From: Balazs Jojart (jojartb_at_gmail.com)
Date: Tue Feb 23 2010 - 04:27:03 CST
Dear Vlad,
Yes I'm going to test the newest CVS code, and as I'm ready I'm going to
report the results.
Balazs
Vlad Cojocaru wrote:
> Dear Balazs, Dear all,
>
> Is that true that the namd2.7b2 always gives segmentation faults with
> AMBER topology files ?
> Is this the case with the newest CVS code as well ?
>
> I am running here the CVS code from 13.08.2009 compiled with tcl8.4.19
> and I do not see any of the problems reported ...
>
> Unfortunately, I do not have much time to test everything now ...
>
> Balazs, if you manage to test with the newest CVS code, would you
> please let me know if you get rid of the segmentation faults ?
>
> Thanks
> Vlad
>
> Balazs Jojart wrote:
>> Dear Vlad, Francesco and Giacomo,
>> I faced to the same problem, and as Vlad suggested we compiled the
>> namd source code against tcl8.5, and we didn't obtained the ("FATAL
>> ERROR: syntax error in expression " $mdSteps == 0 && $mdStart eq
>> "yes" " ) errors.
>> Unfortunatelly, the simulation stop with Segmentation Fault error
>> message, and it was reported previously by others, that there is
>> problems with the amber parm7/rst file using the namd2.7beta2 source
>> code. It means, that we have to use the CVS code?
>> Thank you for youer help in advance!
>> Balazs
>>
>>
>> Vlad Cojocaru wrote:
>>> Francesco, Giacomo,
>>>
>>> As I know this is an error coming from my RAMD scripts, I will curve
>>> in here .. (I changed the subject of the mail for the list archive)
>>>
>>> Recently users noticed that the RAMD scripts require tcl8.4 or
>>> above. I don't know what is the reason for that as I have never
>>> tested it against tcl 8.3 ... While running myself the scripts (self
>>> compiled NAMD against tcl8.4), I have never noticed the error
>>> Francesco and other users reported.
>>>
>>> The error is a complaint ("FATAL ERROR: syntax error in expression "
>>> $mdSteps == 0 && $mdStart eq "yes" " )
>>> about the following if statement at line 106 in the
>>> 'ramd-4.0_script.tcl':
>>>
>>> if { $mdSteps == 0 && $mdStart eq "yes" } {
>>> print "RAMD: WARNING: 'mdStart' has no meaning for pure RAMD
>>> simulation"
>>> }
>>>
>>> I do not see any problem with this if statement. Do any of you
>>> notice something in this statement that might not be compatible with
>>> tcl8.3 ?
>>> But maybe the error message is misleading ...
>>>
>>> Francesco, I don't know if this is too much of a trouble for you ...
>>> But if its possible, could you compile yourself the NAMD code
>>> against tcl8.4 or above and see if you get rid of the problem ? In
>>> the meantime, I will look to see if I can find the reason for this
>>> error .
>>>
>>> Cheers
>>> Vlad
>>>
>>>
>>> Giacomo Fiorin wrote:
>>>> Hi Francesco, if it were compiled against version 8.3 and you only
>>>> had 8.4 installed in the system, NAMD wouldn't find the 8.3 library
>>>> and wouldn't run at all. And even then, you can still install the
>>>> tcl8.3 package from lenny and try that out.
>>>>
>>>> Is it a tcl error or something else? NAMD's and Linux's version
>>>> are secondary informations, without the type of error message, it's
>>>> nearly impossible to help you.
>>>>
>>>> Giacomo
>>>>
>>>>
>>>> ---- ----
>>>> Giacomo Fiorin
>>>> ICMS - Institute for Computational Molecular Science
>>>> Temple University
>>>> 1900 N 12 th Street, Philadelphia, PA 19122
>>>> work phone: (+1)-215-204-4216
>>>> mobile: (+1)-267-324-7676
>>>> mail: giacomo.fiorin_at_gmail.com <mailto:giacomo.fiorin_at_gmail.com>
>>>> ---- ----
>>>>
>>>>
>>>> On Mon, Feb 22, 2010 at 9:38 AM, Francesco Pietra
>>>> <chiendarret_at_gmail.com <mailto:chiendarret_at_gmail.com>> wrote:
>>>>
>>>> Adding to myself, I have now tried NAMD_CVS_Linux-x86_64
>>>> 2010-02-21
>>>> nightly build in place of namd_2.7b2. The TCL script does not work
>>>> either. Therefore, either the nightly build was compiled to
>>>> TCL <8.4
>>>> (which would be surprising to me), or there is a problem with
>>>> the TCL
>>>> script on Debian Linux amd64 lenny (stable).
>>>>
>>>> francesco
>>>>
>>>> On Mon, Feb 22, 2010 at 5:53 PM, Francesco Pietra
>>>> <chiendarret_at_gmail.com <mailto:chiendarret_at_gmail.com>> wrote:
>>>> > Please, which version of TCL was used in building amd64 binary
>>>> > namd_2.7b2? If <8.4, is the 22 Feb2010 nightly build compiled
>>>> against
>>>> > TCL 8.4?
>>>> >
>>>> > The problem is that a TCL script using version 8.4 does not
>>>> work with
>>>> > namd_2.7b2 (amd64).
>>>> >
>>>> > Thanks
>>>> >
>>>> > francesco pietra
>>>> >
>>>> >
>>>> >
>>>>
>>>>
>>>
>>> --
>>> ----------------------------------------------------------------------------
>>>
>>> Dr. Vlad Cojocaru
>>>
>>> Heidelberg Institute for Theoretical Studies
>>> HITS gGmbH
>>> Molecular and Cellular Modelling Group
>>> Schloss-Wolfsbrunnenweg 35
>>> 69118 Heidelberg
>>>
>>> Tel: ++49-6221-533202
>>> Fax: ++49-6221-533298
>>>
>>> e-mail:Vlad.Cojocaru[at]h-its.org
>>>
>>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>>
>>> ----------------------------------------------------------------------------
>>>
>>> Amtgericht Mannheim / HRB 337446
>>> Managing Directors: Dr. h.c. Klaus Tschira, Prof. Dr.-Ing. Andreas
>>> Reuter
>>> http://www.h-its.org (http://eml-research.de)
>>> ----------------------------------------------------------------------------
>>>
>>>
>>
>>
>
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