Re: namd cvs compilation

From: Anirban Ghosh (anirbang_at_cdac.in)
Date: Thu Nov 27 2008 - 22:46:34 CST

Hello Bin,

Are you getting the same error for Nxg Nxg Nxg also?
If so, the I thin Anton or Peter can answer that one better, because some
coefficient values are also associated with these angle parameters.

For "Bad global exclusion count", you can try to run a constant volume
simulation, that might help.

Regards,

> Hi, Anirban:
> Can I do the same thing for Nxg Nxg Nxg?
> Also, I kept getting the error: "FATAL ERROR: Bad global
> exclusion count!" while running the CGMD using NAMD CVS version with
> "cosangles on".
> Does anyone know why this is happening?
> I also checked the NAMD troubleshooting page, (http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting
> ), which said "These errors generally indicate that two atoms that are
> (ususally implicitly) excluded are on non-neighboring patches or are
> more than the cutoff distance apart"
> Can anyone explain, at what situation, this will happen?
>
> Thanks a lot.
> Bin
>
>
> On Nov 27, 2008, at 12:27 AM, Anirban Ghosh wrote:
>
>>
>> Hi,
>>
>> Add the following line to youparameter file, in the section "ANGLES":
>>
>> Nxg Nxx Nxg 2.988 92
>>
>> These parameters are pretty much universal for the protein backbone in
>> the RBCG model (the angle Nxg Nxx Nxg corresponds to the connection
>> glycine-arbitrary amino acid-glycine).
>> Or you can use the older .par and .top files successfully.
>>
>> I was facing the same problem and Anton told me to do this. Hope it
>> helps.
>>
>> Regards,
>>
>>
>>
>>
>>> Sorry about this, but I think that's the problem.
>>> Now I can compile namd, but when I tried to run the CG model, one
>>> peculiar
>>> error occured:
>>>
>>> "Unable to find angle parameter for Nxg Nxx Nxg"
>>>
>>> Is this a reasonable error ?
>>>
>>> Thanks .
>>> Bin
>>>
>>> On Wed, Nov 26, 2008 at 5:24 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>>>
>>>> Hi, Axel:
>>>>
>>>> I just saw your response to the thread "NAMD crashed with
>>>> TclForce
>>>> turned on"
>>>>
>>>>> the namd cvs code defines USE_COMPAT_CONST in the headers that
>>>>> include tcl.h. defining USE_NON_CONST is incompatible with that
>>>>> (see tcl.h). that same should be true for tcl8.4 if you compile
>>>>> the cvs. hence my suspicion that you compiled against an
>>>>> inconsistent version of the tcl header. this can easily cause
>>>>> segfaults regardless of the compiler.
>>>>
>>>> Does this mean when I try to compile cvs version of NAMD, the
>>>> *.tcl
>>>> file in the arch folder should no longer use "TCLFLAGS=-DNAMD_TCL
>>>> -DUSE_NON_CONST", but instead should be :
>>>> "TCLFLAGS=-DNAMD_TCL"?(-DUSE_NON_CONST no longer needed)
>>>> Thanks a lot and Happy Thanksgiving.
>>>>
>>>> Bin
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Nov 26, 2008, at 4:55 PM, BIN ZHANG wrote:
>>>>
>>>> Hi, all:
>>>>> I was trying to build NAMD CVS version(downloaded yesterday) on
>>>>> a linux
>>>>> cluster, with the arch file:
>>>>>
>>>>> ==========================================
>>>>> NAMD_ARCH = Linux-amd64
>>>>> CHARMARCH = mpi-linux-amd64-icc-mpich
>>>>> CHARMOPTS = -thread context -memory os
>>>>>
>>>>> FLOATOPTS = -O3 -fno-rtti -ipo0 -xW -mtune=pentium4
>>>>>
>>>>> CXX = /opt/mpich/infiniband/intel/bin/mpiCC
>>>>> CC = /opt/mpich/infiniband/intel/bin/mpicc
>>>>> CXXOPTS = -static-intel $(FLOATOPTS)
>>>>> CXXNOALIASOPTS = -fno-alias $(FLOATOPTS)
>>>>> COPTS = -static-intel $(FLOATOPTS)
>>>>> ==========================================
>>>>>
>>>>> But it failed with the error:
>>>>>
>>>>> /usr/include/tcl.h(256): catastrophic error: #error directive:
>>>>> define at
>>>>> most one of USE_NON_CONST and USE_COMPAT_CONST
>>>>> # error define at most one of USE_NON_CONST and
>>>>> USE_COMPAT_CONST
>>>>> ^
>>>>>
>>>>> compilation aborted for src/mainfunc.C (code 4)
>>>>> make: *** [obj/mainfunc.o] Error 4
>>>>>
>>>>> Does anyone know what is this error about? How to solve the
>>>>> problem
>>>>> then?
>>>>>
>>>>> Thanks a lot and Happy Thanksgiving.
>>>>> Bin
>>>>>
>>>>> PS: the same configuration works for NAMD-2.6
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------------
>>>>> The tree of liberty must be refreshed from time to time with the
>>>>> blood of
>>>>> patriots and tyrants.
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------------
>>>> The tree of liberty must be refreshed from time to time with the
>>>> blood of
>>>> patriots and tyrants.
>>>>
>>>>
>>>
>>
>> --
>> Anirban Ghosh
>> Grade Based Engineer
>> Bioinformatics Team
>> Scientific & Engineering Computing Group
>> Centre for Development of Advanced Computing
>> Pune, India
>>
>>
>
>
>
>
>
>
>
>
>
> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood
> of patriots and tyrants.
>

-- 
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Scientific & Engineering Computing Group
Centre for Development of Advanced Computing
Pune, India

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