Troubles when trying to update firedrake
Dear Firedrakers, I installed firedrake with the following options few months ago : python3 firedrake-install --disable-ssh --mpiexec mpirun.openmpi --mpicc mpicc.openmpi --mpicxx mpicxx.openmpi --mpif90 mpif90.openmpi I am now trying to update the code. So I am activating the virtualenv and I run : firedrake-update I then get the error : Running firedrake-update --verbose Traceback (most recent call last): File "firedrake-update", line 1254, in <module> mpiexec_loc = shutil.which(args.mpiexec) AttributeError: 'Namespace' object has no attribute 'mpiexec' But if I run the following in a python script, everything seems OK :
import shutil shutil.which('mpiexec') '/home/mylogin/dev/Firedrake/firedrake/bin/mpiexec'
What is going wrong? Nicolas
On 14 Oct 2020, at 15:49, Karin&NiKo <niko.karin@gmail.com> wrote:
Dear Firedrakers,
I installed firedrake with the following options few months ago : python3 firedrake-install --disable-ssh --mpiexec mpirun.openmpi --mpicc mpicc.openmpi --mpicxx mpicxx.openmpi --mpif90 mpif90.openmpi
I am now trying to update the code. So I am activating the virtualenv and I run : firedrake-update I then get the error : Running firedrake-update --verbose Traceback (most recent call last): File "firedrake-update", line 1254, in <module> mpiexec_loc = shutil.which(args.mpiexec) AttributeError: 'Namespace' object has no attribute 'mpiexec'
This error is that the "args" object has no "mpiexec" attribute. I'm not sure how that happens. Does it help to try and recover from a broken update script following the advice here: https://www.firedrakeproject.org/download.html#recovering-from-a-broken-inst... Lawrence
Mmm... No it does not help. I see that python3.5.3 is used in my firedrake install since it is the default python3 version on my computer. Is python3.6 *really* mandatory? Nicolas Le mer. 14 oct. 2020 à 18:42, Lawrence Mitchell <wence@gmx.li> a écrit :
On 14 Oct 2020, at 15:49, Karin&NiKo <niko.karin@gmail.com> wrote:
Dear Firedrakers,
I installed firedrake with the following options few months ago : python3 firedrake-install --disable-ssh --mpiexec mpirun.openmpi --mpicc mpicc.openmpi --mpicxx mpicxx.openmpi --mpif90 mpif90.openmpi
I am now trying to update the code. So I am activating the virtualenv and I run : firedrake-update I then get the error : Running firedrake-update --verbose Traceback (most recent call last): File "firedrake-update", line 1254, in <module> mpiexec_loc = shutil.which(args.mpiexec) AttributeError: 'Namespace' object has no attribute 'mpiexec'
This error is that the "args" object has no "mpiexec" attribute. I'm not sure how that happens.
Does it help to try and recover from a broken update script following the advice here:
https://www.firedrakeproject.org/download.html#recovering-from-a-broken-inst...
Lawrence
And an extra question : do you have some experience on how to set-up a python version (say 3.6.5) on a computer on which you do not have root privileges that could be used in roder to build firedrake? Le jeu. 15 oct. 2020 à 08:53, Karin&NiKo <niko.karin@gmail.com> a écrit :
Mmm... No it does not help. I see that python3.5.3 is used in my firedrake install since it is the default python3 version on my computer. Is python3.6 *really* mandatory?
Nicolas
Le mer. 14 oct. 2020 à 18:42, Lawrence Mitchell <wence@gmx.li> a écrit :
On 14 Oct 2020, at 15:49, Karin&NiKo <niko.karin@gmail.com> wrote:
Dear Firedrakers,
I installed firedrake with the following options few months ago : python3 firedrake-install --disable-ssh --mpiexec mpirun.openmpi --mpicc mpicc.openmpi --mpicxx mpicxx.openmpi --mpif90 mpif90.openmpi
I am now trying to update the code. So I am activating the virtualenv and I run : firedrake-update I then get the error : Running firedrake-update --verbose Traceback (most recent call last): File "firedrake-update", line 1254, in <module> mpiexec_loc = shutil.which(args.mpiexec) AttributeError: 'Namespace' object has no attribute 'mpiexec'
This error is that the "args" object has no "mpiexec" attribute. I'm not sure how that happens.
Does it help to try and recover from a broken update script following the advice here:
https://www.firedrakeproject.org/download.html#recovering-from-a-broken-inst...
Lawrence
Hi Nicolas, Python 3.6 is indeed a hard requirement. Firedrake uses f strings which aren’t part of Python 3.5 so you’ll get syntax errors if you use 3.5. If you don’t have root on a machine then it’s fairly simple to just build Python from source, and in fact that’s what we do on the UK national supercomputer. Python provide instructions for doing this: https://docs.python.org/3/using/unix.html Our Python build script for ARCHER, which might be a useful reference but does contain a lot of system-specific details, is here: https://github.com/firedrakeproject/firedrake-archer/blob/master/build_pytho... Regards, David From: <firedrake-bounces@imperial.ac.uk> on behalf of Karin&NiKo <niko.karin@gmail.com> Date: Thursday, 15 October 2020 at 09:33 To: Lawrence Mitchell <wence@gmx.li> Cc: firedrake <firedrake@imperial.ac.uk> Subject: Re: [firedrake] Troubles when trying to update firedrake And an extra question : do you have some experience on how to set-up a python version (say 3.6.5) on a computer on which you do not have root privileges that could be used in roder to build firedrake? Le jeu. 15 oct. 2020 à 08:53, Karin&NiKo <niko.karin@gmail.com<mailto:niko.karin@gmail.com>> a écrit : Mmm... No it does not help. I see that python3.5.3 is used in my firedrake install since it is the default python3 version on my computer. Is python3.6 *really* mandatory? Nicolas Le mer. 14 oct. 2020 à 18:42, Lawrence Mitchell <wence@gmx.li<mailto:wence@gmx.li>> a écrit :
On 14 Oct 2020, at 15:49, Karin&NiKo <niko.karin@gmail.com<mailto:niko.karin@gmail.com>> wrote:
Dear Firedrakers,
I installed firedrake with the following options few months ago : python3 firedrake-install --disable-ssh --mpiexec mpirun.openmpi --mpicc mpicc.openmpi --mpicxx mpicxx.openmpi --mpif90 mpif90.openmpi
I am now trying to update the code. So I am activating the virtualenv and I run : firedrake-update I then get the error : Running firedrake-update --verbose Traceback (most recent call last): File "firedrake-update", line 1254, in <module> mpiexec_loc = shutil.which(args.mpiexec) AttributeError: 'Namespace' object has no attribute 'mpiexec'
This error is that the "args" object has no "mpiexec" attribute. I'm not sure how that happens. Does it help to try and recover from a broken update script following the advice here: https://www.firedrakeproject.org/download.html#recovering-from-a-broken-inst... Lawrence
Thank you very much for the information David. I will install by hand a specific version of python. I also notice that you have the chance that your supercomputer benefits from an internet access! The supercomputers I am using do not have this privilege! Thanks again, Nicolas Le jeu. 15 oct. 2020 à 10:44, Ham, David A <david.ham@imperial.ac.uk> a écrit :
Hi Nicolas,
Python 3.6 is indeed a hard requirement. Firedrake uses f strings which aren’t part of Python 3.5 so you’ll get syntax errors if you use 3.5. If you don’t have root on a machine then it’s fairly simple to just build Python from source, and in fact that’s what we do on the UK national supercomputer. Python provide instructions for doing this: https://docs.python.org/3/using/unix.html Our Python build script for ARCHER, which might be a useful reference but does contain a lot of system-specific details, is here: https://github.com/firedrakeproject/firedrake-archer/blob/master/build_pytho...
Regards,
David
*From: *<firedrake-bounces@imperial.ac.uk> on behalf of Karin&NiKo < niko.karin@gmail.com> *Date: *Thursday, 15 October 2020 at 09:33 *To: *Lawrence Mitchell <wence@gmx.li> *Cc: *firedrake <firedrake@imperial.ac.uk> *Subject: *Re: [firedrake] Troubles when trying to update firedrake
And an extra question : do you have some experience on how to set-up a python version (say 3.6.5) on a computer on which you do not have root privileges that could be used in roder to build firedrake?
Le jeu. 15 oct. 2020 à 08:53, Karin&NiKo <niko.karin@gmail.com> a écrit :
Mmm... No it does not help. I see that python3.5.3 is used in my firedrake install since it is the default python3 version on my computer.
Is python3.6 *really* mandatory?
Nicolas
Le mer. 14 oct. 2020 à 18:42, Lawrence Mitchell <wence@gmx.li> a écrit :
On 14 Oct 2020, at 15:49, Karin&NiKo <niko.karin@gmail.com> wrote:
Dear Firedrakers,
I installed firedrake with the following options few months ago : python3 firedrake-install --disable-ssh --mpiexec mpirun.openmpi --mpicc mpicc.openmpi --mpicxx mpicxx.openmpi --mpif90 mpif90.openmpi
I am now trying to update the code. So I am activating the virtualenv and I run : firedrake-update I then get the error : Running firedrake-update --verbose Traceback (most recent call last): File "firedrake-update", line 1254, in <module> mpiexec_loc = shutil.which(args.mpiexec) AttributeError: 'Namespace' object has no attribute 'mpiexec'
This error is that the "args" object has no "mpiexec" attribute. I'm not sure how that happens.
Does it help to try and recover from a broken update script following the advice here:
https://www.firedrakeproject.org/download.html#recovering-from-a-broken-inst...
Lawrence
Dear David, I installed python 3.7.0 using the Archer script (slightly modified) and the installation procedure did succeed. Nevertheless, when trying to import firedrake, I get the following error : Python 3.7.0 (default, Oct 15 2020, 11:45:50) [GCC 6.3.0 20170516] on linux Type "help", "copyright", "credits" or "license" for more information.
import firedrake
It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): setting topology failed --> Returned value Error (-1) instead of ORTE_SUCCESS -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_init failed --> Returned value Error (-1) instead of ORTE_SUCCESS -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): ompi_mpi_init: ompi_rte_init failed --> Returned "Error" (-1) instead of "Success" (0) -------------------------------------------------------------------------- *** An error occurred in MPI_Init_thread *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [machineName:31007] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! It clearly comes from openMPI but I do not see why it happens since I can run other mpi processes (like "mpirun -n2 ls"). Any help would be appreciated. Nicolas Le jeu. 15 oct. 2020 à 11:32, Karin&NiKo <niko.karin@gmail.com> a écrit :
Thank you very much for the information David. I will install by hand a specific version of python. I also notice that you have the chance that your supercomputer benefits from an internet access! The supercomputers I am using do not have this privilege! Thanks again, Nicolas
Le jeu. 15 oct. 2020 à 10:44, Ham, David A <david.ham@imperial.ac.uk> a écrit :
Hi Nicolas,
Python 3.6 is indeed a hard requirement. Firedrake uses f strings which aren’t part of Python 3.5 so you’ll get syntax errors if you use 3.5. If you don’t have root on a machine then it’s fairly simple to just build Python from source, and in fact that’s what we do on the UK national supercomputer. Python provide instructions for doing this: https://docs.python.org/3/using/unix.html Our Python build script for ARCHER, which might be a useful reference but does contain a lot of system-specific details, is here: https://github.com/firedrakeproject/firedrake-archer/blob/master/build_pytho...
Regards,
David
*From: *<firedrake-bounces@imperial.ac.uk> on behalf of Karin&NiKo < niko.karin@gmail.com> *Date: *Thursday, 15 October 2020 at 09:33 *To: *Lawrence Mitchell <wence@gmx.li> *Cc: *firedrake <firedrake@imperial.ac.uk> *Subject: *Re: [firedrake] Troubles when trying to update firedrake
And an extra question : do you have some experience on how to set-up a python version (say 3.6.5) on a computer on which you do not have root privileges that could be used in roder to build firedrake?
Le jeu. 15 oct. 2020 à 08:53, Karin&NiKo <niko.karin@gmail.com> a écrit :
Mmm... No it does not help. I see that python3.5.3 is used in my firedrake install since it is the default python3 version on my computer.
Is python3.6 *really* mandatory?
Nicolas
Le mer. 14 oct. 2020 à 18:42, Lawrence Mitchell <wence@gmx.li> a écrit :
On 14 Oct 2020, at 15:49, Karin&NiKo <niko.karin@gmail.com> wrote:
Dear Firedrakers,
I installed firedrake with the following options few months ago : python3 firedrake-install --disable-ssh --mpiexec mpirun.openmpi --mpicc mpicc.openmpi --mpicxx mpicxx.openmpi --mpif90 mpif90.openmpi
I am now trying to update the code. So I am activating the virtualenv and I run : firedrake-update I then get the error : Running firedrake-update --verbose Traceback (most recent call last): File "firedrake-update", line 1254, in <module> mpiexec_loc = shutil.which(args.mpiexec) AttributeError: 'Namespace' object has no attribute 'mpiexec'
This error is that the "args" object has no "mpiexec" attribute. I'm not sure how that happens.
Does it help to try and recover from a broken update script following the advice here:
https://www.firedrakeproject.org/download.html#recovering-from-a-broken-inst...
Lawrence
On 15 Oct 2020, at 12:15, Karin&NiKo <niko.karin@gmail.com> wrote:
Dear David, I installed python 3.7.0 using the Archer script (slightly modified) and the installation procedure did succeed. Nevertheless, when trying to import firedrake, I get the following error :
Python 3.7.0 (default, Oct 15 2020, 11:45:50) [GCC 6.3.0 20170516] on linux Type "help", "copyright", "credits" or "license" for more information.
import firedrake
It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer):
setting topology failed --> Returned value Error (-1) instead of ORTE_SUCCESS -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer):
orte_ess_init failed --> Returned value Error (-1) instead of ORTE_SUCCESS -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer):
ompi_mpi_init: ompi_rte_init failed --> Returned "Error" (-1) instead of "Success" (0) -------------------------------------------------------------------------- *** An error occurred in MPI_Init_thread *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [machineName:31007] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
It clearly comes from openMPI but I do not see why it happens since I can run other mpi processes (like "mpirun -n2 ls").
Does mpirun -n 2 python -c "import firedrake" work? On some supercomputers you always have to run MPI-enabled programs via the mpirun system. Lawrence
participants (3)
-
Ham, David A
-
Karin&NiKo
-
Lawrence Mitchell