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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Feb 24 2010 - 15:57:17 CST

Hello Vlad:

Back from the roof, I have just checked that the CVS nightly build
works fine like namd_2.7b2 with my system, CHARMM topologies, charmm
ff. From what you write now, it seems that you assume that namd
binaries, including nightly builds, are compiled for tcl < 8.4

Debian lenny:
tclsh
% info tclversion
8.4

>From the tk console of VMD 1.8.7, tcl version is 8.5

I must say that I am now rather confused about all these versions, but
if you want that I try the tcl8.3 version of ramd with my system with
charmm topologies, please make it available, or send it to me. I'll
try (although I don't expect it will turn useful).

As to the error messages when using ramd with my (perfectly
equilibrated) system, charmm topologies, with both builds of namd:

###############
Fatal error on PE 0> FATAL ERROR: syntax error in expression "
$mdSteps == 0 && $mdStart eq "yes" "
    ("if" test expression)
    while compiling
"if { $mdSteps == 0 && $mdStart eq "yes" } {
  print "RAMD: WARNING: 'mdStart' has no meaning for pure RAMD simulation"
 }"
    (in namespace eval "::RAMD" script line 65)
    invoked from within
"namespace eval ::RAMD {
 print RAMD:
 print RAMD: -------------------------------------------------------------------
 print RAMD: Random Accele..."
    (file "/home/francesco/ramd-4.0/scripts/ramd-4.0_script.tcl" line 42)
###############

Compare the above with the error you reported to Giacomo:

&&&&&&&&&&&&&&&&
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 vaguely remember that, instinctively, I removed the

if { $mdSteps == 0 && $mdStart eq "yes" } statement

from your script, as it did not apply to my system. But I got errors
from other "if" statements.

Regards
francesco

On Wed, Feb 24, 2010 at 12:52 PM, Vlad Cojocaru <Vlad.Cojocaru_at_h-its.org> wrote:
> Balazs,
>
> Great ! Thanks for the effort to compile .
> To use the AMBER force field, it looks as if you need to compile older CVS
> code (8 August 2009 works for sure) of namd2.7 or namd 2.6 .
>
> Francesco,
>
> So it seems that if the new CVS code is compiled against tcl8.4.19, the RAMD
> scripts run with the CHARMM force field with no error message. Could you
> confirm that as well ?
> I also have a new version of the RAMD that is compatible with tcl8.3 ... It
> seems that tcl8.3 does not like the "eq" operand and some if statements with
> multiple tests ... Don't ask me why ...
>
> other NAMD users,
>
> Is there anybody that is able to run the new CVS code with AMBER topology
> files ?
>
> Greetings
> Vlad
>
> Balazs Jojart wrote:
>>
>> 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
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>>
>
> --
> ----------------------------------------------------------------------------
> 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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>
>

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