Re: charmrun not found

From: Alexandre A. Vakhrouchev (makaveli.lcf_at_gmail.com)
Date: Tue Jun 24 2008 - 22:50:45 CDT

Hi Diego!

If you run from working directory you should point to charmrun as
follows './charmrun', or you can install it in directories stored in
PATH variable.

You errors are due to you didn't include in NAMD configuration file
required options

ERROR: 'exclude' is a required configuration option
ERROR: exclude defines: Electrostatic exclusion policy
ERROR: 'outputname' is a required configuration option
ERROR: outputname defines: prefix for the final PDB position and
velocity filenames
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

2008/6/25, Diego Alejandro Vargas <vardiego9_at_gmail.com>:
> Hi all,
> I installed NAMD not so long ago and have been trying to run it. I am
> working on a linux amd64 cluster with Rocks. I have been attempting to run a
> small simulation folding alanine through the configuration file that comes
> with NAMD. But when I try to use the command 'charmrun', it is not being
> found even though the executable is present in the working directory.
>
> I am able to run it in one processor using mpirun, but it keeps arriving at
> a fatal error: Error in the configuration file. The error is copied after my
> name, in case it may be of use.
>
> Is this due to a failure in translation of charmrun options into mpirun
> options?
>
> Thank you for your attention,
> Diego A. Vargas
>
> Charm++: standalone mode (not using charmrun)
> Info: NAMD 2.6 for Linux-amd64
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 50900 for net-linux-amd64-iccstatic
> Info: Built Wed Aug 30 12:54:51 CDT 2006 by jim on belfast.ks.uiuc.edu
> Info: 1 NAMD 2.6 Linux-amd64 1 Zlab-cluster.bme.utexas.edu Diego
> Info: Running on 1 processors.
> Info: 7476 kB of memory in use.
> Info: Memory usage based on mallinfo
> Info: Changed directory to lib/replica/example
> Info: Configuration file is fold_alanin.conf
> TCL: spawn_namd_ssh {cd
> /home/Diego/Diego/NAMD_2.6_Linux-amd64/lib/replica/example;
> /Projects/namd2/bin/current/Linux64/namd2 +netpoll} {beirut
> belfast}
> TCL: Suspending until startup complete.
> ERROR: 'exclude' is a required configuration option
> ERROR: exclude defines: Electrostatic exclusion policy
> ERROR: 'outputname' is a required configuration option
> ERROR: outputname defines: prefix for the final PDB position and velocity
> filenames
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>
> Stack Traceback:
> [0] CmiAbort+0x4f [0x7eb405]
> [1] _Z8NAMD_diePKc+0x62 [0x4b31e2]
> [2]
> _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x73
> [0x72343f]
> [3] _ZN9NamdState14configListInitEP10ConfigList+0x391
> [0x6ae59b]
> [4] _ZN9ScriptTcl9initcheckEv+0x5e [0x6ff8ac]
> [5] _ZN9ScriptTcl3runEPc+0xb5 [0x6fba3f]
> [6] main+0x21b [0x4b69c3]
> [7] __libc_start_main+0xdb [0x3fbb11c3fb]
> [8] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b2b5a]
> Charm++ fatal error:
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>
>

-- 
Best regards,
Dr. Alexander Vakhrushev
Institute of Applied Mechanics
Dep. of Mech. and Phys.-Chem.
of heterogeneous mediums
UB of Russian Academy of Sciences
34 T. Baramzinoy St.
Izhevsk, Russia 426067
----------------------------------
С уважением,
    Вахрушев Александр Александрович
к.ф.-м.н., с.н.с.
Институт прикладной механики
Уральского Отделения
Российской Академии Наук
426067, г. Ижевск
ул. Т. Барамзиной 34
+7(3412)21-45-83

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