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Subject: Re: [OMPI users] errors testing openmpi1.6.5 ----
From: Gus Correa (gus_at_[hidden])
Date: 2013-07-25 19:21:55


Hi Yuping

Something seems to be broken in the way you set your environment
variables.
We use .bashrc/.tcshrc for this.
For what is worth, the bash man page says:

***
"When bash is invoked as an interactive login shell, or as a non-inter-
active shell with the --login option, it first reads and executes com-
mands from the file /etc/profile, if that file exists. After reading
that file, it looks for ~/.bash_profile, ~/.bash_login, and ~/.profile,
in that order, and reads and executes commands from the first one that
exists and is readable. The --noprofile option may be used when the
shell is started to inhibit this behavior.

When a login shell exits, bash reads and executes commands from the
file ~/.bash_logout, if it exists.

When an interactive shell that is not a login shell is started, bash
reads and executes commands from ~/.bashrc, if that file exists. This
may be inhibited by using the --norc option. The --rcfile file option
will force bash to read and execute commands from file instead of
~/.bashrc. "
***

Notice the difference between interactive login shells,
and interactive shell that is not a login shell.

However, it is hard to guess what it is going on.
We (the OMPI list) don't even know if you are running the
job in a single machine, or on a cluster, or on a few networked
workstations.
It would help if you tell more.

Anyway, you could try to pass along the environment variables
the mpiexec command line.

Something like this:

***
export PATH=... (whatever you use)
export LD_LIBRARY_PATH=... (whatever you use)
mpiexec -x PATH -x LD_LIBRARY_PATH -np 4 ./my_program

***

See 'man mpiexec" for details.

**

In any case, in my humble opinion,
the best approach is to fix for good the problems with
your environment.
They will haunt you sooner or later.

I hope this helps,
Gus Correa

On 07/25/2013 05:58 PM, Yuping Sun wrote:
>
> Hi Gus:
>
> Thank you. I did these as I use .bash_profile to add the path and LD, but it did not help. Thank you.
> Is there anything else you can think of?
>
> Best regards,
>
> Yuping
>
> -----Original Message-----
> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf Of Gus Correa
> Sent: Thursday, July 25, 2013 4:51 PM
> To: Open MPI Users
> Subject: Re: [OMPI users] errors testing openmpi1.6.5 ----
>
> Hi Yuping
>
> A simple way to do it is to put in your initialization files, which are hidden ("dot files") in your home directory.
>
> It depends on the shell you use (do 'echo $SHELL' to see).
>
> If bash,
> .bashrc
>
> export PATH=/usr/local/openmpi1.6.5/bin:${PATH}
> export LD_LIBRARY_PATH=/usr/local/openmpi1.6.5/lib:${LD_LIBRARY_PATH}
>
> If csh/tcsh
> .cshrc/.tcshrc
>
> setenv PATH /usr/local/openmpi1.6.5/bin:${PATH}
> setenv LD_LIBRARY_PATH /usr/local/openmpi1.6.5/lib:${LD_LIBRARY_PATH}
>
> Are you running the programs in a single machine, or is it a cluster or some farm or networked machines?
> In the second case, you need to make sure your home directory is shared across the machines, or if it is not shared, you need to make the modifications above in each machine.
>
> I hope this helps.
>
> Gus Correa
>
> On 07/25/2013 03:11 PM, Yuping Sun wrote:
>> Hi Gus:
>>
>> I went back and set the PATH and LD_LIBRARY_PATH following the FAQ answer. However, it did not change anything.
>>
>> What else can you suggest?
>>
>> Thank you.
>>
>> Yuping
>>
>> -----Original Message-----
>> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]]
>> On Behalf Of Gus Correa
>> Sent: Wednesday, July 24, 2013 8:28 PM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] errors testing openmpi1.6.5 ----
>>
>> Hi Yuping
>>
>> Did you set your PATH and LD_LIBRARY_PATH?
>> Please, see these FAQ:
>> http://www.open-mpi.org/faq/?category=running#run-prereqs
>> http://www.open-mpi.org/faq/?category=running#adding-ompi-to-path
>>
>> I hope this helps,
>> Gus Correa
>>
>> On 07/24/2013 08:09 PM, Yuping Sun wrote:
>>> Dear All:
>>>
>>> I downloaded openmpi1.5.6 and installed on my linux workstation with
>>> the help of NASA engineer. Then I tried to test the openmpi
>>> installation, but get the following error message:
>>>
>>> [ysun_at_ysunrh mpi]$ which mpiexec
>>>
>>> /usr/local/openmpi1.6.5/bin/mpiexec
>>>
>>> [ysun_at_ysunrh mpi]$ mpiexec utils/MPIcheck/mpicheck
>>>
>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_paffinity_hwloc: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_carto_auto_detect:
>>> lt_dlerror() returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_carto_file: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_shmem_mmap: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_shmem_posix: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_shmem_sysv: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> ---------------------------------------------------------------------
>>> -
>>> ----
>>>
>>> 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_shmem_base_select failed
>>>
>>> --> Returned value -1 instead of OPAL_SUCCESS
>>>
>>> ---------------------------------------------------------------------
>>> -
>>> ----
>>>
>>> [ysunrh.fdwt.com:24905] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in
>>> file runtime/orte_init.c at line 79
>>>
>>> [ysunrh.fdwt.com:24905] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in
>>> file orterun.c at line 694
>>>
>>> I also try the use ompi_info to get more information, and it give me
>>> a lot error messages and I listed some below:
>>>
>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_osc_pt2pt: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_osc_rdma: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_btl_self: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_btl_sm: lt_dlerror() returned
>>> NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_btl_tcp: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_topo_unity: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_pubsub_orte: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open
>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_dpm_orte: lt_dlerror()
>>> returned NULL! (ignored)
>>>
>>> MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.6.5)
>>>
>>> MCA memory: linux (MCA v2.0, API v2.0, Component v1.6.5)
>>>
>>> MCA timer: linux (MCA v2.0, API v2.0, Component v1.6.5)
>>>
>>> MCA installdirs: env (MCA v2.0, API v2.0, Component v1.6.5)
>>>
>>> MCA installdirs: config (MCA v2.0, API v2.0, Component v1.6.5)
>>>
>>> MCA hwloc: hwloc132 (MCA v2.0, API v2.0, Component v1.6.5)
>>>
>>> Could anyone of you give me some help, and tell me what I need to do
>>> to install openmpi correctly or give me some instructions to make it
>>> working? Thank you.
>>>
>>> */Yuping Sun/*
>>>
>>>
>>> FloDesign Wind Turbine Corp
>>>
>>> 242 Sturbridge Road
>>>
>>> Charlton, MA 01507
>>> Direct: 508-434-1507
>>>
>>> Cell: 713-456-9420
>>> ysun_at_[hidden]<mailto:ysun_at_[hidden]>
>>>
>>> Description: cid:3300779197_294562
>>>
>>>
>>>
>>> _______________________________________________
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>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
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