[mpich-discuss] MPICH error on CentOS

Ricardo Román Brenes roman.ricardo at gmail.com
Wed Nov 6 21:25:37 CST 2013 

yup.


On Wed, Nov 6, 2013 at 9:25 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> Okay .. thanks but right now my simulation is running and if I use the
> command that you both mentioned would ultimately lead to the stoppage of my
> simulations .. right ?? May be I can try reinstalling the new version after
> finishing the simulations
>
>
> On Thu, Nov 7, 2013 at 12:21 PM, Ricardo Román Brenes <
> roman.ricardo at gmail.com> wrote:
>
>> both will coexiste, you ahve to "yum remove mpich2-x-x-x.x84_64"
>>
>>
>> On Wed, Nov 6, 2013 at 9:20 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:
>>
>>> But how to remove the older version or reinstalling the new one will
>>> override the changes
>>>
>>>
>>> On Thu, Nov 7, 2013 at 12:18 PM, Pavan Balaji <balaji at mcs.anl.gov>wrote:
>>>
>>>>
>>>> Wow.  1.2.1p1 is ancient.  It was used by dinosaurs and such when they
>>>> still roamed the earth.
>>>>
>>>> I don’t use CentOS, but don’t the rpm’s from this page work?
>>>>
>>>> http://www.mpich.org/downloads/
>>>>
>>>> If not, then source compile is always possible.  :-)  It’s an
>>>> open-source project.
>>>>
>>>>   —- Pavan
>>>>
>>>> On Nov 6, 2013, at 6:56 PM, bharat gupta <bharat.85.monu at gmail.com>
>>>> wrote:
>>>>
>>>> > 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
>>>> > >
>>>> > >
>>>> > >
>>>> > > _______________________________________________
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>>>> > >
>>>> > > _______________________________________________
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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:
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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
>>>> > >
>>>> > >
>>>> > >
>>>> > >
>>>> > > --
>>>> > > 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:
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>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > 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:
>>>> > 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
>>>> >
>>>> > _______________________________________________
>>>> > 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
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>
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