) RuntimeError: 256 ---------------------------------------- Command "/home/fgidel/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-2fa0Ik-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-OxfBa5-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/fgidel/firedrake/include/site/python2.7/petsc" failed with error code 1 in /tmp/pip-2fa0Ik-build/ Traceback (most recent call last): File "firedrake-install", line 884, in <module> install("petsc/") File "firedrake-install", line 491, in install run_pip_install(["--ignore-installed", package]) File "firedrake-install", line 354, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 205, in check_call subprocess.check_call(arguments, env=env) File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/fgidel/firedrake/bin/pip', 'install', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero exit status 1 Should I try with the option --with-mpi ? The OSError and AttributeError (where N is defined as a positive integer) occur when I load the old MPI. I cannot try without loading the old MPI since Firedrake isn't installed correctly in that case. The ValueError ("ValueError: Number of cells must be a positive integer") for N is fixed when I put an integer instead of N. Then the file runs correctly. However, I don't know how to overcome the OSError in my other program ("OSError: [Errno 12] Cannot allocate memory"). I tried on another machine with the same installation of Firedrake and loading the same openmpi, and it gives the same error so I don't think it comes from a lack of memory. In another program, I also get an error that I don't get on my laptop (where an older version of firedrake is installed): wf1_solver = NonlinearVariationalSolver(wf1_problem) File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", line 74, in _merge_loops while isinstance(loop_b.children[0], (Block, For)): IndexError: list index out of range Exception AttributeError: "'NonlinearVariationalSolver' object has no attribute '_parameters'" in <bound method NonlinearVariationalSolver.__del__ of <firedrake.variational_solver.NonlinearVariationalSolver object at 0x4f4d490>> ignored Maybe the program editor is causing problem ? I remember, last year I had errors due to an old version of Xcode on Mac. But I guess the installation would have raised an error if a dependency was missing or not recent enough... ________________________________ De : Miklós Homolya <m.homolya14@imperial.ac.uk> Envoyé : mardi 30 août 2016 11:20:37 À : Floriane Gidel [RPG]; firedrake Objet : Re: [firedrake] Saving txt files while running in parallel Do you have any MPI available if you don't load the old MPI? What does "mpicc -v" say in that case? What is the installation error you get if you don't load MPI? Yes, if you installed with a specific MPI, you must have the same MPI when sourcing Firedrake. More importantly, what about the other errors you had? (OSError: allocation failed, N isn't a positive integer etc.) On 30/08/16 11:13, Floriane Gidel [RPG] wrote: If I do not load the old openmpi before the installation, the installation breaks. It only works if I run module load/mpi/compat-openmpi16-x86_64 python firedrake-install --no-package-manager --disable-ssh With this installation, if I do not load the old openmpi before sourcing Firedrake, I have an mpi error. This is why I run module load/mpi/compat-openmpi16-x86_64 source firedrake/bin/activate before running my programs. So it does not work without loading the old openmpi... ________________________________ De : Miklós Homolya <m.homolya14@imperial.ac.uk><mailto:m.homolya14@imperial.ac.uk> Envoyé : mardi 30 août 2016 10:59:45 À : Floriane Gidel [RPG]; firedrake Objet : Re: [firedrake] Saving txt files while running in parallel OK, in this case you don't even need to load the old OpenMPI anymore. Does it work now? On 30/08/16 10:57, Floriane Gidel [RPG] wrote: This is what I have done: delete Firedrake and re-install it with the command : python firedrake-install --no-package-manager --disable-ssh ________________________________ De : Homolya, Miklós <m.homolya14@imperial.ac.uk><mailto:m.homolya14@imperial.ac.uk> Envoyé : mardi 30 août 2016 10:53:52 À : Floriane Gidel [RPG]; firedrake Objet : Re: [firedrake] Saving txt files while running in parallel OK, so in case of a system upgrade which brings new versions (not just bugfixes) of the C compiler, MPI library etc. I suggest doing a fresh installation of Firedrake. Currently, this isn't a scenario that firedrake-update can correctly handle. ________________________________ From: Floriane Gidel [RPG] <mmfg@leeds.ac.uk><mailto:mmfg@leeds.ac.uk> Sent: 30 August 2016 10:47:36 To: Homolya, Miklós; firedrake Subject: RE: [firedrake] Saving txt files while running in parallel Hi Miklós, Basically I had installed Firedrake on my linux machine and the programs were running correctly, but later on it stopped working. I asked the IT and they said : "It seems that Firedrake got broken after an update of one of it's many dependencies. Firedrake requires an older version of OpenMPI to function correctly. You need to load the module mpi/compat-openmpi16-x86_64 to activate this older version." By doing this, I have no error coming from mpi, but other errors as those I sent earlier (OSError, ValueError...), and I don't have them on my laptop. It is not on a cluster. ________________________________ De : Miklós Homolya <m.homolya14@imperial.ac.uk><mailto:m.homolya14@imperial.ac.uk> Envoyé : mardi 30 août 2016 10:07:42 À : firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk>; Floriane Gidel [RPG] Objet : Re: [firedrake] Saving txt files while running in parallel Answers inlined below. On 30/08/16 07:11, Floriane Gidel [RPG] wrote: mesh = UnitIntervalMesh(N) raises the error ValueError: Number of cells must be a positive integer while the file runs correctly on my laptop with another version of Firedrake. Well, what is the value of N? I did not encounter any issue while running the installation script, but I know that Firedrake requires a version of OpenMPI different from the one installed on my machine, It's not correct to say that Firedrake requires a specific MPI implementation or that it requires a specific version of OpenMPI. Firedrake, in principle at least, should work with any MPI implementation. The install script happens to install OpenMPI on Ubuntu and Mac OS X, but that's just for convenience. If you have another MPI implementation installed, with the --no-package-manager option firedrake-install should just pick that up and use it. so I load the required version before sourcing Firedrake. Maybe this is not enough for Firedrake to access the required version? Below are the commands I used to load the module and install Firedrake: module load/mpi/compat-openmpi16-x86_64 python firedrake-install --no-package-manager --disable-ssh and to source the Firedrake environment before running simulations: module load/mpi/compat-openmpi16-x86_64 source firedrake/bin/activate Does Firedrake use the loaded version of openmpi with these commands, or is there something missing? Firedrake uses whatever MPI implementation provides mpicc and similar command. You can check e.g. what $ mpicc -v says. It is important to use the same MPI when installing and when using Firedrake, but you seem to have done this correctly. I wonder though why did you load an OpenMPI implementation... If this is on a cluster, you should use whatever the "native" MPI of that cluster is.