Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts

From: Balazs Jojart (jojartb_at_gmail.com)
Date: Wed Feb 24 2010 - 05:41:28 CST

Dear Vlad,
The namd-CVS version was compiled against Tcl8.4.19.
The RAMD calculations runs with charmm psf files, without any error
message, but with this compilation I obtain again a segmentation fault
error with the amber topology files.
Don't worry about the troubles, we thank for your work to implement the
code into namd.
Cheers,
Balazs

Vlad Cojocaru wrote:
> Dear Balazs,
>
> Did you try to run the tcl forces tutorials from the NAMD website? Do
> they run correctly ? If you did not, I suggest you do that first. Like
> this we will see if you have a general tcl problem or its only the
> RAMD scripts. Let me know about it ... I am saying this because I had
> similar problems with tcl 8.5 with other tcl scripts I have been using
> ( like the former ABF module )...
>
> If the tcl forces tutorials exit with the same type of errors, then
> there is a general problem with your compilation. If these errors only
> appear while running RAMD, then the next test would be if you could
> compile against tcl 8.4.19 ...
>
> Actually maybe to put a correct diagnostic, you could compile namd 2.6
> both against tcl 8.4.19 and 8.5 and try the RAMD scripts with this
> NAMD code ....
>
> What is actually interesting that you don't get the seg faults anymore
> although you are using AMBER topology. ....
>
> I am also trying to test against different tcl versions to see what is
> actually going wrong . ....
>
> Sorry for the troubles .... but we are running these scripts so
> successfully here that I didn't even imagine that all these errors
> could appear ...
>
> Vlad
>
> Balazs Jojart wrote:
>> Dear Vlad,
>> I think the topology is OK, because it was used in a former
>> simulation only using standard MD. In the output file (RAMD), the the
>> structure information looks ok. I tested the loadcoords part as well,
>> by adding "puts coordinates(1)" lines in the tcl code, and the
>> coordinates are also missing - same error "no such element in array".
>> Our system administrator compiled the newest CVS of namd against
>> tcl8.5, fortunately I don't obtain any segfault error, but
>> unfortunately, the same error was occurred with the example files as
>> well, as described below. The outputs are attached.
>> Do we have to compile with another version of tcl (for example
>> Tcl8.4.19)?
>> Cheers,
>> Balazs
>>
>> Cojocaru,Vlad wrote:
>>> Dear Balazs,
>>>
>>> This is a more friendly error ...
>>> It looks as if your definition of the ramd and/or protein atoms is
>>> somehow wrong .. You have an atom that somehow does not have a mass
>>> .. Can you double check ?
>>>
>>> Otherwise, if you could send me a zipped file with the files
>>> required to reproduce your problem (topology, coordinates, box info
>>> files) I can try to see what is wrong ..
>>>
>>> vlad
>>>
>>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: Balazs Jojart [mailto:jojartb_at_gmail.com]
>>> Gesendet: Di 23.02.2010 17:05
>>> An: Cojocaru,Vlad
>>> Betreff: Re: namd-l: update: segmentation faults with AMBER topology
>>> and RAMD tcl scripts
>>>
>>> Dear Vlad,
>>> Using the RAMD method with the compiled namd2.7beta2 against Tcl8.5
>>> and charmm topologies I obtain the following error message:
>>>
>>> TCL: can't read "masses(5962)": no such element in array
>>> FATAL ERROR: can't read "masses(5962)": no such element in array
>>> while executing
>>> "expr $ligMass + $masses($ramdAtom)"
>>> ("foreach" body line 2)
>>>
>>> the whole error message is attached.
>>> I'm going to test the charmm topologies, with the namd2.6 + tcl8.5
>>> version compilation.
>>> Cheers,
>>> Balazs
>>>
>>>
>>> Vlad Cojocaru wrote:
>>>> Dear all,
>>>>
>>>> To test the errors I've been commenting on recently I compiled
>>>> today's CVS code of NAMD (23 February 2010) using exactly the same
>>>> protocol as for my last running compilation (13 August 2009). Tcl
>>>> version is tcl8.4.19. Architecture: x86_64 + infniband + intel 11.0
>>>> compiler + mvapich1.4rc1. The compilation worked absolutely fine.
>>>>
>>>> Then I ran the RAMD tests which resulted in "Segmentation
>>>> violation" . Then I tested the new executable for one of my
>>>> standard MD simulation using AMBER topology. The same undefined
>>>> error occurred.
>>>>
>>>> To conclude, the latest CVS code produces segmentation faults on
>>>> AMBER topologies regardless whether RAMD is switched on or not.
>>>> Therefore, this error apparently has nothing to do with the RAMD
>>>> scripts. It looks as if the amber topology is read correctly but
>>>> the program exists with segmentation violation immediately after
>>>> reading the topology (below last lines of the output)
>>>>
>>>> I could not test against CHARMM topologies as I don't have one but
>>>> another NAMD user mentioned recently that the code runs fine on
>>>> CHARMM topologies while observing the same errors with AMBER
>>>> topologies.
>>>>
>>>> To test the RAMD scripts until the problem with the AMBER
>>>> topologies will be fixed, I suggest to compile namd 2.6 against
>>>> tcl8.4.19 or above.
>>>> If you still see errors, please let me know.
>>>>
>>>> Cheers
>>>> Vlad
>>>>
>>>> -----------------output sample------------------------------
>>>> Reading parm file (1r9o_1.top) ...
>>>> PARM file in AMBER 7 format
>>>> Warning: Encounter 10-12 H-bond term
>>>> Warning: Found 18886 H-H bonds.
>>>> Info: SUMMARY OF PARAMETERS:
>>>> Info: 62 BONDS
>>>> Info: 131 ANGLES
>>>> Info: 49 DIHEDRAL
>>>> Info: 0 IMPROPER
>>>> Info: 0 CROSSTERM
>>>> Info: 0 VDW
>>>> Info: 210 VDW_PAIRS
>>>> Info: TIME FOR READING PDB FILE: 0.158216
>>>> Info:
>>>> Info: Reading from binary file 1r9o_1_eq10_rst.500000.coor
>>>> Info: ****************************
>>>> Info: STRUCTURE SUMMARY:
>>>> Info: 64265 ATOMS
>>>> Info: 64360 BONDS
>>>> Info: 13994 ANGLES
>>>> Info: 29662 DIHEDRALS
>>>> Info: 0 IMPROPERS
>>>> Info: 0 CROSSTERMS
>>>> Info: 98534 EXCLUSIONS
>>>> Info: 60475 RIGID BONDS
>>>> Info: 132320 DEGREES OF FREEDOM
>>>> Info: 22676 HYDROGEN GROUPS
>>>> Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
>>>> Info: 22676 MIGRATION GROUPS
>>>> Info: 4 ATOMS IN LARGEST MIGRATION GROUP
>>>> Info: TOTAL MASS = 394234 amu
>>>> Info: TOTAL CHARGE = -1.48128e-05 e
>>>> Info: MASS DENSITY = 1.00973 g/cm^3
>>>> Info: ATOM DENSITY = 0.0991208 atoms/A^3
>>>> Info: *****************************
>>>> Info:
>>>> Info: Entering startup at 30.2467 s, 156.332 MB of memory in use
>>>> Info: Startup phase 0 took 0.00019908 s, 156.332 MB of memory in use
>>>>
>>>>
>>>
>>>
>>
>

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