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Subject: Re: [OMPI users] openmpi query
From: Nisha Dhankher -M.Tech(CSE) (nishadhankher-coaeseeit_at_[hidden])
Date: 2014-04-03 13:13:30


i first formatted my database with mpiformatdb command then i ran command :
mpirun -np 64 -machinefile mf mpiblast -d all.fas -p blastn -i query.fas -o
output.txt
but then it gave this error 113 from some hosts and continue to run for
other but with no results even after 2 hours lapsed.....on rocks 6.0
cluster with 12 virtual nodes on pc's ...2 on each using virt-manger , 1 gb
ram to each

On Thu, Apr 3, 2014 at 10:41 PM, Nisha Dhankher -M.Tech(CSE) <
nishadhankher-coaeseeit_at_[hidden]> wrote:

> i also made machine file which contain ip adresses of all compute nodes +
> .ncbirc file for path to mpiblast and shared ,local storage path....
> Sir
> I ran the same command of mpirun on my college supercomputer 8 nodes each
> having 24 processors but it just running....gave no result uptill 3 hours...
>
>
> On Thu, Apr 3, 2014 at 10:39 PM, Nisha Dhankher -M.Tech(CSE) <
> nishadhankher-coaeseeit_at_[hidden]> wrote:
>
>> i first formatted my database with mpiformatdb command then i ran command
>> :
>> mpirun -np 64 -machinefile mf mpiblast -d all.fas -p blastn -i query.fas
>> -o output.txt
>> but then it gave this error 113 from some hosts and continue to run for
>> other but with results even after 2 hours lapsed.....on rocks 6.0 cluster
>> with 12 virtual nodes on pc's ...2 on each using virt-manger , 1 gb ram to
>> each
>>
>>
>>
>> On Thu, Apr 3, 2014 at 8:37 PM, Ralph Castain <rhc_at_[hidden]> wrote:
>>
>>> I'm having trouble understanding your note, so perhaps I am getting this
>>> wrong. Let's see if I can figure out what you said:
>>>
>>> * your perl command fails with "no route to host" - but I don't see any
>>> host in your cmd. Maybe I'm just missing something.
>>>
>>> * you tried running a couple of "mpirun", but the mpirun command wasn't
>>> recognized? Is that correct?
>>>
>>> * you then ran mpiblast and it sounds like it successfully started the
>>> processes, but then one aborted? Was there an error message beyond just the
>>> -1 return status?
>>>
>>>
>>> On Apr 2, 2014, at 11:17 PM, Nisha Dhankher -M.Tech(CSE) <
>>> nishadhankher-coaeseeit_at_[hidden]> wrote:
>>>
>>> error btl_tcp_endpint.c: 638 connection failed due to error 113<http://biosupport.se/questions/696/error-btl_tcp_endpintc-638-connection-failed-due-to-error-113>
>>>
>>> In openmpi: this error came when i run my mpiblast program on rocks
>>> cluster.Connect to hosts failed on ip 10.1.255.236,10.1.255.244 . And when
>>> i run following command linux_shell$ perl -e 'die$!=113' this msg comes:
>>> "No route to host at -e line 1." shell$ mpirun --mca btl ^tcp shell$ mpirun
>>> --mca btl_tcp_if_include eth1,eth2 shell$ mpirun --mca btl_tcp_if_include
>>> 10.1.255.244 was also executed but it did nt recognized these
>>> commands....nd aborted.... what should i do...? When i run my mpiblast
>>> program for the frst time then it give mpi_abort error...bailing out of
>>> signal -1 on rank 2 processor...then i removed my public ethernet
>>> cable....and then give btl_tcp endpint error 113....
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>>
>>
>