November 2013 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] MPICH error on CentOS
by Ricardo Román Brenes 06 Nov '13

06 Nov '13

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(a)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(a)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(a)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(a)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(a)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(a)gmail.com> wrote: >> > Still, try to update to a new mpich asap! :-) >> > >> > On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: >> > Did you start mpd either with mpd or mpdboot? >> > >> > On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <roman.ricardo(a)gmail.com> >> wrote: >> > He has to. Thats an older mpich than mine! :-P >> > >> > On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… >> > > >> > > 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@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(a)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(a)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(a)gmail.com> wrote: >> > > With rwx permission just for root? >> > > >> > > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> >> wrote: >> > > Hi, >> > > >> > > I am getting the following error while using the command - >> > > >> > > [root@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@localhost /]# which mpirun >> > > /usr/bin/mpirun >> > > [root@localhost /]# which mpiexec >> > > /usr/bin/mpiexec >> > > >> > > What could be the problem here ?? >> > > >> > > Thanks >> > > -------- >> > > Bharat >> > > >> > > >> > > >> > > _______________________________________________ >> > > discuss mailing list discuss(a)mpich.org >> > > To manage subscription options or unsubscribe: >> > > https://lists.mpich.org/mailman/listinfo/discuss >> > > >> > > _______________________________________________ >> > > discuss mailing list discuss(a)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(a)mpich.org >> > > To manage subscription options or unsubscribe: >> > > https://lists.mpich.org/mailman/listinfo/discuss >> > > >> > > _______________________________________________ >> > > discuss mailing list discuss(a)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(a)mpich.org >> > > To manage subscription options or unsubscribe: >> > > https://lists.mpich.org/mailman/listinfo/discuss >> > > >> > > _______________________________________________ >> > > discuss mailing list discuss(a)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(a)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(a)mpich.org >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)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(a)mpich.org >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)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(a)mpich.org >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)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(a)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(a)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(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Re: [mpich-discuss] MPICH error on CentOS
by Pavan Balaji 06 Nov '13

06 Nov '13

Does this not work? % yum remove mpich2 On Nov 6, 2013, at 9:20 PM, bharat gupta <bharat.85.monu(a)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(a)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(a)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(a)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(a)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(a)gmail.com> wrote: > > Still, try to update to a new mpich asap! :-) > > > > On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: > > Did you start mpd either with mpd or mpdboot? > > > > On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <roman.ricardo(a)gmail.com> wrote: > > He has to. Thats an older mpich than mine! :-P > > > > On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… > > > > > > 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@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(a)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(a)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(a)gmail.com> wrote: > > > With rwx permission just for root? > > > > > > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: > > > Hi, > > > > > > I am getting the following error while using the command - > > > > > > [root@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@localhost /]# which mpirun > > > /usr/bin/mpirun > > > [root@localhost /]# which mpiexec > > > /usr/bin/mpiexec > > > > > > What could be the problem here ?? > > > > > > Thanks > > > -------- > > > Bharat > > > > > > > > > > > > _______________________________________________ > > > discuss mailing list discuss(a)mpich.org > > > To manage subscription options or unsubscribe: > > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > _______________________________________________ > > > discuss mailing list discuss(a)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(a)mpich.org > > > To manage subscription options or unsubscribe: > > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > _______________________________________________ > > > discuss mailing list discuss(a)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(a)mpich.org > > > To manage subscription options or unsubscribe: > > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > _______________________________________________ > > > discuss mailing list discuss(a)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(a)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(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)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(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)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(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)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(a)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(a)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(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] MPICH error on CentOS
by bharat gupta 06 Nov '13

06 Nov '13

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(a)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(a)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(a)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(a)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(a)gmail.com> wrote: > > Still, try to update to a new mpich asap! :-) > > > > On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: > > Did you start mpd either with mpd or mpdboot? > > > > On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <roman.ricardo(a)gmail.com> > wrote: > > He has to. Thats an older mpich than mine! :-P > > > > On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… > > > > > > 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@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(a)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(a)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(a)gmail.com> wrote: > > > With rwx permission just for root? > > > > > > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> > wrote: > > > Hi, > > > > > > I am getting the following error while using the command - > > > > > > [root@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@localhost /]# which mpirun > > > /usr/bin/mpirun > > > [root@localhost /]# which mpiexec > > > /usr/bin/mpiexec > > > > > > What could be the problem here ?? > > > > > > Thanks > > > -------- > > > Bharat > > > > > > > > > > > > _______________________________________________ > > > discuss mailing list discuss(a)mpich.org > > > To manage subscription options or unsubscribe: > > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > _______________________________________________ > > > discuss mailing list discuss(a)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(a)mpich.org > > > To manage subscription options or unsubscribe: > > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > _______________________________________________ > > > discuss mailing list discuss(a)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(a)mpich.org > > > To manage subscription options or unsubscribe: > > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > _______________________________________________ > > > discuss mailing list discuss(a)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(a)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(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)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(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)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(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)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(a)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(a)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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Re: [mpich-discuss] MPICH error on CentOS
by Pavan Balaji 06 Nov '13

06 Nov '13

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(a)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(a)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(a)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(a)gmail.com> wrote: > Still, try to update to a new mpich asap! :-) > > On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: > Did you start mpd either with mpd or mpdboot? > > On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <roman.ricardo(a)gmail.com> wrote: > He has to. Thats an older mpich than mine! :-P > > On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… > > > > 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@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(a)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(a)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(a)gmail.com> wrote: > > With rwx permission just for root? > > > > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: > > Hi, > > > > I am getting the following error while using the command - > > > > [root@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@localhost /]# which mpirun > > /usr/bin/mpirun > > [root@localhost /]# which mpiexec > > /usr/bin/mpiexec > > > > What could be the problem here ?? > > > > Thanks > > -------- > > Bharat > > > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)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(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)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(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)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(a)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(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)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(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)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(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)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(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] MPICH error on CentOS
by bharat gupta 06 Nov '13

06 Nov '13

Okay.. Thanks a lot for your time and help.. On Thu, Nov 7, 2013 at 9:54 AM, Ricardo Román Brenes < roman.ricardo(a)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(a)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(a)gmail.com> wrote: >> >>> Still, try to update to a new mpich asap! :-) >>> On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: >>>>> >>>>>> Did you start mpd either with mpd or mpdboot? >>>>>> On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" < >>>>>> roman.ricardo(a)gmail.com> wrote: >>>>>> >>>>>>> He has to. Thats an older mpich than mine! :-P >>>>>>> On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… >>>>>>>> > >>>>>>>> > 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@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(a)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(a)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(a)gmail.com> wrote: >>>>>>>> > With rwx permission just for root? >>>>>>>> > >>>>>>>> > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> >>>>>>>> wrote: >>>>>>>> > Hi, >>>>>>>> > >>>>>>>> > I am getting the following error while using the command - >>>>>>>> > >>>>>>>> > [root@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@localhost /]# which mpirun >>>>>>>> > /usr/bin/mpirun >>>>>>>> > [root@localhost /]# which mpiexec >>>>>>>> > /usr/bin/mpiexec >>>>>>>> > >>>>>>>> > What could be the problem here ?? >>>>>>>> > >>>>>>>> > Thanks >>>>>>>> > -------- >>>>>>>> > Bharat >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > _______________________________________________ >>>>>>>> > discuss mailing list discuss(a)mpich.org >>>>>>>> > To manage subscription options or unsubscribe: >>>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>>>>> > >>>>>>>> > _______________________________________________ >>>>>>>> > discuss mailing list discuss(a)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(a)mpich.org >>>>>>>> > To manage subscription options or unsubscribe: >>>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>>>>> > >>>>>>>> > _______________________________________________ >>>>>>>> > discuss mailing list discuss(a)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(a)mpich.org >>>>>>>> > To manage subscription options or unsubscribe: >>>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>>>>> > >>>>>>>> > _______________________________________________ >>>>>>>> > discuss mailing list discuss(a)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(a)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(a)mpich.org >>>>>>>> To manage subscription options or unsubscribe: >>>>>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> discuss mailing list discuss(a)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(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>> >>> _______________________________________________ >>> discuss mailing list discuss(a)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(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > _______________________________________________ > discuss mailing list discuss(a)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

1 0

Re: [mpich-discuss] MPICH error on CentOS
by Ricardo Román Brenes 06 Nov '13

06 Nov '13

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(a)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(a)gmail.com> wrote: > >> Still, try to update to a new mpich asap! :-) >> On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: >>>> >>>>> Did you start mpd either with mpd or mpdboot? >>>>> On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" < >>>>> roman.ricardo(a)gmail.com> wrote: >>>>> >>>>>> He has to. Thats an older mpich than mine! :-P >>>>>> On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… >>>>>>> > >>>>>>> > 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@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(a)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(a)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(a)gmail.com> wrote: >>>>>>> > With rwx permission just for root? >>>>>>> > >>>>>>> > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> >>>>>>> wrote: >>>>>>> > Hi, >>>>>>> > >>>>>>> > I am getting the following error while using the command - >>>>>>> > >>>>>>> > [root@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@localhost /]# which mpirun >>>>>>> > /usr/bin/mpirun >>>>>>> > [root@localhost /]# which mpiexec >>>>>>> > /usr/bin/mpiexec >>>>>>> > >>>>>>> > What could be the problem here ?? >>>>>>> > >>>>>>> > Thanks >>>>>>> > -------- >>>>>>> > Bharat >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > _______________________________________________ >>>>>>> > discuss mailing list discuss(a)mpich.org >>>>>>> > To manage subscription options or unsubscribe: >>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>>>> > >>>>>>> > _______________________________________________ >>>>>>> > discuss mailing list discuss(a)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(a)mpich.org >>>>>>> > To manage subscription options or unsubscribe: >>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>>>> > >>>>>>> > _______________________________________________ >>>>>>> > discuss mailing list discuss(a)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(a)mpich.org >>>>>>> > To manage subscription options or unsubscribe: >>>>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>>>> > >>>>>>> > _______________________________________________ >>>>>>> > discuss mailing list discuss(a)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(a)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(a)mpich.org >>>>>>> To manage subscription options or unsubscribe: >>>>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>>>>> >>>>>> >>>>> _______________________________________________ >>>>> discuss mailing list discuss(a)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(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >> >> _______________________________________________ >> discuss mailing list discuss(a)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(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

1 0

Re: [mpich-discuss] MPICH error on CentOS
by bharat gupta 06 Nov '13

06 Nov '13

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(a)gmail.com> wrote: > Still, try to update to a new mpich asap! :-) > On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: >>> >>>> Did you start mpd either with mpd or mpdboot? >>>> On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <roman.ricardo(a)gmail.com> >>>> wrote: >>>> >>>>> He has to. Thats an older mpich than mine! :-P >>>>> On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… >>>>>> > >>>>>> > 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@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(a)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(a)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(a)gmail.com> wrote: >>>>>> > With rwx permission just for root? >>>>>> > >>>>>> > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> >>>>>> wrote: >>>>>> > Hi, >>>>>> > >>>>>> > I am getting the following error while using the command - >>>>>> > >>>>>> > [root@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@localhost /]# which mpirun >>>>>> > /usr/bin/mpirun >>>>>> > [root@localhost /]# which mpiexec >>>>>> > /usr/bin/mpiexec >>>>>> > >>>>>> > What could be the problem here ?? >>>>>> > >>>>>> > Thanks >>>>>> > -------- >>>>>> > Bharat >>>>>> > >>>>>> > >>>>>> > >>>>>> > _______________________________________________ >>>>>> > discuss mailing list discuss(a)mpich.org >>>>>> > To manage subscription options or unsubscribe: >>>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>>> > >>>>>> > _______________________________________________ >>>>>> > discuss mailing list discuss(a)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(a)mpich.org >>>>>> > To manage subscription options or unsubscribe: >>>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>>> > >>>>>> > _______________________________________________ >>>>>> > discuss mailing list discuss(a)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(a)mpich.org >>>>>> > To manage subscription options or unsubscribe: >>>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>>> > >>>>>> > _______________________________________________ >>>>>> > discuss mailing list discuss(a)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(a)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(a)mpich.org >>>>>> To manage subscription options or unsubscribe: >>>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>>>> >>>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)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(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > _______________________________________________ > discuss mailing list discuss(a)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

1 0

Re: [mpich-discuss] MPICH error on CentOS
by Ricardo Román Brenes 06 Nov '13

06 Nov '13

Still, try to update to a new mpich asap! :-) On Nov 6, 2013 6:45 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> wrote: >> >>> Did you start mpd either with mpd or mpdboot? >>> On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <roman.ricardo(a)gmail.com> >>> wrote: >>> >>>> He has to. Thats an older mpich than mine! :-P >>>> On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… >>>>> > >>>>> > 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@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(a)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(a)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(a)gmail.com> wrote: >>>>> > With rwx permission just for root? >>>>> > >>>>> > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> >>>>> wrote: >>>>> > Hi, >>>>> > >>>>> > I am getting the following error while using the command - >>>>> > >>>>> > [root@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@localhost /]# which mpirun >>>>> > /usr/bin/mpirun >>>>> > [root@localhost /]# which mpiexec >>>>> > /usr/bin/mpiexec >>>>> > >>>>> > What could be the problem here ?? >>>>> > >>>>> > Thanks >>>>> > -------- >>>>> > Bharat >>>>> > >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > discuss mailing list discuss(a)mpich.org >>>>> > To manage subscription options or unsubscribe: >>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>> > >>>>> > _______________________________________________ >>>>> > discuss mailing list discuss(a)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(a)mpich.org >>>>> > To manage subscription options or unsubscribe: >>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>> > >>>>> > _______________________________________________ >>>>> > discuss mailing list discuss(a)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(a)mpich.org >>>>> > To manage subscription options or unsubscribe: >>>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>>> > >>>>> > _______________________________________________ >>>>> > discuss mailing list discuss(a)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(a)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(a)mpich.org >>>>> To manage subscription options or unsubscribe: >>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>>> >>>> >>> _______________________________________________ >>> discuss mailing list discuss(a)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(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Re: [mpich-discuss] MPICH error on CentOS
by bharat gupta 06 Nov '13

06 Nov '13

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(a)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(a)gmail.com> wrote: > >> Did you start mpd either with mpd or mpdboot? >> On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <roman.ricardo(a)gmail.com> >> wrote: >> >>> He has to. Thats an older mpich than mine! :-P >>> On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… >>>> > >>>> > 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@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(a)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(a)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(a)gmail.com> wrote: >>>> > With rwx permission just for root? >>>> > >>>> > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> >>>> wrote: >>>> > Hi, >>>> > >>>> > I am getting the following error while using the command - >>>> > >>>> > [root@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@localhost /]# which mpirun >>>> > /usr/bin/mpirun >>>> > [root@localhost /]# which mpiexec >>>> > /usr/bin/mpiexec >>>> > >>>> > What could be the problem here ?? >>>> > >>>> > Thanks >>>> > -------- >>>> > Bharat >>>> > >>>> > >>>> > >>>> > _______________________________________________ >>>> > discuss mailing list discuss(a)mpich.org >>>> > To manage subscription options or unsubscribe: >>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>> > >>>> > _______________________________________________ >>>> > discuss mailing list discuss(a)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(a)mpich.org >>>> > To manage subscription options or unsubscribe: >>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>> > >>>> > _______________________________________________ >>>> > discuss mailing list discuss(a)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(a)mpich.org >>>> > To manage subscription options or unsubscribe: >>>> > https://lists.mpich.org/mailman/listinfo/discuss >>>> > >>>> > _______________________________________________ >>>> > discuss mailing list discuss(a)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(a)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(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>> >> _______________________________________________ >> discuss mailing list discuss(a)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

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Re: [mpich-discuss] MPICH error on CentOS
by bharat gupta 06 Nov '13

06 Nov '13

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(a)gmail.com> wrote: > Did you start mpd either with mpd or mpdboot? > On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <roman.ricardo(a)gmail.com> > wrote: > >> He has to. Thats an older mpich than mine! :-P >> On Nov 6, 2013 6:34 PM, "Pavan Balaji" <balaji(a)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(a)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(a)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/… >>> > >>> > 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@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(a)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(a)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(a)gmail.com> wrote: >>> > With rwx permission just for root? >>> > >>> > On Nov 6, 2013 6:00 PM, "bharat gupta" <bharat.85.monu(a)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(a)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(a)gmail.com> >>> wrote: >>> > Hi, >>> > >>> > I am getting the following error while using the command - >>> > >>> > [root@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@localhost /]# which mpirun >>> > /usr/bin/mpirun >>> > [root@localhost /]# which mpiexec >>> > /usr/bin/mpiexec >>> > >>> > What could be the problem here ?? >>> > >>> > Thanks >>> > -------- >>> > Bharat >>> > >>> > >>> > >>> > _______________________________________________ >>> > discuss mailing list discuss(a)mpich.org >>> > To manage subscription options or unsubscribe: >>> > https://lists.mpich.org/mailman/listinfo/discuss >>> > >>> > _______________________________________________ >>> > discuss mailing list discuss(a)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(a)mpich.org >>> > To manage subscription options or unsubscribe: >>> > https://lists.mpich.org/mailman/listinfo/discuss >>> > >>> > _______________________________________________ >>> > discuss mailing list discuss(a)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(a)mpich.org >>> > To manage subscription options or unsubscribe: >>> > https://lists.mpich.org/mailman/listinfo/discuss >>> > >>> > _______________________________________________ >>> > discuss mailing list discuss(a)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(a)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(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >> > _______________________________________________ > discuss mailing list discuss(a)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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