infomap-nlp-users

[infomap-nlp-users] infomap-build causes segmentation fault

[Armin W. <arm...@un...>]

Hello,

infomap-build -s /home/awegner/Corpora/kjbible.txt kjbible

causes a segmentation fault. The output is as follows:

Sourcing param file "/home/awegner/share/infomap-nlp/default-params"
Sourcing extra param file "/tmp/infomap-build.V22807"
Contents are:
Removing extra param file
WORKING_DATA_DIR = "/home/awegner/Infomap/kjbible"
CORPUS_DIR = "/home/awegner/Corpora"
CORPUS_FILE = "/home/awegner/Corpora/kjbible.txt"
FNAMES_FILE = ""
ROWS = "20000"
COLUMNS = "1000"
SINGVALS = "100"
SVD_ITER = "100"
PRE_CONTEXT_SIZE = "15"
POST_CONTEXT_SIZE = "15"
WRITE_MATLAB_FORMAT = "0"
VALID_CHARS_FILE = "/home/awegner/share/infomap-nlp/valid_chars.en"
STOPLIST_FILE = "/home/awegner/share/infomap-nlp/stop.list"
COL_LABELS_FROM_FILE = "0"
COL_LABEL_FILE = ""
echo "Making datadir"
Making datadir
mkdir -p /home/awegner/Infomap/kjbible

==================================================
Building target: /home/awegner/Infomap/kjbible/wordlist
Prerequisites: /home/awegner/Corpora/kjbible.txt
Tue Jan 16 10:16:23 CET 2007
..................................................
prepare_corpus \
-cdir "/home/awegner/Corpora" \
	-mdir "/home/awegner/Infomap/kjbible" \
	-cfile "/home/awegner/Corpora/kjbible.txt" \
	-fnfile "" \
	-chfile "/home/awegner/share/infomap-nlp/valid_chars.en" \
	-slfile "/home/awegner/share/infomap-nlp/stop.list" \
	-rptfile "" 
Locale set to en_US.
Opening File for "r":
	"/home/awegner/share/infomap-nlp/valid_chars.en"
Opening File for "r":
	""
my_fopen: No such file or directory
Opening File for "r":
	"/home/awegner/share/infomap-nlp/stop.list"
Opening File for "w":
	"/home/awegner/Infomap/kjbible/wordlist"
Opening File for "r":
	"/home/awegner/Corpora/kjbible.txt"
Opening File for "w":
	"/home/awegner/Infomap/kjbible/numDocs"
Typecount = 12805
Preparing to sort ... Sorting ... Done.
Opening File for "w":
	"/home/awegner/Infomap/kjbible/dic"
..................................................
Finishing target: /home/awegner/Infomap/kjbible/wordlist
==================================================


==================================================
Building target: /home/awegner/Infomap/kjbible/coll
Prerequisites: /home/awegner/Infomap/kjbible/wordlist /home/awegner/Infomap/kjbible/dic /home/awegner/Infomap/kjbible/numDocs
Tue Jan 16 10:16:24 CET 2007
..................................................
count_wordvec \
-mdir /home/awegner/Infomap/kjbible \
-matlab 0 \
-precontext 15 \
-postcontext 15 \
-rows 20000 \
-columns 1000 \
-col_labels_from_file 0 \
-col_label_file ""
model data dir is "/home/awegner/Infomap/kjbible".
Reading the dictionary... Opening File for "r":
	"/home/awegner/Infomap/kjbible/dic"
Opening File for "r":
	"/home/awegner/Infomap/kjbible/numDocs"
Initializing row indices...Done.
Initializing column indices...Done.
Allocating matrix memory...done.
Initializing matrix...done.
model data dir is "/home/awegner/Infomap/kjbible".
count_wordvec.c: about to call process_wordlist
Entering process_wordlist.
About to call initialize_wordlist.
Opening File for "r":
	"/home/awegner/Infomap/kjbible/wordlist"
Returned from initialize_wordlist.
Writing the co-occurrence matrix.
Opening File for "w":
	"/home/awegner/Infomap/kjbible/coll"
Opening File for "w":
	"/home/awegner/Infomap/kjbible/indx"
count_wordvec.c: looking for 12805 rows
which had better match 12805
Entering write_matrix_svd; rows = 12805 and columns = 1000.
..................................................
Finishing target: /home/awegner/Infomap/kjbible/coll
==================================================


==================================================
Building target: /home/awegner/Infomap/kjbible/left
Prerequisites: /home/awegner/Infomap/kjbible/coll /home/awegner/Infomap/kjbible/indx
Tue Jan 16 10:16:26 CET 2007
..................................................
cd /home/awegner/Infomap/kjbible && rm -f svd_diag left \
			rght sing
cd /home/awegner/Infomap/kjbible && svdinterface \
        -singvals 100 \
        -iter 100

  This is svdinterface.

  Writing to: left
  Writing to: rght
  Writing to: sing
  Writing to: svd_diag
  Reading: indx
  Reading: indx
  Reading: coll
/bin/sh: line 1: 22852 Segmentation fault      svdinterface -singvals 100 -iter 100
make: *** [/home/awegner/Infomap/kjbible/left] Error 139

Can you help me, please?

Re: [infomap-nlp-users] infomap-build causes segmentation fault

[Scott C. <ced...@gm...>]

Hi Armin,

    Are you using a 64-bit machine?  I think I may have seen this error before.

    Also, are you familiar with gdb?


                 Scott

On 1/16/07, Armin Wegner <arm...@un...> wrote:
> Hello,
>
> infomap-build -s /home/awegner/Corpora/kjbible.txt kjbible
>
> causes a segmentation fault. The output is as follows:
>
> Sourcing param file "/home/awegner/share/infomap-nlp/default-params"
> Sourcing extra param file "/tmp/infomap-build.V22807"
> Contents are:
> Removing extra param file
> WORKING_DATA_DIR = "/home/awegner/Infomap/kjbible"
> CORPUS_DIR = "/home/awegner/Corpora"
> CORPUS_FILE = "/home/awegner/Corpora/kjbible.txt"
> FNAMES_FILE = ""
> ROWS = "20000"
> COLUMNS = "1000"
> SINGVALS = "100"
> SVD_ITER = "100"
> PRE_CONTEXT_SIZE = "15"
> POST_CONTEXT_SIZE = "15"
> WRITE_MATLAB_FORMAT = "0"
> VALID_CHARS_FILE = "/home/awegner/share/infomap-nlp/valid_chars.en"
> STOPLIST_FILE = "/home/awegner/share/infomap-nlp/stop.list"
> COL_LABELS_FROM_FILE = "0"
> COL_LABEL_FILE = ""
> echo "Making datadir"
> Making datadir
> mkdir -p /home/awegner/Infomap/kjbible
>
> ==================================================
> Building target: /home/awegner/Infomap/kjbible/wordlist
> Prerequisites: /home/awegner/Corpora/kjbible.txt
> Tue Jan 16 10:16:23 CET 2007
> ..................................................
> prepare_corpus \
> -cdir "/home/awegner/Corpora" \
>         -mdir "/home/awegner/Infomap/kjbible" \
>         -cfile "/home/awegner/Corpora/kjbible.txt" \
>         -fnfile "" \
>         -chfile "/home/awegner/share/infomap-nlp/valid_chars.en" \
>         -slfile "/home/awegner/share/infomap-nlp/stop.list" \
>         -rptfile ""
> Locale set to en_US.
> Opening File for "r":
>         "/home/awegner/share/infomap-nlp/valid_chars.en"
> Opening File for "r":
>         ""
> my_fopen: No such file or directory
> Opening File for "r":
>         "/home/awegner/share/infomap-nlp/stop.list"
> Opening File for "w":
>         "/home/awegner/Infomap/kjbible/wordlist"
> Opening File for "r":
>         "/home/awegner/Corpora/kjbible.txt"
> Opening File for "w":
>         "/home/awegner/Infomap/kjbible/numDocs"
> Typecount = 12805
> Preparing to sort ... Sorting ... Done.
> Opening File for "w":
>         "/home/awegner/Infomap/kjbible/dic"
> ..................................................
> Finishing target: /home/awegner/Infomap/kjbible/wordlist
> ==================================================
>
>
> ==================================================
> Building target: /home/awegner/Infomap/kjbible/coll
> Prerequisites: /home/awegner/Infomap/kjbible/wordlist /home/awegner/Infomap/kjbible/dic /home/awegner/Infomap/kjbible/numDocs
> Tue Jan 16 10:16:24 CET 2007
> ..................................................
> count_wordvec \
> -mdir /home/awegner/Infomap/kjbible \
> -matlab 0 \
> -precontext 15 \
> -postcontext 15 \
> -rows 20000 \
> -columns 1000 \
> -col_labels_from_file 0 \
> -col_label_file ""
> model data dir is "/home/awegner/Infomap/kjbible".
> Reading the dictionary... Opening File for "r":
>         "/home/awegner/Infomap/kjbible/dic"
> Opening File for "r":
>         "/home/awegner/Infomap/kjbible/numDocs"
> Initializing row indices...Done.
> Initializing column indices...Done.
> Allocating matrix memory...done.
> Initializing matrix...done.
> model data dir is "/home/awegner/Infomap/kjbible".
> count_wordvec.c: about to call process_wordlist
> Entering process_wordlist.
> About to call initialize_wordlist.
> Opening File for "r":
>         "/home/awegner/Infomap/kjbible/wordlist"
> Returned from initialize_wordlist.
> Writing the co-occurrence matrix.
> Opening File for "w":
>         "/home/awegner/Infomap/kjbible/coll"
> Opening File for "w":
>         "/home/awegner/Infomap/kjbible/indx"
> count_wordvec.c: looking for 12805 rows
> which had better match 12805
> Entering write_matrix_svd; rows = 12805 and columns = 1000.
> ..................................................
> Finishing target: /home/awegner/Infomap/kjbible/coll
> ==================================================
>
>
> ==================================================
> Building target: /home/awegner/Infomap/kjbible/left
> Prerequisites: /home/awegner/Infomap/kjbible/coll /home/awegner/Infomap/kjbible/indx
> Tue Jan 16 10:16:26 CET 2007
> ..................................................
> cd /home/awegner/Infomap/kjbible && rm -f svd_diag left \
>                         rght sing
> cd /home/awegner/Infomap/kjbible && svdinterface \
>         -singvals 100 \
>         -iter 100
>
>   This is svdinterface.
>
>   Writing to: left
>   Writing to: rght
>   Writing to: sing
>   Writing to: svd_diag
>   Reading: indx
>   Reading: indx
>   Reading: coll
> /bin/sh: line 1: 22852 Segmentation fault      svdinterface -singvals 100 -iter 100
> make: *** [/home/awegner/Infomap/kjbible/left] Error 139
>
> Can you help me, please?
>
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