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Subject: Re: [OMPI users] openmpi query
From: Nisha Dhankher -M.Tech(CSE) (nishadhankher-coaeseeit_at_[hidden])
Date: 2014-04-05 03:04:49


sorry Ralph my mistake its not names...it is "it does not happen on same
nodes."

On Sat, Apr 5, 2014 at 12:33 PM, Nisha Dhankher -M.Tech(CSE) <
nishadhankher-coaeseeit_at_[hidden]> wrote:

> same vm on all machines that is virt-manager
>
>
> On Sat, Apr 5, 2014 at 12:32 PM, Nisha Dhankher -M.Tech(CSE) <
> nishadhankher-coaeseeit_at_[hidden]> wrote:
>
>> 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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>>>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
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>>>>>>
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>>>>>
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>>>>>
>>>>>
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>>>>
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>>
>