namd-l: AW: rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs AW: rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs From: Norman Geist (norman.geist_at_uni-greifswald.de) Date: Mon Oct 14 2013 - 01:15:13 CDT Next message: Vidhya Sankar: "Re: About Usage of Topolgy and Parameter" Previous message: Kenno Vanommeslaeghe: "Re: About Usage of Topolgy and Parameter" In reply to: Thomas C. Bishop: "rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] Hi, you are trying to start 256 processes. This is not a problem, but most linux distributions don't allow that much connections by default. If you have a smp compile of NAMD, you should set "+p" as you did before, but use "+ppn" additionally, to use the shared memory parallelism layer of namd, this will save you processes. You need to benchmark the best ratio between distributed memory (processes) and shared memory (threads) for your configuration. A good starting point is to start one process per cpu socket and fork over all its cores. <- this is the most easiest way to solve this Another option might be, as it seems you are using rsh to connect the processes currently, try to use with charmrun "++remote-shell ssh". Nonetheless you will have to modify the ssh settings to allow more connections. I guess it's something like "MaxStartups" in /etc/ssh/sshd_config. Good luck Norman Geist. Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Thomas C. Bishop Gesendet: Montag, 14. Oktober 2013 05:30 An: namd-l_at_ks.uiuc.edu Betreff: namd-l: rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs Dear NAMD, I'm trying to run a job w/ 256 core (4way SMP systems w/ infiniband) using NAMD_2.9_Linux-x86_64-ibverbs and following command line $CHARM ++timeout 120 ++nodelist nodes ++p $NP $NAMD $CONF where $CHARM and $NAMD are the charmrun and namd executables and nodes is the list of nodes allocated by pbs NOTE nodes lists all hosts 4x since 4way SMP. I get messages similar to following when try to start a job on 256 core but not when I use say 64 core... suggestions? rcmd: socket: All ports in use rcmd: socket: All ports in use rcmd: socket: All ports in use rcmd: socket: All ports in use Charmrun> Error 1 returned from rsh (poseidon106:247) Thanks in advance, Tom
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Thomas C. Bishop
Tel: 318-257-5209
Fax: 318-257-3823
www.latech.edu/~bishop
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Next message: Vidhya Sankar: "Re: About Usage of Topolgy and Parameter" Previous message: Kenno Vanommeslaeghe: "Re: About Usage of Topolgy and Parameter" In reply to: Thomas C. Bishop: "rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:49 CST
