Re: errno = 2

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:

------
[mriv209-01:~/MD/NAMD/NAMD_2.6b1_MacOSX-PPC] bo% ./charmrun ./namd2
++local +p1 ubq_wb_eq.conf > ubq_wb_eq.log
------

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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