[mpich-discuss] MPICH error on CentOS

bharat gupta bharat.85.monu at gmail.com
Wed Nov 6 18:56:10 CST 2013 

Okay.. Thanks a lot for your time and help..


On Thu, Nov 7, 2013 at 9:54 AM, Ricardo Román Brenes <
roman.ricardo at gmail.com> wrote:

> You have to either remove the old rpm and compile a new version or remove
> the old version and create an rpm from the source. Maybe fedora or suse
> have a newer version in their repos but I havent checked
> On Nov 6, 2013 6:48 PM, "bharat gupta" <bharat.85.monu at gmail.com> wrote:
>
>> How can that be done in CentOS 6.0, I used the command yum search mpich
>> and installed the one that it showed ...
>>
>>
>> On Thu, Nov 7, 2013 at 9:47 AM, Ricardo Román Brenes <
>> roman.ricardo at gmail.com> wrote:
>>
>>> Still, try to update to a new mpich asap! :-)
>>> On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu at gmail.com> wrote:
>>>
>>>> Thanks for the command. After issuing mpdboot and making file mdp.conf
>>>> with line secretword=<> in /etc folder solved the problem..
>>>>
>>>> Thanks a lot
>>>>
>>>>
>>>> On Thu, Nov 7, 2013 at 9:43 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:
>>>>
>>>>> I didn't use any of these command , I issued the command 'mpirun -np
>>>>> 24 mdrun -v -deffnm mdrun' for running the gromacs' and after using this
>>>>> command I got those errors
>>>>>
>>>>>
>>>>> On Thu, Nov 7, 2013 at 9:42 AM, Ricardo Román Brenes <
>>>>> roman.ricardo at gmail.com> wrote:
>>>>>
>>>>>> Did you start mpd either with mpd or mpdboot?
>>>>>> On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <
>>>>>> roman.ricardo at gmail.com> wrote:
>>>>>>
>>>>>>> He has to. Thats an older mpich than mine!  :-P
>>>>>>> On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji at mcs.anl.gov> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> Looks like I’m late to this email chain.
>>>>>>>>
>>>>>>>> Please don’t use mpd.  mpd has been deprecated for many releases of
>>>>>>>> mpich now.  You might be using a very old version of mpich.
>>>>>>>>
>>>>>>>>   —- Pavan
>>>>>>>>
>>>>>>>> On Nov 6, 2013, at 6:26 PM, bharat gupta <bharat.85.monu at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> > DO I need to add some command in mpd.hosts file
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > On Thu, Nov 7, 2013 at 9:22 AM, bharat gupta <
>>>>>>>> bharat.85.monu at gmail.com> wrote:
>>>>>>>> > I don't know much about mpi , as I am using gromacs which was
>>>>>>>> complied with mpi option. , But I read somewhere that
>>>>>>>> >
>>>>>>>> >  " If a file named .mpd.conf is available in the user's home
>>>>>>>> directory, only the user can have read and write privileges. The file must
>>>>>>>> minimally contain a line with secretword=<secretword>. If you want to run
>>>>>>>> MPD as root, create the mpd.conf file in the /etc directory instead of
>>>>>>>> .mpd.conf in the root's home directory to run mpd as root. Avoid starting
>>>>>>>> the MPD ring under the root account." Here'e the link
>>>>>>>> http://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Multipurpose_Daemon_Commands.htm
>>>>>>>> >
>>>>>>>> > And after using chmod 700 , I still get the same error, but when
>>>>>>>> I create a file mpd.conf in /etc I get the and added the
>>>>>>>> secretword=<secretword> line in the file and run the same command, I get
>>>>>>>> this error:-
>>>>>>>> >
>>>>>>>> > root at localhost INGT]# mpirun -np 24 mdrun -v -deffnm mdrun
>>>>>>>> > mpdroot: perror msg: No such file or directory
>>>>>>>> > mpdroot: cannot connect to local mpd at: /tmp/mpd2.console_root
>>>>>>>> >     probable cause:  no mpd daemon on this machine
>>>>>>>> >     possible cause:  unix socket /tmp/mpd2.console_root has been
>>>>>>>> removed
>>>>>>>> >
>>>>>>>> > mpiexec_localhost.localdomain (__init__ 1208): forked process
>>>>>>>> failed; status=255
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > On Thu, Nov 7, 2013 at 9:11 AM, Ricardo Román Brenes <
>>>>>>>> roman.ricardo at gmail.com> wrote:
>>>>>>>> > Try using chmod 700.  Can you run any other mpi example? Like
>>>>>>>> cpi.c
>>>>>>>> >
>>>>>>>> > On Nov 6, 2013 6:08 PM, "bharat gupta" <bharat.85.monu at gmail.com>
>>>>>>>> wrote:
>>>>>>>> > It have changed the file permission (rw) for root , ls -l
>>>>>>>> mpd.hosts gives the output
>>>>>>>> > -rw-r--r--, 1 root root
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > On Thu, Nov 7, 2013 at 9:02 AM, Ricardo Román Brenes <
>>>>>>>> roman.ricardo at gmail.com> wrote:
>>>>>>>> > With rwx permission just for root?
>>>>>>>> >
>>>>>>>> > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu at gmail.com>
>>>>>>>> wrote:
>>>>>>>> > I have created the file mpd.hosts in /etc folder in the root ,
>>>>>>>> but still it shows the same error ... /usr/bin/mpdroot: open failed for
>>>>>>>> root's mpd conf filempiexec_localhost.localdomain (__init__ 1208): forked
>>>>>>>> process failed; status=255
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > On Thu, Nov 7, 2013 at 8:45 AM, Ricardo Román Brenes <
>>>>>>>> roman.ricardo at gmail.com> wrote:
>>>>>>>> > You need to create a mpd.hosts in /etc if you want to run mpd as
>>>>>>>> root
>>>>>>>> >
>>>>>>>> > On Nov 6, 2013 5:41 PM, "bharat gupta" <bharat.85.monu at gmail.com>
>>>>>>>> wrote:
>>>>>>>> > Hi,
>>>>>>>> >
>>>>>>>> > I am getting the following error while using the command -
>>>>>>>> >
>>>>>>>> > [root at localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt
>>>>>>>> >
>>>>>>>> > Error -
>>>>>>>> >
>>>>>>>> > /usr/bin/mpdroot: open failed for root's mpd conf
>>>>>>>> filempiexec_localhost.localdomain (__init__ 1208): forked process failed;
>>>>>>>> status=255
>>>>>>>> >
>>>>>>>> > I complied gromacs using - ./configure --enable-shared
>>>>>>>> --enable-mpi. I have installed the mpich package , this is what I get when
>>>>>>>> I check for mpirun and mpiexec -
>>>>>>>> >
>>>>>>>> > [root at localhost /]# which mpirun
>>>>>>>> > /usr/bin/mpirun
>>>>>>>> > [root at localhost /]# which mpiexec
>>>>>>>> > /usr/bin/mpiexec
>>>>>>>> >
>>>>>>>> > What could be the problem here ??
>>>>>>>> >
>>>>>>>> > Thanks
>>>>>>>> > --------
>>>>>>>> > Bharat
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > discuss mailing list     discuss at mpich.org
>>>>>>>> > To manage subscription options or unsubscribe:
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>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > discuss mailing list     discuss at mpich.org
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>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > --
>>>>>>>> > Bharat
>>>>>>>> > Ph.D. Candidate
>>>>>>>> > Biomolecular Engineering Laboratory
>>>>>>>> > Pusan National University
>>>>>>>> > South Korea
>>>>>>>> > Mobile no. - 010-5818-3680
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > discuss mailing list     discuss at mpich.org
>>>>>>>> > To manage subscription options or unsubscribe:
>>>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > discuss mailing list     discuss at mpich.org
>>>>>>>> > To manage subscription options or unsubscribe:
>>>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > --
>>>>>>>> > Bharat
>>>>>>>> > Ph.D. Candidate
>>>>>>>> > Biomolecular Engineering Laboratory
>>>>>>>> > Pusan National University
>>>>>>>> > South Korea
>>>>>>>> > Mobile no. - 010-5818-3680
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > discuss mailing list     discuss at mpich.org
>>>>>>>> > To manage subscription options or unsubscribe:
>>>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > discuss mailing list     discuss at mpich.org
>>>>>>>> > To manage subscription options or unsubscribe:
>>>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > --
>>>>>>>> > Bharat
>>>>>>>> > Ph.D. Candidate
>>>>>>>> > Biomolecular Engineering Laboratory
>>>>>>>> > Pusan National University
>>>>>>>> > South Korea
>>>>>>>> > Mobile no. - 010-5818-3680
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > --
>>>>>>>> > Bharat
>>>>>>>> > Ph.D. Candidate
>>>>>>>> > Biomolecular Engineering Laboratory
>>>>>>>> > Pusan National University
>>>>>>>> > South Korea
>>>>>>>> > Mobile no. - 010-5818-3680
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > discuss mailing list     discuss at mpich.org
>>>>>>>> > To manage subscription options or unsubscribe:
>>>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss
>>>>>>>>
>>>>>>>> --
>>>>>>>> Pavan Balaji
>>>>>>>> http://www.mcs.anl.gov/~balaji
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> discuss mailing list     discuss at mpich.org
>>>>>>>> To manage subscription options or unsubscribe:
>>>>>>>> https://lists.mpich.org/mailman/listinfo/discuss
>>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> discuss mailing list     discuss at mpich.org
>>>>>> To manage subscription options or unsubscribe:
>>>>>> https://lists.mpich.org/mailman/listinfo/discuss
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Bharat
>>>>> Ph.D. Candidate
>>>>> Biomolecular Engineering Laboratory
>>>>> Pusan National University
>>>>> South Korea
>>>>> Mobile no. - 010-5818-3680
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Bharat
>>>> Ph.D. Candidate
>>>> Biomolecular Engineering Laboratory
>>>> Pusan National University
>>>> South Korea
>>>> Mobile no. - 010-5818-3680
>>>>
>>>>
>>>> _______________________________________________
>>>> discuss mailing list     discuss at mpich.org
>>>> To manage subscription options or unsubscribe:
>>>> https://lists.mpich.org/mailman/listinfo/discuss
>>>>
>>>
>>> _______________________________________________
>>> discuss mailing list     discuss at mpich.org
>>> To manage subscription options or unsubscribe:
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>>>
>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Biomolecular Engineering Laboratory
>> Pusan National University
>> South Korea
>> Mobile no. - 010-5818-3680
>>
>>
>> _______________________________________________
>> discuss mailing list     discuss at mpich.org
>> To manage subscription options or unsubscribe:
>> https://lists.mpich.org/mailman/listinfo/discuss
>>
>
> _______________________________________________
> discuss mailing list     discuss at mpich.org
> To manage subscription options or unsubscribe:
> https://lists.mpich.org/mailman/listinfo/discuss
>



-- 
Bharat
Ph.D. Candidate
Biomolecular Engineering Laboratory
Pusan National University
South Korea
Mobile no. - 010-5818-3680
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