[infomap-nlp-users] Problems getting INFOMAP going

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Hi

I am having problem starting using infomap. In particular i get an "fsign"=
=20
error during exectuion of "coll". Do you know what the problem is?

I would really appreciate help getting this software running, because my=20
research progress is dependent on it!!!!!

The output from infomap-build is below:

Is this an installation problem? I am not confident that i did the=20
configure command correct, i did get the following 'no' following the=20
configure command (I pasted all output during installation below):

checking whether we are cross compiling... no
checking ndbm.h usability... no
checking ndbm.h presence... no
checking for ndbm.h... no
checking whether stat accepts an empty string... no

INFOMAP-BUILD COMMAND:

[sverker@sccn ~]$ infomap-build -s /home/sverker/test.txt test5
Sourcing param file "/home/sverker/install/share/infomap-nlp/default-params"
Sourcing extra param file "/tmp/infomap-build.xF4114"
Contents are:
Removing extra param file
WORKING_DATA_DIR =3D "/home/sverker/infomap_models/test5"
CORPUS_DIR =3D "/home/sverker"
CORPUS_FILE =3D "/home/sverker/test.txt"
FNAMES_FILE =3D ""
ROWS =3D "20000"
COLUMNS =3D "1000"
SINGVALS =3D "100"
SVD_ITER =3D "100"
PRE_CONTEXT_SIZE =3D "15"
POST_CONTEXT_SIZE =3D "15"
WRITE_MATLAB_FORMAT =3D "0"
VALID_CHARS_FILE =3D=
 "/home/sverker/install/share/infomap-nlp/valid_chars.en"
STOPLIST_FILE =3D "/home/sverker/install/share/infomap-nlp/stop.list"
COL_LABELS_FROM_FILE =3D "0"
COL_LABEL_FILE =3D ""
echo "Making datadir"
Making datadir
mkdir -p /home/sverker/infomap_models/test5

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Building target: /home/sverker/infomap_models/test5/wordlist
Prerequisites: /home/sverker/test.txt
Fri Jan 19 11:55:12 PST 2007
..................................................
prepare_corpus \
-cdir "/home/sverker" \
         -mdir "/home/sverker/infomap_models/test5" \
         -cfile "/home/sverker/test.txt" \
         -fnfile "" \
         -chfile "/home/sverker/install/share/infomap-nlp/valid_chars.en" \
         -slfile "/home/sverker/install/share/infomap-nlp/stop.list" \
         -rptfile ""
Locale set to en_US.
Opening File for "r":
         "/home/sverker/install/share/infomap-nlp/valid_chars.en"
Opening File for "r":
         ""
my_fopen: No such file or directory
Opening File for "r":
         "/home/sverker/install/share/infomap-nlp/stop.list"
Opening File for "w":
         "/home/sverker/infomap_models/test5/wordlist"
Opening File for "r":
         "/home/sverker/test.txt"
Opening File for "w":
         "/home/sverker/infomap_models/test5/numDocs"
Typecount =3D 826
Preparing to sort ... Sorting ... Done.
Opening File for "w":
         "/home/sverker/infomap_models/test5/dic"
..................................................
Finishing target: /home/sverker/infomap_models/test5/wordlist
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Building target: /home/sverker/infomap_models/test5/coll
Prerequisites: /home/sverker/infomap_models/test5/wordlist=20
/home/sverker/infomap_models/test5/dic=20
/home/sverker/infomap_models/test5/numDocs
Fri Jan 19 11:55:12 PST 2007
..................................................
count_wordvec \
-mdir /home/sverker/infomap_models/test5 \
-matlab 0 \
-precontext 15 \
-postcontext 15 \
-rows 20000 \
-columns 1000 \
-col_labels_from_file 0 \
-col_label_file ""
model data dir is "/home/sverker/infomap_models/test5".
count_wordvec.c: looking for 826 rows
which had better match 826
Reading the dictionary... Opening File for "r":
         "/home/sverker/infomap_models/test5/dic"
Opening File for "r":
         "/home/sverker/infomap_models/test5/numDocs"
Initializing row indices...Done.
Initializing column indices...Done.
Allocating matrix memory...done.
Initializing matrix...done.
model data dir is "/home/sverker/infomap_models/test5".
count_wordvec.c: about to call process_wordlist
Entering process_wordlist.
About to call initialize_wordlist.
Opening File for "r":
         "/home/sverker/infomap_models/test5/wordlist"
Returned from initialize_wordlist.
Writing the co-occurrence matrix.
Entering write_matrix_svd; rows =3D 826 and columns =3D 1000.
Opening File for "w":
         "/home/sverker/infomap_models/test5/coll"
Opening File for "w":
         "/home/sverker/infomap_models/test5/indx"
..................................................
Finishing target: /home/sverker/infomap_models/test5/coll
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Building target: /home/sverker/infomap_models/test5/left
Prerequisites: /home/sverker/infomap_models/test5/coll=20
/home/sverker/infomap_models/test5/indx
Fri Jan 19 11:55:12 PST 2007
..................................................
cd /home/sverker/infomap_models/test5 && rm -f svd_diag left \
                         rght sing
cd /home/sverker/infomap_models/test5 && 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

   ERROR:

   fsign

make: *** [/home/sverker/infomap_models/test5/left] Error 1
[sverker@sccn ~]$

CONFIGUREING / INSTALLATION:

[sverker@sccn ~/infomap-nlp-0.8.6]$ ./configure=
 --prefix=3D/home/sverker/install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... (cached) yes
checking for sqrt in -lm... yes
checking for dbm_open in -lgdbm... yes
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking ndbm.h usability... no
checking ndbm.h presence... no
checking for ndbm.h... no
checking gdbm/ndbm.h usability... yes
checking gdbm/ndbm.h presence... yes
checking for gdbm/ndbm.h... yes
checking for an ANSI C-conforming const... yes
checking for off_t... yes
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking whether lstat dereferences a symlink specified with a trailing=20
slash... yes
checking whether stat accepts an empty string... no
checking for getcwd... yes
checking for memset... yes
checking for setlocale... yes
checking for sqrt... yes
checking for strchr... yes
checking for strdup... yes
checking for strstr... yes
checking for dbm_open... yes
checking for dbm_close... yes
checking for dbm_fetch... yes
checking for dbm_store... yes
configure: creating ./config.status
./config.status: line 305: NLP config.status 0.8.6
configured by ./configure, generated by GNU Autoconf 2.59,
   with options "'--prefix=3D/home/sverker/install'"

Copyright (C) 2003 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it.: No such file=
=20
or directory
config.status: creating Makefile
config.status: creating preprocessing/Makefile
config.status: creating search/Makefile
config.status: creating svd/Makefile
config.status: creating svd/svdinterface/Makefile
config.status: creating lib/Makefile
config.status: creating admin/Makefile
config.status: creating admin/infomap-build
config.status: creating admin/infomap-install
config.status: creating admin/Makefile.data
config.status: creating admin/default-params
config.status: creating doc/Makefile
config.status: creating doc/man/Makefile
config.status: creating doc/man/man1/Makefile
config.status: creating doc/man/man5/Makefile
config.status: creating doc/html/Makefile
config.status: creating doc/html/tutorial/Makefile
config.status: creating util/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
[sverker@sccn ~/infomap-nlp-0.8.6]$

MAKE COMMANDE:

[sverker@sccn ~/infomap-nlp-0.8.6]$ make
make  all-recursive
make[1]: Entering directory `/home/sverker/infomap-nlp-0.8.6'
Making all in .
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6'
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6'
Making all in admin
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/admin'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/admin'
Making all in lib
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/lib'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/lib'
Making all in search
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/search'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/search'
Making all in preprocessing
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/preprocessing'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/preprocessing'
Making all in svd
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/svd'
Making all in svdinterface
make[3]: Entering directory=
 `/home/sverker/infomap-nlp-0.8.6/svd/svdinterface'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory=
 `/home/sverker/infomap-nlp-0.8.6/svd/svdinterface'
make[3]: Entering directory `/home/sverker/infomap-nlp-0.8.6/svd'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/svd'
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/svd'
Making all in doc
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/doc'
Making all in man
make[3]: Entering directory `/home/sverker/infomap-nlp-0.8.6/doc/man'
Making all in man1
make[4]: Entering directory `/home/sverker/infomap-nlp-0.8.6/doc/man/man1'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/doc/man/man1'
Making all in man5
make[4]: Entering directory `/home/sverker/infomap-nlp-0.8.6/doc/man/man5'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/doc/man/man5'
make[4]: Entering directory `/home/sverker/infomap-nlp-0.8.6/doc/man'
make[4]: Nothing to be done for `all-am'.
make[4]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/doc/man'
make[3]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/doc/man'
Making all in html
make[3]: Entering directory `/home/sverker/infomap-nlp-0.8.6/doc/html'
Making all in .
make[4]: Entering directory `/home/sverker/infomap-nlp-0.8.6/doc/html'
make[4]: Nothing to be done for `all-am'.
make[4]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/doc/html'
Making all in tutorial
make[4]: Entering directory=
 `/home/sverker/infomap-nlp-0.8.6/doc/html/tutorial'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory=
 `/home/sverker/infomap-nlp-0.8.6/doc/html/tutorial'
make[3]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/doc/html'
make[3]: Entering directory `/home/sverker/infomap-nlp-0.8.6/doc'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/doc'
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/doc'
Making all in util
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/util'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/util'
make[1]: Leaving directory `/home/sverker/infomap-nlp-0.8.6'
[sverker@sccn ~/infomap-nlp-0.8.6]$ ~

MAKE INSTALL COMMANDE:

[sverker@sccn ~/infomap-nlp-0.8.6]$ make install
Making install in .
make[1]: Entering directory `/home/sverker/infomap-nlp-0.8.6'
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6'
make[1]: Leaving directory `/home/sverker/infomap-nlp-0.8.6'
Making install in admin
make[1]: Entering directory `/home/sverker/infomap-nlp-0.8.6/admin'
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/admin'
/bin/sh ../mkinstalldirs /home/sverker/install/bin
  /usr/bin/install -c infomap-install=
 /home/sverker/install/bin/infomap-install
  /usr/bin/install -c infomap-build /home/sverker/install/bin/infomap-build
mv infomap-install infomap-install.old
sed -e "s,^prefix=3D,prefix=3D/home/sverker/install," \
            infomap-install.old >infomap-install
/usr/bin/install -c infomap-install=
 /home/sverker/install/bin/infomap-install
mv infomap-build infomap-build.old
sed -e "s,^prefix=3D,prefix=3D/home/sverker/install," \
     -e "s,^exec_prefix=3D,exec_prefix=3D/home/sverker/install," \
    infomap-build.old >infomap-build
/usr/bin/install -c infomap-build /home/sverker/install/bin/infomap-build
make  install-exec-hook
make[3]: Entering directory `/home/sverker/infomap-nlp-0.8.6/admin'
mv -f infomap-install.old infomap-install
mv -f infomap-build.old infomap-build
make[3]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/admin'
mv Makefile.data Makefile.data.old
sed -e "s,^prefix=3D,prefix=3D/home/sverker/install," \
    Makefile.data.old >Makefile.data
mkdir -p /home/sverker/install/share/infomap-nlp
/usr/bin/install -c Makefile.data=20
/home/sverker/install/share/infomap-nlp/Makefile.data
mv default-params default-params.old
sed -e "s,^prefix=3D,prefix=3D/home/sverker/install," \
    default-params.old >default-params
mkdir -p /home/sverker/install/share/infomap-nlp
/usr/bin/install -c default-params=20
/home/sverker/install/share/infomap-nlp/Makefile.data
/bin/sh ../mkinstalldirs /home/sverker/install/share/infomap-nlp
  /usr/bin/install -c -m 644 Makefile.data=20
/home/sverker/install/share/infomap-nlp/Makefile.data
  /usr/bin/install -c -m 644 Makefile.filenames=20
/home/sverker/install/share/infomap-nlp/Makefile.filenames
  /usr/bin/install -c -m 644 install.control=20
/home/sverker/install/share/infomap-nlp/install.control
  /usr/bin/install -c -m 644 default-params=20
/home/sverker/install/share/infomap-nlp/default-params
  /usr/bin/install -c -m 644 stop.list=20
/home/sverker/install/share/infomap-nlp/stop.list
  /usr/bin/install -c -m 644 valid_chars.en=20
/home/sverker/install/share/infomap-nlp/valid_chars.en
make  install-data-hook
make[3]: Entering directory `/home/sverker/infomap-nlp-0.8.6/admin'
mv -f Makefile.data.old Makefile.data
mv -f default-params.old default-params
make[3]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/admin'
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/admin'
make[1]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/admin'
Making install in lib
make[1]: Entering directory `/home/sverker/infomap-nlp-0.8.6/lib'
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/lib'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/lib'
make[1]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/lib'
Making install in search
make[1]: Entering directory `/home/sverker/infomap-nlp-0.8.6/search'
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/search'
/bin/sh ../mkinstalldirs /home/sverker/install/bin
   /usr/bin/install -c associate /home/sverker/install/bin/associate
   /usr/bin/install -c print_doc /home/sverker/install/bin/print_doc
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/search'
make[1]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/search'
Making install in preprocessing
make[1]: Entering directory `/home/sverker/infomap-nlp-0.8.6/preprocessing'
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/preprocessing'
/bin/sh ../mkinstalldirs /home/sverker/install/bin
   /usr/bin/install -c prepare_corpus=
 /home/sverker/install/bin/prepare_corpus
   /usr/bin/install -c count_wordvec /home/sverker/install/bin/count_wordvec
   /usr/bin/install -c encode_wordvec=
 /home/sverker/install/bin/encode_wordvec
   /usr/bin/install -c count_artvec /home/sverker/install/bin/count_artvec
   /usr/bin/install -c write_text_params=20
/home/sverker/install/bin/write_text_params
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/preprocessing'
make[1]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/preprocessing'
Making install in svd
make[1]: Entering directory `/home/sverker/infomap-nlp-0.8.6/svd'
Making install in svdinterface
make[2]: Entering directory=
 `/home/sverker/infomap-nlp-0.8.6/svd/svdinterface'
make[3]: Entering directory=
 `/home/sverker/infomap-nlp-0.8.6/svd/svdinterface'
/bin/sh ../../mkinstalldirs /home/sverker/install/bin
   /usr/bin/install -c svdinterface /home/sverker/install/bin/svdinterface
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory=
 `/home/sverker/infomap-nlp-0.8.6/svd/svdinterface'
make[2]: Leaving directory=
 `/home/sverker/infomap-nlp-0.8.6/svd/svdinterface'
make[2]: Entering directory `/home/sverker/infomap-nlp-0.8.6/svd'
make[3]: Entering directory `/home/sverker/infomap-nlp-0.8.6/svd'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/svd'
make[2]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/svd'
make[1]: Leaving directory `/home/sverker/infomap-nlp-0.8.6/svd'
Making install in doc
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Making install in man
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/bin/sh ../../../mkinstalldirs /home/sverker/install/man/man1
  /usr/bin/install -c -m 644 ./associate.1=20
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Making install in man5
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/bin/sh ../../mkinstalldirs /home/sverker/install/share/doc/infomap-nlp
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Making install in tutorial
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Making install in util
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/bin/sh ../mkinstalldirs /home/sverker/install/bin
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[sverker@sccn ~/infomap-nlp-0.8.6]$

Docent Sverker Sikstr=F6m, Kognitionsavdelningen, Kungshuset, Lundag=E5rd,=
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s-22222 Lund, ++46-46-2220923 (work Lund), ++46-70-3614333 (mobile+SMS),=20
040-692 84 07 (home) http://www.lucs.lu.se/People/Sverker.Sikstrom