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Subject: Re: [OMPI users] mpirun tries to ssh to local machine
From: Reuti (reuti_at_[hidden])
Date: 2013-08-29 05:49:55


Am 29.08.2013 um 10:41 schrieb Federico Carotenuto:

> Kind Reuti,
>
> the output of which mpicc is that such program may be found in various packages (which can be installed with apt-get), while which mpiexec outputs nothing (goes back to the prompt).

You can compile and install Open MPI directly from source - even without being root. You are not limited to what the distribution offers at all.

-- Reuti

> Seems like no mpicc and mpiexec are set on the system...
>
>
> Reuti <reuti_at_[hidden]> ha scritto:
>
>> Hi,
>>
>> Am 26.08.2013 um 18:10 schrieb Federico Carotenuto:
>>
>>> Kind Reuti,
>>>
>>> as you suggested I proceeded to install Openmpi 1.6.5
>>
>> Good.
>>
>>
>>> and changed the environmental variable MPI_ROOT
>>
>> No, there is no such variable necessary to be set (at least from Open MPI points of view).
>>
>>
>>> to the new folder, should I know source the commands in .bashrc to be sure to be able to execute the right mpirun and mpiexec (something like source
>>
>> Please check with:
>>
>> which mpicc
>> which mpiexec
>>
>> which you are using. It's also necessary to recompile the application with the new MPI library.
>>
>> -- Reuti
>>
>>
>>> /home/modelstation/Software/openmpi1.6.5/mpirun, where the directory is the installation directory)?
>>>
>>> Thanks!
>>>
>>> Reuti <reuti_at_[hidden]> ha scritto:
>>>
>>>> Am 26.08.2013 um 14:33 schrieb Federico Carotenuto:
>>>>
>>>>> Kind Reuti,
>>>>>
>>>>> I'm start thinking I've got some compilation issue with MPI: I'm afraid I've got the MPICH 1 coming with the PGI compiler installation, because if I try to run mpiexec the terminal answers with "The program 'mpiexec' can be found in the following packages: *lam-runtime *mpich2 *openmpi-bin *openmpi1.6-bin. Try: sudo apt-get install <selected package>".
>>>>>
>>>>> I've also tried to modify the machinefile that comes by default under /opt/pgi/linux86-64/13.4/mpi/mpich/share/machinefile.LINUX adding the line "modelstation:8", but still mpirun prompts for the password 8 times.
>>>>
>>>> This was normal at that time: one rsh/ssh per parallel instance. Nowadays Open MPI and MPICH2/3 will use only one `rsh`/`ssh` per host and start all other parallel tasks as thread (i.e: on a local machine they don't need a local `rsh` or `ssh` at all). Although you could either adjust `rsh` to disregard passwords (deprecated) or route `rsh` to `ssh` and enable passphraseless login:
>>>>
>>>> MPICH(1) is outdated (released 2005) and I suggested already to Portland to exclude it from the package. IMO this adds more confusion than it help.
>>>>
>>>> Hence, please install a recent version of Open MPI or MPICH2/3 and then we can look into it again on the appropriate list.
>>>>
>>>> -- Reuti
>>>>
>>>> PS: The above mentioned LAM/MPI is outdated too.
>>>>
>>>>
>>>>> Thanks for your help and patience
>>>>>
>>>>>
>>>>> Reuti <reuti_at_[hidden]> ha scritto:
>>>>>
>>>>>> Am 26.08.2013 um 12:53 schrieb Federico Carotenuto:
>>>>>>
>>>>>>> Kind Reuti,
>>>>>>>
>>>>>>> Thanks for your quick reply!
>>>>>>>
>>>>>>>
>>>>>>> I'm afraid I didn't set a machinefile...that may be the problem: I'm fairly new to MPI and SSH and I'm still quite confused even after reading some tutorials.
>>>>>>
>>>>>> There is a default. But you can also specify it on the command line to test it:
>>>>>>
>>>>>> mpiexec -host modelstation -np 2 mpihello
>>>>>>
>>>>>> -- Reuti
>>>>>>
>>>>>>
>>>>>>> My etc/hosts contains: 127.0.0.1 localhost and 127.0.1.1 modelstation (modelstation is the machine name I was mentioning in the previous mail)
>>>>>>>
>>>>>>> if I type hostname the terminal returns modelstation
>>>>>>>
>>>>>>> Cheers
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Reuti <reuti_at_[hidden]> ha scritto:
>>>>>>>
>>>>>>>> Am 26.08.2013 um 12:15 schrieb Federico Carotenuto:
>>>>>>>>
>>>>>>>>> I'm currently having this issue with mpirun: I want to launch a program only on the cores of the local machine, but every time I run an mpi program it says that the host 127.0.0.1 <local_machine_name> with it's associated key is unkown and asks me if I want to add it to the list of ssh known hosts.
>>>>>>>>>
>>>>>>>>> By chowing/chmodding the .ssh file I was able to permanently add this "host" to the list of known hosts, but my problem is that every program that I try to run ask me to insert a password (the actual local user password) n times where n is equal to the -np parameter (i.e.: if I run the program on 8 cores I receive 8 successive password pronts).
>>>>>>>>>
>>>>>>>>> If I insert the password everything runs fine, but it's quite annoying and I wish to bypass such step: is there a way to have mpirun memorize the password? Or make him understand that the 8 nodes are actually 8 cores on the local machine and not 8 different hosts?
>>>>>>>>
>>>>>>>> Which hostname do you specify in your machinefile?
>>>>>>>> Which hostnames are set in /etc/hosts for your local machine?
>>>>>>>> What is the output of `hostname`? Does it match the one in the machinefile?
>>>>>>>>
>>>>>>>> For systemd there is a new command `hostnamectl --static set-hostname [NAME]` to set it.
>>>>>>>>
>>>>>>>> -- Reuti
>>>>>>>> _______________________________________________
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>>>>>>>>
>>>>>>>
>>>>>>>
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