[mpich-discuss] MPICH error on CentOS

bharat gupta bharat.85.monu at gmail.com
Wed Nov 6 21:25:06 CST 2013 

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:
>>> > > https://lists.mpich.org/mailman/listinfo/discuss
>>> > >
>>> > > _______________________________________________
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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
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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
>>> >
>>> > --
>>> > 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:
>>> > 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:
> 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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