<div dir="ltr">yup.</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Nov 6, 2013 at 9:25 PM, bharat gupta <span dir="ltr"><<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Okay .. thanks but right now my simulation is running and if I use the command that you both mentioned would ultimately lead to the stoppage of my simulations .. right ?? May be I can try reinstalling the new version after finishing the simulations </div>
<div class="HOEnZb"><div class="h5">
<div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Nov 7, 2013 at 12:21 PM, Ricardo Román Brenes <span dir="ltr"><<a href="mailto:roman.ricardo@gmail.com" target="_blank">roman.ricardo@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">both will coexiste, you ahve to "yum remove mpich2-x-x-x.x84_64"</div><div><div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Nov 6, 2013 at 9:20 PM, bharat gupta <span dir="ltr"><<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">But how to remove the older version or reinstalling the new one will override the changes</div><div>
<div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Nov 7, 2013 at 12:18 PM, Pavan Balaji <span dir="ltr"><<a href="mailto:balaji@mcs.anl.gov" target="_blank">balaji@mcs.anl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Wow. 1.2.1p1 is ancient. It was used by dinosaurs and such when they still roamed the earth.<br>
<br>
I don’t use CentOS, but don’t the rpm’s from this page work?<br>
<br>
<a href="http://www.mpich.org/downloads/" target="_blank">http://www.mpich.org/downloads/</a><br>
<br>
If not, then source compile is always possible. :-) It’s an open-source project.<br>
<span><font color="#888888"><br>
—- Pavan<br>
</font></span><div><div><br>
On Nov 6, 2013, at 6:56 PM, bharat gupta <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>> wrote:<br>
<br>
> Okay.. Thanks a lot for your time and help..<br>
><br>
><br>
> On Thu, Nov 7, 2013 at 9:54 AM, Ricardo Román Brenes <<a href="mailto:roman.ricardo@gmail.com" target="_blank">roman.ricardo@gmail.com</a>> wrote:<br>
> 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<br>
><br>
> On Nov 6, 2013 6:48 PM, "bharat gupta" <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>> wrote:<br>
> How can that be done in CentOS 6.0, I used the command yum search mpich and installed the one that it showed ...<br>
><br>
><br>
> On Thu, Nov 7, 2013 at 9:47 AM, Ricardo Román Brenes <<a href="mailto:roman.ricardo@gmail.com" target="_blank">roman.ricardo@gmail.com</a>> wrote:<br>
> Still, try to update to a new mpich asap! :-)<br>
><br>
> On Nov 6, 2013 6:45 PM, "bharat gupta" <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>> wrote:<br>
> Thanks for the command. After issuing mpdboot and making file mdp.conf with line secretword=<> in /etc folder solved the problem..<br>
><br>
> Thanks a lot<br>
><br>
><br>
> On Thu, Nov 7, 2013 at 9:43 AM, bharat gupta <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>> wrote:<br>
> 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<br>
><br>
><br>
> On Thu, Nov 7, 2013 at 9:42 AM, Ricardo Román Brenes <<a href="mailto:roman.ricardo@gmail.com" target="_blank">roman.ricardo@gmail.com</a>> wrote:<br>
> Did you start mpd either with mpd or mpdboot?<br>
><br>
> On Nov 6, 2013 6:39 PM, "Ricardo Román Brenes" <<a href="mailto:roman.ricardo@gmail.com" target="_blank">roman.ricardo@gmail.com</a>> wrote:<br>
> He has to. Thats an older mpich than mine! :-P<br>
><br>
> On Nov 6, 2013 6:34 PM, "Pavan Balaji" <<a href="mailto:balaji@mcs.anl.gov" target="_blank">balaji@mcs.anl.gov</a>> wrote:<br>
><br>
> Looks like I’m late to this email chain.<br>
><br>
> 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.<br>
><br>
> —- Pavan<br>
><br>
> On Nov 6, 2013, at 6:26 PM, bharat gupta <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>> wrote:<br>
><br>
> > DO I need to add some command in mpd.hosts file<br>
> ><br>
> ><br>
> > On Thu, Nov 7, 2013 at 9:22 AM, bharat gupta <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>> wrote:<br>
> > I don't know much about mpi , as I am using gromacs which was complied with mpi option. , But I read somewhere that<br>
> ><br>
> > " 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 <a href="http://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Multipurpose_Daemon_Commands.htm" target="_blank">http://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Multipurpose_Daemon_Commands.htm</a><br>
> ><br>
> > 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:-<br>
> ><br>
> > root@localhost INGT]# mpirun -np 24 mdrun -v -deffnm mdrun<br>
> > mpdroot: perror msg: No such file or directory<br>
> > mpdroot: cannot connect to local mpd at: /tmp/mpd2.console_root<br>
> > probable cause: no mpd daemon on this machine<br>
> > possible cause: unix socket /tmp/mpd2.console_root has been removed<br>
> ><br>
> > mpiexec_localhost.localdomain (__init__ 1208): forked process failed; status=255<br>
> ><br>
> ><br>
> > On Thu, Nov 7, 2013 at 9:11 AM, Ricardo Román Brenes <<a href="mailto:roman.ricardo@gmail.com" target="_blank">roman.ricardo@gmail.com</a>> wrote:<br>
> > Try using chmod 700. Can you run any other mpi example? Like cpi.c<br>
> ><br>
> > On Nov 6, 2013 6:08 PM, "bharat gupta" <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>> wrote:<br>
> > It have changed the file permission (rw) for root , ls -l mpd.hosts gives the output<br>
> > -rw-r--r--, 1 root root<br>
> ><br>
> ><br>
> > On Thu, Nov 7, 2013 at 9:02 AM, Ricardo Román Brenes <<a href="mailto:roman.ricardo@gmail.com" target="_blank">roman.ricardo@gmail.com</a>> wrote:<br>
> > With rwx permission just for root?<br>
> ><br>
> > On Nov 6, 2013 6:00 PM, "bharat gupta" <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>> wrote:<br>
> > 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<br>
> ><br>
> ><br>
> > On Thu, Nov 7, 2013 at 8:45 AM, Ricardo Román Brenes <<a href="mailto:roman.ricardo@gmail.com" target="_blank">roman.ricardo@gmail.com</a>> wrote:<br>
> > You need to create a mpd.hosts in /etc if you want to run mpd as root<br>
> ><br>
> > On Nov 6, 2013 5:41 PM, "bharat gupta" <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>> wrote:<br>
> > Hi,<br>
> ><br>
> > I am getting the following error while using the command -<br>
> ><br>
> > [root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt<br>
> ><br>
> > Error -<br>
> ><br>
> > /usr/bin/mpdroot: open failed for root's mpd conf filempiexec_localhost.localdomain (__init__ 1208): forked process failed; status=255<br>
> ><br>
> > 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 -<br>
> ><br>
> > [root@localhost /]# which mpirun<br>
> > /usr/bin/mpirun<br>
> > [root@localhost /]# which mpiexec<br>
> > /usr/bin/mpiexec<br>
> ><br>
> > What could be the problem here ??<br>
> ><br>
> > Thanks<br>
> > --------<br>
> > Bharat<br>
> ><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > discuss mailing list <a href="mailto:discuss@mpich.org" target="_blank">discuss@mpich.org</a><br>
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> ><br>
> > _______________________________________________<br>
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> ><br>
> ><br>
> ><br>
> > --<br>
> > Bharat<br>
> > Ph.D. Candidate<br>
> > Biomolecular Engineering Laboratory<br>
> > Pusan National University<br>
> > South Korea<br>
> > Mobile no. - 010-5818-3680<br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > discuss mailing list <a href="mailto:discuss@mpich.org" target="_blank">discuss@mpich.org</a><br>
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> ><br>
> > _______________________________________________<br>
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> ><br>
> ><br>
> ><br>
> > --<br>
> > Bharat<br>
> > Ph.D. Candidate<br>
> > Biomolecular Engineering Laboratory<br>
> > Pusan National University<br>
> > South Korea<br>
> > Mobile no. - 010-5818-3680<br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > discuss mailing list <a href="mailto:discuss@mpich.org" target="_blank">discuss@mpich.org</a><br>
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> ><br>
> > _______________________________________________<br>
> > discuss mailing list <a href="mailto:discuss@mpich.org" target="_blank">discuss@mpich.org</a><br>
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> ><br>
> ><br>
> ><br>
> > --<br>
> > Bharat<br>
> > Ph.D. Candidate<br>
> > Biomolecular Engineering Laboratory<br>
> > Pusan National University<br>
> > South Korea<br>
> > Mobile no. - 010-5818-3680<br>
> ><br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > Bharat<br>
> > Ph.D. Candidate<br>
> > Biomolecular Engineering Laboratory<br>
> > Pusan National University<br>
> > South Korea<br>
> > Mobile no. - 010-5818-3680<br>
> ><br>
> > _______________________________________________<br>
> > discuss mailing list <a href="mailto:discuss@mpich.org" target="_blank">discuss@mpich.org</a><br>
> > To manage subscription options or unsubscribe:<br>
> > <a href="https://lists.mpich.org/mailman/listinfo/discuss" target="_blank">https://lists.mpich.org/mailman/listinfo/discuss</a><br>
><br>
> --<br>
> Pavan Balaji<br>
> <a href="http://www.mcs.anl.gov/~balaji" target="_blank">http://www.mcs.anl.gov/~balaji</a><br>
><br>
> _______________________________________________<br>
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><br>
><br>
><br>
> --<br>
> Bharat<br>
> Ph.D. Candidate<br>
> Biomolecular Engineering Laboratory<br>
> Pusan National University<br>
> South Korea<br>
> Mobile no. - 010-5818-3680<br>
><br>
><br>
><br>
><br>
> --<br>
> Bharat<br>
> Ph.D. Candidate<br>
> Biomolecular Engineering Laboratory<br>
> Pusan National University<br>
> South Korea<br>
> Mobile no. - 010-5818-3680<br>
><br>
><br>
> _______________________________________________<br>
> discuss mailing list <a href="mailto:discuss@mpich.org" target="_blank">discuss@mpich.org</a><br>
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><br>
><br>
><br>
> --<br>
> Bharat<br>
> Ph.D. Candidate<br>
> Biomolecular Engineering Laboratory<br>
> Pusan National University<br>
> South Korea<br>
> Mobile no. - 010-5818-3680<br>
><br>
><br>
> _______________________________________________<br>
> discuss mailing list <a href="mailto:discuss@mpich.org" target="_blank">discuss@mpich.org</a><br>
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><br>
><br>
><br>
> --<br>
> Bharat<br>
> Ph.D. Candidate<br>
> Biomolecular Engineering Laboratory<br>
> Pusan National University<br>
> South Korea<br>
> Mobile no. - 010-5818-3680<br>
><br>
> _______________________________________________<br>
> discuss mailing list <a href="mailto:discuss@mpich.org" target="_blank">discuss@mpich.org</a><br>
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<br>
--<br>
Pavan Balaji<br>
<a href="http://www.mcs.anl.gov/~balaji" target="_blank">http://www.mcs.anl.gov/~balaji</a><br>
<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Bharat<br>Ph.D. Candidate<br>Biomolecular Engineering Laboratory<br>Pusan National University<br>South Korea<br>Mobile no. - 010-5818-3680<br><div>
<br></div>
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<a href="https://lists.mpich.org/mailman/listinfo/discuss" target="_blank">https://lists.mpich.org/mailman/listinfo/discuss</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Bharat<br>Ph.D. Candidate<br>
Biomolecular Engineering Laboratory<br>Pusan National University<br>South Korea<br>Mobile no. - 010-5818-3680<br><div><br></div>
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