From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Tue Feb 23 2010 - 09:52:30 CST
To further confirm the problem regarding the segfault when using amber
generated topologies with namd2.7b2 or later, I just wanted to say that
I made a test on a cray xt5 and the behavior is the same. Whatever I
reported yesterday were tests made on Intel/Linux machines at MSI.
If anyone on the developers side can give us any suggestion, I'll be
happy to make the tests right away.
All the best,
George
Balazs Jojart wrote:
> 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)
>>>> ----------------------------------------------------------------------------
>>>>
>>>>
>>>
>>>
>>
>
-- ________________________________________________________________________ George Madalin Giambasu PhD Student University of Minnesota Phone : (612) 625-6317 Department of Chemistry Fax : (612) 626-7541 207 Pleasant St. SE e-mail: Minneapolis, MN USA 55455-0431 GeorgeMGiambasu_at_umn.edu York Research Group giambasu_at_gmail.com http://theory.chem.umn.edu/~giambasu ________________________________________________________________________
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