ESYS Installation -permission denied

Hi Tao,

I would recommend you to use packaged version of Esys-Particle. It is
"more correct" way to install software into the standard paths (/usr).

https://answers.launchpad.net/esys-particle/+faq/1792

Anton

On Tue, Jan 31, 2012 at 7:55 PM, Tao
<email address hidden> wrote:
> New question #186430 on ESyS-Particle:
> https://answers.launchpad.net/esys-particle/+question/186430
>
> Dear all,
> I am trying to install ESyS-Particle-2.1 in one of my computer, but I met one problem when I try to type "sudo make install" at the final stage. The error message is shown as below:
>
> ----------------------------------------------------------------------
> make[3]: Nothing to be done for `install-data-am'.
> make[3]: Leaving directory `/home/tao/ESyS-Particle-2.1/Python/BoostPythonUtil'
> make[2]: Leaving directory `/home/tao/ESyS-Particle-2.1/Python/BoostPythonUtil'
> Making install in esys
> make[2]: Entering directory `/home/tao/ESyS-Particle-2.1/Python/esys'
> Making install in lsm
> make[3]: Entering directory `/home/tao/ESyS-Particle-2.1/Python/esys/lsm'
> Making install in doc
> make[4]: Entering directory `/home/tao/ESyS-Particle-2.1/Python/esys/lsm/doc'
> make[5]: Entering directory `/home/tao/ESyS-Particle-2.1/Python/esys/lsm/doc'
> make[5]: Nothing to be done for `install-exec-am'.
> test -z "/usr/local/lib/python2.6/dist-packages/esys/lsm/doc" || /bin/mkdir -p "/usr/local/lib/python2.6/dist-packages/esys/lsm/doc"
>  /usr/bin/install -c -m 644 __init__.py Installation.py InitialConfigTut.py GravityTut.py Overview.py Util.py VisualisationTut.py '/usr/local/lib/python2.6/dist-packages/esys/lsm/doc'
> /bin/bash: line 16: ../../../../py-compile: Permission denied
> make[5]: *** [install-lsmdocPYTHON] Error 126
> make[5]: Leaving directory `/home/tao/ESyS-Particle-2.1/Python/esys/lsm/doc'
> make[4]: *** [install-am] Error 2
> make[4]: Leaving directory `/home/tao/ESyS-Particle-2.1/Python/esys/lsm/doc'
> make[3]: *** [install-recursive] Error 1
> make[3]: Leaving directory `/home/tao/ESyS-Particle-2.1/Python/esys/lsm'
> make[2]: *** [install-recursive] Error 1
> make[2]: Leaving directory `/home/tao/ESyS-Particle-2.1/Python/esys'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory `/home/tao/ESyS-Particle-2.1/Python'
> make: *** [install-recursive] Error 1
> tao@tao-desktop:~/ESyS-Particle-2.1$
> --------------------------------------------------------------------------------------------------------
>
> I am using Ubuntu 10.04, 32 bit in a virtual machine.
> I think the error is really wired sinece I executed the command as root. I do not know why it happened "/bin/bash: line 16: ../../../../py-compile: Permission denied".
>
> Please can anybody give me any suggestion?
>
> Thanks!
>
> Yours,
> Tao
>
> --
> You received this question notification because you are an answer
> contact for ESyS-Particle.

Hi Anton,
Thanks for your suggestion. I also tried the daily version. However, I got the error message as below:

tao@tao-desktop:~/Dropbox/project/consolidation/1e-6$ mpirun -np 3 esysparticle consolidation.py
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during opal_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):

  opal_paffinity_base_select failed
  --> Returned value -13 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
[tao-desktop:21154] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file ../../../orte/runtime/orte_init.c at line 77
--------------------------------------------------------------------------
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 "Not found" (-13) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[tao-desktop:21154] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during opal_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):

  opal_paffinity_base_select failed
  --> Returned value -13 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
[tao-desktop:21155] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file ../../../orte/runtime/orte_init.c at line 77
--------------------------------------------------------------------------
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 "Not found" (-13) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[tao-desktop:21155] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during opal_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):

  opal_paffinity_base_select failed
  --> Returned value -13 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
[tao-desktop:21156] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file ../../../orte/runtime/orte_init.c at line 77
--------------------------------------------------------------------------
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 "Not found" (-13) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[tao-desktop:21156] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------

I am running the code in a virtual machine on a linux server. I do not know what causes this problem. Previously, I installed ESyS on a Ubuntu 10.04 machine without any problem. I still want to try to compile the ESyS source code but I do not know how to fix the "permission denied" problem as listed above.

Does anybody meet the same problem before? Please help me out.

Thanks.

Tao

Hi Tao.

The permission denial I have not seen before when installing ESyS-Particle. The only thing I can say for now is that you have an OS installation problem on your VM, or at least there is something wrong with sudo. I don't think that ESyS-Particle is to blame in this instance.

Vince

Thanks Dion Weatherley, that solved my question.