neal skinner wrote: > Zheng, Lieven, WBR and Fellow MEEP users, > > Your suggestions were right on the money. When I got rsh enabled and > started specifying the full path to meep-mpi, things started working. > Unfortunately, I am dissapointed by the decrease in execution times I > have experienced so far. For example, the best speed up I have seen is > only 10 - 15% when using up to 4 processors. > > While running on multiple processors, I can go into the system monitor > and see multiple instances of meep-mpi and it looks like the memory > required for the job is split among these processes, but with no big > speed increase. I understand that sometimes MPI does not show any > significant decrease in processing times for small problems, so I have > tried several sizes of problems - all with similar results. > > I am not complaining, 10 - 15 % more speed is better than what I had, > but I was expecting maybe something like 50% less time required for 4 > processors. > > Do you have any other suggestions that I might try. Once again, I > thank you for your help. > > Best regards, > > Neal > > On Wed, Nov 19, 2008 at 11:51 PM, Zheng Li > <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > neal skinner wrote: >> Zheng, >> >> I am running a quad core pentium (Q6600). When I enter rsh >> localhost, it asks for a password and I get the following: >> >> >> [EMAIL PROTECTED]:~/meep/pec-reflector$ rsh localhost >> Password: >> Last login: Wed Nov 19 22:07:49 CST 2008 from localhost on pts/2 >> Linux blackie 2.6.18-6-amd64 #1 SMP Wed Oct 15 10:07:11 UTC 2008 >> x86_64 >> >> The programs included with the Debian GNU/Linux system are free >> software; >> the exact distribution terms for each program are described in the >> individual files in /usr/share/doc/*/copyright. >> >> Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent >> permitted by applicable law. >> You have new mail. >> [EMAIL PROTECTED]:~$ >> >> then, when I type exit, i get >> >> [EMAIL PROTECTED]:~/meep/pec-reflector$ ssh localhost >> ssh: connect to host localhost port 22: Connection refused >> [EMAIL PROTECTED]:~/meep/pec-reflector$ >> >> Nothing much happens with ssh: >> >> [EMAIL PROTECTED]:~/meep/pec-reflector$ ssh localhost >> ssh: connect to host localhost port 22: Connection refused >> [EMAIL PROTECTED]:~/meep/pec-reflector$ >> >> So, I think the conclusion is I can log in with rsh, but not ssh. >> >> Thanks again! >> >> Neal >> >> >> On Wed, Nov 19, 2008 at 7:48 PM, Zheng Li >> <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>> wrote: >> >> neal skinner wrote: >>> Thank you for your help, but I tried your suggestions, and >>> it still does not work. Both mpirun and meep-mpi are in >>> /usr/bin. Here is the response I now get when I add the full >>> path to meep-mpi as well as to mpirun: >>> >>> [EMAIL PROTECTED]:~/meep/pec-reflector$ /usr/bin/mpirun -np 2 >>> /usr/bin/meep-mpi pec-reflector-50.ctl >>> Permission denied. >>> p0_20989: p4_error: Child process exited while making >>> connection to remote process on localhost: 0 >>> p0_20989: (2.007812) net_send: could not write to fd=4, >>> errno = 32 >>> [EMAIL PROTECTED]:~/meep/pec-reflector$ >>> >>> I get a permission denied error message. I get the same >>> message if I sign on as superuser. Any more thoughts on what >>> I can do to get meep-mpi to work? >>> >>> Once again, I thank you in advance of your help. >>> >>> Best regards, >>> >>> Neal >>> >>> >>> >>> >>> On Wed, Nov 19, 2008 at 3:37 AM, Zheng Li >>> <[EMAIL PROTECTED] >>> <mailto:[EMAIL PROTECTED]>> wrote: >>> >>> neal skinner wrote: >>>> Folks, >>>> >>>> I have been experimenting with MEEP for several months >>>> now and cannot get meep-mpi to work. I am running a >>>> quad core Pentium (Q6600) system and think I have >>>> downloaded all the right files. When I try to run >>>> meep-mpi for two processors this is what I get: >>>> >>>> [EMAIL PROTECTED]:~/meep/pec-reflector$ mpirun -np 2 >>>> meep-mpi pec-reflector-50.ctl >>>> Warning: Command line arguments for program should be given >>>> after the program name. Assuming that >>>> pec-reflector-50.ctl is a >>>> command line argument for the program. >>>> Missing: program name >>>> Program meep-mpi either does not exist, is not >>>> executable, or is an erroneous argument to mpirun. >>>> >>>> I think this error message is saying that meep-mpi is >>>> not present, but I can run meep-mpi >>>> >>>> >>>> [EMAIL PROTECTED]:~/meep/pec-reflector$ meep-mpi >>>> pec-reflector-50.ctl >>>> Using MPI version 1.2, 1 processes >>>> ----------- >>>> >>>> and everything works like normal meep. >>>> >>>> Obviously I'm missing something somewhere. I am new to >>>> Linux and parallel processing, so any help to get me >>>> pointed in the right direction would be appreciated. >>>> >>>> Thanks in advance, >>>> >>>> Neal >>>> _______________________________________________ >>>> meep-discuss mailing list >>>> [email protected] >>>> <mailto:[email protected]> >>>> http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss >>> Hi, >>> >>> You should tell mpi-run the absolute path or the one >>> relative to >>> the current working path of meep-mpi like >>> mpi-run -np 2 /usr/bin/meep-mpi a.ctl >>> or >>> mpi-run -np 2 ../bin/meep-mpi a.ctl. >>> >>> Yet, when you type meep-mpi in bash/csh, the shell can >>> guess >>> the absolute path for you via searching the paths >>> provided by >>> the environment variable PATH. >>> For example: >>> PATH=~/apps/bin:/usr/local/bin:/usr/bin >>> then bash/csh "tries" >>> ~/apps/bin/meep-mpi, >>> /usr/local/bin/meep-mpi, >>> and /usr/bin/meep-mpi one by one. >>> Once the shell finds meep-mpi, meep-mpi is called. >>> >>> Yours >>> Zheng >>> 2008-11-19 >>> >>> >> Hi, neal skinner: >> What linux box and which mpi system do you use. It seems like >> that you can not login remotely. >> Try: >> rsh localhost >> or >> ssh localhost >> Can you successfully login? >> >> Zheng >> 2008-11-20 >> >> > Since debian uses mpich to compile meep-mpi, there is something > wrong with your rsh. See > http://www-unix.mcs.anl.gov/mpi/mpich1/docs/faq.htm#permdenied > for further informations. > > Good luck for you. > Zheng > 2008-11-20 > > Hi neal
You should find the bottleneck by yourself to speed up meep-mpi. Yet, two tools may be useful: a: top/htop to show your CPU and MEM usage; b: sudo iptraf to show your network usage. Zheng 2008-11-25
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