<div dir="ltr">Thanks for the command. After issuing mpdboot and making file mdp.conf with line secretword=<> in /etc folder solved the problem..<div><br></div><div>Thanks a lot</div></div><div class="gmail_extra"><br>
<br><div class="gmail_quote">On Thu, Nov 7, 2013 at 9:43 AM, 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">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</div><div class="HOEnZb">
<div class="h5"><div class="gmail_extra">
<br><br><div class="gmail_quote">On Thu, Nov 7, 2013 at 9:42 AM, 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">
<p dir="ltr">Did you start mpd either with mpd or mpdboot? </p><div><div>
<div class="gmail_quote">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 type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<p dir="ltr">He has to. Thats an older mpich than mine! :-P </p>
<div class="gmail_quote">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 type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<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>
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><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>
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><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>
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><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>
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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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</blockquote></div>
</blockquote></div>
</div></div><br>_______________________________________________<br>
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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>
</div>
</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>
</div>