Re: [firedrake] firedrake-install on macOS Sierra
I think we've seen this occasionally on new macs. I think it's caused by the virtualenv getting installed in a different python installation from the one which is being used to install Firedrake. Try the following: Open a new terminal (this is to try to avoid any bash path caching effects) Type "which python". The answer you want is /usr/local/bin/python run python and check that you can import virtualenv If all the above works, try running firedrake-install in the new shell. If anything above fails, tell us. Regards, David On Tue, 21 Mar 2017 at 10:28 Anna Kalogirou <A.Kalogirou@leeds.ac.uk> wrote:
Dear all,
I am installing firedrake on my new laptop from scratch (running macOS Sierra).
The installation script runs and installs virtualenv, up to the point where I get this:
Virtual env installed. Please run firedrake-install again.
But when I run
python firedrake-install
again, it just does the same thing (similar to the previous step) and does not install firedrake (and petsc etc..). What shall I do?
Best, Anna.
-- Dr David Ham Department of Mathematics Imperial College London
Thank you David, You suggestion indeed solved the issue and the installation has finished. However, when I test the installation I get the following without any more info: make alltest Building extension modules Linting firedrake codebase Linting firedrake test suite Linting firedrake scripts Running all regression tests make: *** [test] Error 1 Also, when running the helmholtz.py example, I get something weird: [UEADGKT4HGBGG7F:12658] [[29900,0],0] ORTE_ERROR_LOG: Bad parameter in file orted/pmix/pmix_server.c at line 262 [UEADGKT4HGBGG7F:12658] [[29900,0],0] ORTE_ERROR_LOG: Bad parameter in file ess_hnp_module.c at line 666 -------------------------------------------------------------------------- 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): pmix server init failed --> Returned value Bad parameter (-5) instead of ORTE_SUCCESS -------------------------------------------------------------------------- [UEADGKT4HGBGG7F:12651] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 575 [UEADGKT4HGBGG7F:12651] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 165 -------------------------------------------------------------------------- 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 Unable to start a daemon on the local node (-127) 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 "Unable to start a daemon on the local node" (-127) 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) [UEADGKT4HGBGG7F:12651] 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! ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of David Ham <David.Ham@imperial.ac.uk> Sent: 21 March 2017 10:52:55 To: firedrake Subject: Re: [firedrake] firedrake-install on macOS Sierra I think we've seen this occasionally on new macs. I think it's caused by the virtualenv getting installed in a different python installation from the one which is being used to install Firedrake. Try the following: Open a new terminal (this is to try to avoid any bash path caching effects) Type "which python". The answer you want is /usr/local/bin/python run python and check that you can import virtualenv If all the above works, try running firedrake-install in the new shell. If anything above fails, tell us. Regards, David On Tue, 21 Mar 2017 at 10:28 Anna Kalogirou <A.Kalogirou@leeds.ac.uk<mailto:A.Kalogirou@leeds.ac.uk>> wrote: Dear all, I am installing firedrake on my new laptop from scratch (running macOS Sierra). The installation script runs and installs virtualenv, up to the point where I get this: Virtual env installed. Please run firedrake-install again. But when I run python firedrake-install again, it just does the same thing (similar to the previous step) and does not install firedrake (and petsc etc..). What shall I do? Best, Anna. -- Dr David Ham Department of Mathematics Imperial College London
Ok I fixed it. It is a problem with openmpi on macOS Sierra https://www.open-mpi.org/faq/?category=osx It was fixed by setting a shorter name for the openmpi temp directory: export TMPDIR=/tmp ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Anna Kalogirou <A.Kalogirou@leeds.ac.uk> Sent: 21 March 2017 12:03:41 To: firedrake Subject: Re: [firedrake] firedrake-install on macOS Sierra Thank you David, You suggestion indeed solved the issue and the installation has finished. However, when I test the installation I get the following without any more info: make alltest Building extension modules Linting firedrake codebase Linting firedrake test suite Linting firedrake scripts Running all regression tests make: *** [test] Error 1 Also, when running the helmholtz.py example, I get something weird: [UEADGKT4HGBGG7F:12658] [[29900,0],0] ORTE_ERROR_LOG: Bad parameter in file orted/pmix/pmix_server.c at line 262 [UEADGKT4HGBGG7F:12658] [[29900,0],0] ORTE_ERROR_LOG: Bad parameter in file ess_hnp_module.c at line 666 -------------------------------------------------------------------------- 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): pmix server init failed --> Returned value Bad parameter (-5) instead of ORTE_SUCCESS -------------------------------------------------------------------------- [UEADGKT4HGBGG7F:12651] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 575 [UEADGKT4HGBGG7F:12651] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 165 -------------------------------------------------------------------------- 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 Unable to start a daemon on the local node (-127) 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 "Unable to start a daemon on the local node" (-127) 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) [UEADGKT4HGBGG7F:12651] 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! ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of David Ham <David.Ham@imperial.ac.uk> Sent: 21 March 2017 10:52:55 To: firedrake Subject: Re: [firedrake] firedrake-install on macOS Sierra I think we've seen this occasionally on new macs. I think it's caused by the virtualenv getting installed in a different python installation from the one which is being used to install Firedrake. Try the following: Open a new terminal (this is to try to avoid any bash path caching effects) Type "which python". The answer you want is /usr/local/bin/python run python and check that you can import virtualenv If all the above works, try running firedrake-install in the new shell. If anything above fails, tell us. Regards, David On Tue, 21 Mar 2017 at 10:28 Anna Kalogirou <A.Kalogirou@leeds.ac.uk<mailto:A.Kalogirou@leeds.ac.uk>> wrote: Dear all, I am installing firedrake on my new laptop from scratch (running macOS Sierra). The installation script runs and installs virtualenv, up to the point where I get this: Virtual env installed. Please run firedrake-install again. But when I run python firedrake-install again, it just does the same thing (similar to the previous step) and does not install firedrake (and petsc etc..). What shall I do? Best, Anna. -- Dr David Ham Department of Mathematics Imperial College London
participants (2)
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Anna Kalogirou
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David Ham