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Subject: Re: [OMPI users] openmpi query
From: Nisha Dhankher -M.Tech(CSE) (nishadhankher-coaeseeit_at_[hidden])
Date: 2014-04-05 03:02:48


opmpi version 1.4.3

On Fri, Apr 4, 2014 at 8:13 PM, Ralph Castain <rhc_at_[hidden]> wrote:

> Okay, so if you run mpiBlast on all the non-name nodes, everything is
> okay? What do you mean by "names nodes"?
>
>
> On Apr 4, 2014, at 7:32 AM, Nisha Dhankher -M.Tech(CSE) <
> nishadhankher-coaeseeit_at_[hidden]> wrote:
>
> no it does not happen on names nodes
>
>
> On Fri, Apr 4, 2014 at 7:51 PM, Ralph Castain <rhc_at_[hidden]> wrote:
>
>> Hi Nisha
>>
>> I'm sorry if my questions appear abrasive - I'm just a little frustrated
>> at the communication bottleneck as I can't seem to get a clear picture of
>> your situation. So you really don't need to keep calling me "sir" :-)
>>
>> The error you are hitting is very unusual - it means that the processes
>> are able to make a connection, but are failing to correctly complete a
>> simple handshake exchange of their process identifications. There are only
>> a few ways that can happen, and I'm trying to get you to test for them.
>>
>> So let's try and see if we can narrow this down. You mention that it
>> works on some machines, but not all. Is this consistent - i.e., is it
>> always the same machines that work, and the same ones that generate the
>> error? If you exclude the ones that show the error, does it work? If so,
>> what is different about those nodes? Are they a different architecture?
>>
>>
>> On Apr 3, 2014, at 11:09 PM, Nisha Dhankher -M.Tech(CSE) <
>> nishadhankher-coaeseeit_at_[hidden]> wrote:
>>
>> sir
>> smae virt-manager is bein used by all pc's.no i did n't enable
>> openmpi-hetro.Yes openmpi version is same in all through same kickstart
>> file.
>> ok...actually sir...rocks itself installed,configured openmpi and mpich
>> on it own through hpc roll.
>>
>>
>> On Fri, Apr 4, 2014 at 9:25 AM, Ralph Castain <rhc_at_[hidden]> wrote:
>>
>>>
>>> On Apr 3, 2014, at 8:03 PM, Nisha Dhankher -M.Tech(CSE) <
>>> nishadhankher-coaeseeit_at_[hidden]> wrote:
>>>
>>> thankyou Ralph.
>>> Yes cluster is heterogenous...
>>>
>>>
>>> And did you configure OMPI --enable-heterogeneous? And are you running
>>> it with ---hetero-nodes? What version of OMPI are you using anyway?
>>>
>>> Note that we don't care if the host pc's are hetero - what we care about
>>> is the VM. If all the VMs are the same, then it shouldn't matter. However,
>>> most VM technologies don't handle hetero hardware very well - i.e., you
>>> can't emulate an x86 architecture on top of a Sparc or Power chip or vice
>>> versa.
>>>
>>>
>>> And i haven't made compute nodes on direct physical nodes (pc's) becoz
>>> in college it is not possible to take whole lab of 32 pc's for your work
>>> so i ran on vm.
>>>
>>>
>>> Yes, but at least it would let you test the setup to run MPI across even
>>> a couple of pc's - this is simple debugging practice.
>>>
>>> In Rocks cluster, frontend give the same kickstart to all the pc's so
>>> openmpi version should be same i guess.
>>>
>>>
>>> Guess? or know? Makes a difference - might be worth testing.
>>>
>>> Sir
>>> mpiformatdb is a command to distribute database fragments to different
>>> compute nodes after partitioning od database.
>>> And sir have you done mpiblast ?
>>>
>>>
>>> Nope - but that isn't the issue, is it? The issue is with the MPI setup.
>>>
>>>
>>>
>>> On Fri, Apr 4, 2014 at 4:48 AM, Ralph Castain <rhc_at_[hidden]> wrote:
>>>
>>>> What is "mpiformatdb"? We don't have an MPI database in our system, and
>>>> I have no idea what that command means
>>>>
>>>> As for that error - it means that the identifier we exchange between
>>>> processes is failing to be recognized. This could mean a couple of things:
>>>>
>>>> 1. the OMPI version on the two ends is different - could be you aren't
>>>> getting the right paths set on the various machines
>>>>
>>>> 2. the cluster is heterogeneous
>>>>
>>>> You say you have "virtual nodes" running on various PC's? That would be
>>>> an unusual setup - VM's can be problematic given the way they handle TCP
>>>> connections, so that might be another source of the problem if my
>>>> understanding of your setup is correct. Have you tried running this across
>>>> the PCs directly - i.e., without any VMs?
>>>>
>>>>
>>>> On Apr 3, 2014, at 10:13 AM, 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 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....
>>>>>>> _______________________________________________
>>>>>>> users mailing list
>>>>>>> users_at_[hidden]
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>>
>>>>>>
>>>>>>
>>>>>
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