[infomap-nlp-users] infomap on FreeBSD-current does not run - call for some hints at where to look

[Mathias P. <Mat...@vi...>]

Greetings everybody,

do you have any idea what the following errors might mean?

infomap-0.8.5 compiled cleanly on FreeBSD-current, using either the 
system dbm or gdbm. The only change nessecary was to make "make ..." 
into gmake .... " in infomap-build,

Both version show the same errormessages, one pointing to dbm. That's 
why I tried it with the system dbm and gdbm, without success the version 
used for these test uses gdbm:

venus% ldd /usr/local/bin/prepare_corpus
/usr/local/bin/prepare_corpus:
        libgdbm.so.3 => /usr/local/lib/libgdbm.so.3 (0x28079000)
        libm.so.2 => /lib/libm.so.2 (0x2807f000)
        libc.so.5 => /lib/libc.so.5 (0x28098000)

Any ideas would be very welcome!

Thanks, Mathias

P.S.: here come the two error messages. if I run infomap -m again after 
infomap -s, I get the same error as infomap -s instead of the one shown 
here for infomap -m.

1) first try with infomap -m:

venus% export INFOMAP_WORKING_DIRECTORY=/tmp
venus% rm /tmp/gb/*
zsh: sure you want to delete all the files in /tmp/gb [yn]? y
venus% infomap-build -m gb-corpus.txt gb
Sourcing param file "/usr/local/share/infomap-nlp/default-params"
Sourcing extra param file "/tmp/infomap-build.JDWu66"
Contents are:
Removing extra param file
WORKING_DATA_DIR = "/tmp/gb"
CORPUS_DIR = "."
CORPUS_FILE = ""
FNAMES_FILE = "gb-corpus.txt"
ROWS = "20000"
COLUMNS = "1000"
SINGVALS = "100"
SVD_ITER = "100"
PRE_CONTEXT_SIZE = "15"
POST_CONTEXT_SIZE = "15"
WRITE_MATLAB_FORMAT = "0"
VALID_CHARS_FILE = "/usr/local/share/infomap-nlp/valid_chars.en"
STOPLIST_FILE = "/usr/local/share/infomap-nlp/stop.list"
COL_LABELS_FROM_FILE = "0"
COL_LABEL_FILE = ""
echo "Making datadir"
Making datadir
mkdir -p /tmp/gb

==================================================
Building target: /tmp/gb/wordlist
Prerequisites: gb-corpus.txt
Wed May 19 10:53:49 CEST 2004
..................................................
prepare_corpus \
-cdir "." \
        -mdir "/tmp/gb" \
        -cfile "" \
        -fnfile "gb-corpus.txt" \
        -chfile "/usr/local/share/infomap-nlp/valid_chars.en" \
        -slfile "/usr/local/share/infomap-nlp/stop.list" \
        -rptfile ""
Locale set to (null).
Opening File for "r":
        "/usr/local/share/infomap-nlp/valid_chars.en"
Opening File for "r":
        "gb-corpus.txt"
Opening File for "r":
        "/usr/local/share/infomap-nlp/stop.list"
Opening File for "w":
        "/tmp/gb/wordlist"
Can't open nu2na database
gmake: *** [/tmp/gb/wordlist] Error 1
venus%

------------------------ next error msg 
-------------------------------------------------------

2) infomap -s shows this:venus% infomap-build -s 1.html gb
Sourcing param file "/usr/local/share/infomap-nlp/default-params"
Sourcing extra param file "/tmp/infomap-build.kDVdtJ"
Contents are:
Removing extra param file
WORKING_DATA_DIR = "/tmp/gb"
CORPUS_DIR = "."
CORPUS_FILE = "1.html"
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 = "/usr/local/share/infomap-nlp/valid_chars.en"
STOPLIST_FILE = "/usr/local/share/infomap-nlp/stop.list"
COL_LABELS_FROM_FILE = "0"
COL_LABEL_FILE = ""
echo "Making datadir"
Making datadir
mkdir -p /tmp/gb

==================================================
Building target: /tmp/gb/dic
Prerequisites: 1.html
Wed May 19 10:55:14 CEST 2004
..................................................
prepare_corpus \
-cdir "." \
        -mdir "/tmp/gb" \
        -cfile "1.html" \
        -fnfile "" \
        -chfile "/usr/local/share/infomap-nlp/valid_chars.en" \
        -slfile "/usr/local/share/infomap-nlp/stop.list" \
        -rptfile ""
Locale set to (null).
Opening File for "r":
        "/usr/local/share/infomap-nlp/valid_chars.en"
Opening File for "r":
        ""
my_fopen: No such file or directory
Opening File for "r":
        "/usr/local/share/infomap-nlp/stop.list"
Opening File for "w":
        "/tmp/gb/wordlist"
Opening File for "r":
        "1.html"
Opening File for "w":
        "/tmp/gb/numDocs"
Typecount = 0
Preparing to sort ... Sorting ... Done.
Opening File for "w":
        "/tmp/gb/dic"
..................................................
Finishing target: /tmp/gb/dic
==================================================


==================================================
Building target: /tmp/gb/coll
Prerequisites: /tmp/gb/wordlist /tmp/gb/dic /tmp/gb/numDocs
Wed May 19 10:55:14 CEST 2004
..................................................
count_wordvec \
-mdir /tmp/gb \
-matlab 0 \
-precontext 15 \
-postcontext 15 \
-rows 20000 \
-columns 1000 \
-col_labels_from_file 0 \
-col_label_file ""
model data dir is "/tmp/gb".
count_wordvec.c: looking for 0 rows
which had better match 0
Reading the dictionary... Opening File for "r":
        "/tmp/gb/dic"
Opening File for "r":
        "/tmp/gb/numDocs"
Initializing row indices...Done.
Initializing column indices...Done.
Allocating matrix memory...done.
Initializing matrix...done.
model data dir is "/tmp/gb".
count_wordvec.c: about to call process_wordlist
Entering process_wordlist.
About to call initialize_wordlist.
Opening File for "r":
        "/tmp/gb/wordlist"
Returned from initialize_wordlist.
Writing the co-occurrence matrix.
Entering write_matrix_svd; rows = 0 and columns = 1000.
Opening File for "w":
        "/tmp/gb/coll"
Opening File for "w":
        "/tmp/gb/indx"
..................................................
Finishing target: /tmp/gb/coll
==================================================


==================================================
Building target: /tmp/gb/left
Prerequisites: /tmp/gb/coll /tmp/gb/indx
Wed May 19 10:55:14 CEST 2004
..................................................
cd /tmp/gb && rm svd_diag left \
                        rght sing
rm: svd_diag: No such file or directory
rm: left: No such file or directory
rm: rght: No such file or directory
rm: sing: No such file or directory
gmake: [/tmp/gb/left] Error 1 (ignored)
cd /tmp/gb && 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

  FEWER THAN EXPECTED SINGULAR VALUES
..................................................
Finishing target: /tmp/gb/left
==================================================


==================================================
Building target: /tmp/gb/wordvec.bin
Prerequisites: /tmp/gb/left /tmp/gb/dic
Wed May 19 10:55:14 CEST 2004
..................................................
encode_wordvec \
        -m /tmp/gb
Opening File for "r":
        "/tmp/gb/left"
Can't Open /tmp/gb/word2offset
Failed dbm_open(): Invalid argument
gmake: *** [/tmp/gb/wordvec.bin] Error 1

------------------------------- next error msg 
-------------------------------------

3) running infmap -m again without clearing the working dir

venus% infomap-build -m gb-corpus.txt gb
Sourcing param file "/usr/local/share/infomap-nlp/default-params"
Sourcing extra param file "/tmp/infomap-build.lRMTsa"
Contents are:
Removing extra param file
WORKING_DATA_DIR = "/tmp/gb"
CORPUS_DIR = "."
CORPUS_FILE = ""
FNAMES_FILE = "gb-corpus.txt"
ROWS = "20000"
COLUMNS = "1000"
SINGVALS = "100"
SVD_ITER = "100"
PRE_CONTEXT_SIZE = "15"
POST_CONTEXT_SIZE = "15"
WRITE_MATLAB_FORMAT = "0"
VALID_CHARS_FILE = "/usr/local/share/infomap-nlp/valid_chars.en"
STOPLIST_FILE = "/usr/local/share/infomap-nlp/stop.list"
COL_LABELS_FROM_FILE = "0"
COL_LABEL_FILE = ""
echo "Making datadir"
Making datadir
mkdir -p /tmp/gb

==================================================
Building target: /tmp/gb/wordvec.bin
Prerequisites: /tmp/gb/left /tmp/gb/dic
Wed May 19 10:52:06 CEST 2004
..................................................
encode_wordvec \
        -m /tmp/gb
Opening File for "r":
        "/tmp/gb/left"
Can't Open /tmp/gb/word2offset
Failed dbm_open(): Invalid argument
gmake: *** [/tmp/gb/wordvec.bin] Error 1
venus%