[mpich-discuss] MPICH error on CentOS

Wed Nov 6 18:54:33 CST 2013

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:
>>>>>>> > 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
>>>>>>> >
>>>>>>> > _______________________________________________
>>>>>>> > 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:
>> 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
>
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