Hello,
Thanks a lot to Bozidar and Andras who kindly answered my question about
'memory requirements'. I have checked my parameters that seem to be big enough
and I decided to have a look at things from the beginning, installing the
recent modeller6v1.
I still get a segmentation fault executing the tutorial examples
(initial.top and model-defailt.top) with mod6v1_iris4d on my SGI
Octane workstation ('trace' enclosed).
Could you please tell me on which Silicon Graphics machine (which OS
version) was modeller6 compiled?
I would be grateful for any help.
All the best,
Ada
-------------------------------------------------------------------------
balthus:adap 18>/ext5/usr/local/bin/modeller6v1/bin/mod6v1_iris4d initial
MODELLER 6v1, 17 Jan 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from A. Fiser, R. Sanchez, M.A. Marti-Renom,
B. Jerkovic, A. Badretdinov, F. Melo,
J.P. Overington & E. Feyfant
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, IRIX64 balthus 6.5 IP30
Date and time of compilation : 01/25/2002 20:36:35
Job starting time (YY/MM/DD HH:MM:SS): 2002/01/30 19:25:47.221
TOP_________> 2 2 READ_ALIGNMENT ALIGNMENT_FORMAT = 'PIR', FILE = 'alignmen;
t.ali'
openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali
openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali
Read the alignment from file : alignment.ali
Total number of alignment positions: 106
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 5fd1 106 1 5fd1 ferredoxin
2 1fdx 54 1 1fdx ferredoxin
TOP_________> 3 3 ID_TABLE MATRIX_FILE = 'id.mat'
Segmentation fault
-----------------------------------------------------------------------
and the second one:
balthus:adap 29>$MODINSTALL6v1/bin/mod6v1_iris4d model-default
MODELLER 6v1, 17 Jan 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from A. Fiser, R. Sanchez, M.A. Marti-Renom,
B. Jerkovic, A. Badretdinov, F. Melo,
J.P. Overington & E. Feyfant
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, IRIX64 balthus 6.5 IP30
Date and time of compilation : 01/25/2002 20:36:35
Job starting time (YY/MM/DD HH:MM:SS): 2002/01/30 19:55:04.865
TOP_________> 105 705 SET ALNFILE = 'alignment.ali'
TOP_________> 106 706 SET KNOWNS = '5fd1'
TOP_________> 107 707 SET SEQUENCE = '1fdx'
TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 109 709 SET STARTING_MODEL = 1
TOP_________> 110 710 SET ENDING_MODEL = 1
TOP_________> 111 711 CALL ROUTINE = 'model'
TOP_________> 112 398 CALL ROUTINE = 'getnames'
TOP_________> 113 508 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION;
= 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA;
TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 114 509 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI;
ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE;
NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE;
'
TOP_________> 115 510 STRING_OPERATE OPERATION = 'CONCATENATE', ;
STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE
TOP_________> 116 511 STRING_OPERATE OPERATION = 'CONCATENATE', ;
STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI;
LE
TOP_________> 117 512 SET ROOT_NAME = SEQUENCE
TOP_________> 118 513 RETURN
TOP_________> 119 399 CALL ROUTINE = 'homcsr'
TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;
NCE
Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103
openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali
Dynamically allocated memory at amaxbnd [B,kB,MB]: 3882961 3791.954 3.703
openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali
Read the alignment from file : alignment.ali
Total number of alignment positions: 106
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 5fd1 106 1 5fd1 ferredoxin
2 1fdx 54 1 1fdx ferredoxin
TOP_________> 121 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
Segmentation fault
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