From: bo baker (bo.bybaker_at_gmail.com)
Date: Tue Aug 16 2005 - 19:04:49 CDT
Dear Nav:
I have all executables as well as all the input and output files
in the same directory. I run the files with 1 processor, and I change
'p2' to 'p1;. I try the way as you suggested . Here is how I did:
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[mriv209-01:~/MD/NAMD/NAMD_2.6b1_MacOSX-PPC] bo% ./charmrun ./namd2
++local +p1 ubq_wb_eq.conf > ubq_wb_eq.log
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But I got the same error message as before:
---- Charmrun> error 0 attaching to node: Timeout waiting for node-program to connect ----- Do I have some typing problems? Or the NAMD program just not set in my computer? Thank you for any comments. Regard Bo On 8/16/05, Navratna Vajpai <navratna.vajpai_at_unibas.ch> wrote: > Dear Bo.. > first thing .. > if u have all ur executables as well as all the input and output files > in the same directory then u have to use the command > ./charmrun ./namd2 ++local +p2 ubq_wb_eq.conf > ubq_wb_eq.log > > Are u also running ur file on two processors or two CPU at the same > time .. if yes +p2 will be valid otherwise u have to use +p1 or > depending on number of processors you are using for the MD run. > just try it out .. i hope this should work. > best of luck and regards > nav > > > On Aug 16, 2005, at 9:03 PM, bo baker wrote: > > > Dear Nav: > > > > Thank you very much for your suggestion. I try it on the Mac. Here is > > how I did: > > > > ----- > > [mriv209-01:~/MD/NAMD/NAMD_2.6b1_MacOSX-PPC] bo% > > /Users/bo/MD/NAMD/NAMD_2.6b1_MacOSX-PPC/charmrun > > /Users/bo/MD/NAMD/NAMD_2.6b1_MacOSX-PPC/namd2 ++local +p2 > > ubq_wb_eq.conf > unq_wb_eq.log > > > > ----- > > > > It seems work! But after a while, I got the following message: > > ------- > > Charmrun> error 0 attaching to node: > > Timeout waiting for node-program to connect > > ------- > > > > Could you have any idea on how to fix it? Your advices will be much > > appreciated! > > > > Regards > > > > Bo > > > > > > > > On 8/15/05, Navratna Vajpai <navratna.vajpai_at_unibas.ch> wrote: > >> Dear Bo, > >> Hi. > >> first of all check whether u have the right path for the execution. I > >> also have the same version of the NAMD on my Mac OsX. I use the > >> following command and it works. may be something like this should work > >> at your setup > >> > >> ../../NAMD_2.5_MacOSX-PPC/charmrun ../../NAMD_2.5_MacOSX-PPC/namd2 > >> ++local +p2 pep300r.namd > logmd300r_all > >> > >> depending on the location of the executables u set up the same command > >> and try to run. The last two are input and output file. I am hopeful > >> that it should work. > >> good luck > >> regards > >> Nav > >> > >> > >> On Aug 16, 2005, at 2:05 AM, bo baker wrote: > >> > >>> Hello, NAMD: > >>> > >>> I install the NAMD_2.6b1 into a Mac computer (Mac OSX 10.3.9). I try > >>> to run 'namd2'. Here is what I got: > >>> > >>> ------ > >>> > >>> [mriv209-01:~/MD/NAMD/NAMD_2.6b1_MacOSX-PPC] bo% > >>> /Users/bo/MD/NAMD/NAMD_2.6b1_MacOSX-PPC/namd2 ubq_wb_eq.conf > > >>> unq_wb_eq.log > >>> > >>> dyld: /Users/bo/MD/NAMD/NAMD_2.6b1_MacOSX-PPC/namd2 can't open > >>> library: /opt/ibmcmp/lib/libibmc++.A.dylib (No such file or > >>> directory, errno = 2) > >>> Trace/BPT trap > >>> > >>> ------ > >>> > >>> The 'ubq_wb_eq.conf' is from 'namd-tutorial-files' downloaded from > >>> NAMD website. I have the 'ubq_wb.pdb' and 'ubq_wb.psf' files at the > >>> same directory. It seems that I don't have the NAMD installed > >>> properly. The computer is in mutiple users, and I am not the > >>> adminstrator. > >>> > >>> Thanks for any comments to fix this problem. > >>> > >>> Bo > >>> > >> ***************************************************************** > >> Navratna Vajpai > >> Ph.D student in Prof. Stephan Grzesiek's group > >> NMR in Strukturbiologie, > >> Abt. Strukturbiologie & Biophysik, > >> Biozentrum, > >> CH-4056, Basel, > >> Switzerland > >> Phone - 0041 76 375 2003(M) > >> 0041 61 267 2097(O) > >> > >> > >> > ***************************************************************** > Navratna Vajpai > Ph.D student in Prof. Stephan Grzesiek's group > NMR in Strukturbiologie, > Abt. Strukturbiologie & Biophysik, > Biozentrum, > CH-4056, Basel, > Switzerland > Phone - 0041 76 375 2003(M) > 0041 61 267 2097(O) > >
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