Dorsal

karmic.platform: There was a problem in build setup for petsc-3.0.0-p8.

Asked by Murtazo Nazarov

I am trying to install fenics using dorsal for Ubuntu 9.10: ./dorsal.sh platforms/karmic.platform. But I got the following error:

Unpacking petsc-3.0.0-p8
Building petsc-3.0.0-p8
=================================================================================
             Configuring PETSc to compile on your system
=================================================================================
/afs/nada.kth.se/home/x/u18gh7kx/data/Work/FEniCS_lp/petsc-3.0.0-p8/config/BuildSystem/config/compilers.py:7: DeprecationWarning: the sets module is deprecated
  import sets
/afs/nada.kth.se/home/x/u18gh7kx/data/Work/FEniCS_lp/petsc-3.0.0-p8/config/PETSc/package.py:7: DeprecationWarning: the md5 module is deprecated; use hashlib instead
  import md5
/afs/nada.kth.se/home/x/u18gh7kx/data/Work/FEniCS_lp/petsc-3.0.0-p8/config/BuildSystem/script.py:101: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module.
  import popen2
================================================================================= WARNING! Compiling PETSc with no debugging, this should only be done for timing and production runs. All development should be done when configured using --with-debugging=1 ================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:126) *********************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
---------------------------------------------------------------------------------------
You must specify a path for MPI with --with-mpi-dir=<directory>
If you do not want MPI, then give --with-mpi
*********************************************************************************

Failure with exit status: 1
Exit message: There was a problem in build setup for petsc-3.0.0-p8.

Any help?

murtazo

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Murtazo Nazarov
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Revision history for this message
Murtazo Nazarov (murtazo) said : 		#1

This stage is passed, it seems some packages were missing after the upgrading Ubuntu.

murtazo

Revision history for this message
Harish Narayanan (hnarayanan) said : 		#2

OK. Let me know if something goes wrong.

And you shouldn't need to type ./dorsal.sh platforms/karmic.platform

Just ./dorsal.sh should do.

Revision history for this message
Murtazo Nazarov (murtazo) said : 		#3

After installing necessary packages Dorsal did his job smoothly. I can compile demo programs in Dolfin, but it seems there is something wrong whith mpi:

na48:./demo
[na48:06157] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 269
[na48:06157] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 143
[na48:06157] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132
--------------------------------------------------------------------------
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_set_name failed
  --> Returned value A system-required executable either could not be found or was not executable by this user (-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: orte_init failed
  --> Returned "A system-required executable either could not be found or was not executable by this user" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[na48:6157] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
na48:cpp >

My Openmpi and gcc version is 4.4.1.

Revision history for this message
Harish Narayanan (hnarayanan) said : 		#4

Are you sure you are using the correct MPI, i.e. OpenMPI? If you have multiple MPI libraries installed, make sure

sudo update-alternatives --config mpi

is set to openmpi.

Revision history for this message
Murtazo Nazarov (murtazo) said : 		#5

That is what I am wondering, but I am not sure:

na48:cpp > sudo update-alternatives --config mpi
[sudo] password for murtazo:
There is only one alternative in link group mpi: /usr/lib/openmpi/include
Nothing to configure.

Revision history for this message
Murtazo Nazarov (murtazo) said : 		#6

Compiling and installing openmpi from the source fixed the problem.

Revision history for this message
Florian Rathgeber (florian-rathgeber) said : 		#7

You might also get this error if the openmpi-bin package was not installed.