sample input file that works with IMa2 v12.17?

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Mary Kuhner

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Oct 3, 2012, 1:11:54 PM10/3/12
to isolation-wi...@googlegroups.com
Can anyone email me a sample input file, however trivial, that works with IMa2 v12.17?  I have repeatedly failed to make one; I get a segmentation fault early on for every file I try, including one typed in from the IMa2 documentation.

jhey

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Oct 6, 2012, 10:40:31 AM10/6/12
to Isolation with Migration
sorry you are having trouble with this Mary

Here I've copied the text from the manual (it runs fine)
I also email it as a file, in case it gets copied here with messed up
spacing (e.g. data must begin in column 11)

jhey

Example data for IMa
# example data set
3
pop0 pop1 pop2
((0,1):3,2):4
3
locus1 1 1 2 13 I 0.25 0.0000000008
pop0_1 ACTACTGTCATGA
pop1_1 AGTACTATCACGA
pop2_1 AGTACTATCACGA
pop2_2 AGTACTATCATGA
hapstrexample 2 1 0 4 J1 0.75
pop1_1 13 GTAC
pop1_2 12 GTAT
pop2_1 12 GTAT
strexample 2 2 2 1 S3 1 0.00001 0.000015 0.00008
strpop01a 23 12 9
strpop01b 26 10 11
strpop11a 25 10 9
strpop11b 31 11 9
strpop21a 26 12 11
strpop21b 26 13 1

Gabe Fiorini

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Oct 25, 2012, 8:41:51 PM10/25/12
to isolation-wi...@googlegroups.com
I'm having the same trouble. I'm running the 8/27/2012 update under ubuntu and after running configure and make (make throws up a lot of warnings, but no errors) I get segmentation faults when I try to run the program. I can run the executable and get the help screen which lists the various arguments and parameters that can be set, but whenever I try to run an actual dataset (I have tried the one that comes with the Windows distribution of the program, and also the one you posted above, that I named minisample.txt) all I get is a segmentation fault. Any assistance with this would be greatly appreciated, I feel like it's quite possible that there is something wrong with the environment I'm running it under such that my installation didn't go right, but I don't really know where to look. I've attached config.log in hopes that something useful can be found there by someone more knowledgable than I. Below I also posted the output from my attempts to run IMa2. I was unable to find a log file for the results of the make command but if anybody can tell me where to find it I'd be glad to find it and post it here. The server I am working on is an Amazon EC2 instance running Ubuntu 12.0.4 Server 64-bit, with 32-bit compatibility libraries installed.

Output from running IMa2:

root@ip-10-245-191-114:/home/ubuntu/ima2/src# ls *.u && ls *.txt && ls IMa2
ima2_testinput.u
ima2_priorfile_4pops.txt  minisample.txt
IMa2
root@ip-10-245-191-114:/home/ubuntu/ima2/src# ./IMa2 -i ima2_testinput.u
executing program ...
Segmentation fault (core dumped)
root@ip-10-245-191-114:/home/ubuntu/ima2/src# ./IMa2 -i minisample.txt
executing program ...
Segmentation fault (core dumped)
root@ip-10-245-191-114:/home/ubuntu/ima2/src# root@ip-10-245-191-114:/home/ubuntu/ima2/src# 

I'm afraid that's all I've got. Any assistance would be most appreciated.

Gabe Fiorini

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Oct 25, 2012, 8:44:10 PM10/25/12
to isolation-wi...@googlegroups.com
Hmm, the attachment failed. I've pasted the contents of config.log here, sorry for the length.

////////////////////////////

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by IMa2 configure 8.27.12, which was
generated by GNU Autoconf 2.68.  Invocation command line was

  $ ./configure 

## --------- ##
## Platform. ##
## --------- ##

hostname = ip-10-245-191-114
uname -m = x86_64
uname -r = 3.2.0-31-virtual
uname -s = Linux
uname -v = #50-Ubuntu SMP Fri Sep 7 16:36:36 UTC 2012

/usr/bin/uname -p = unknown
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2212: checking for a BSD-compatible install
configure:2280: result: /usr/bin/install -c
configure:2291: checking whether build environment is sane
configure:2328: result: yes
configure:2455: checking for a thread-safe mkdir -p
configure:2494: result: /bin/mkdir -p
configure:2507: checking for gawk
configure:2537: result: no
configure:2507: checking for mawk
configure:2523: found /usr/bin/mawk
configure:2534: result: mawk
configure:2545: checking whether make sets $(MAKE)
configure:2567: result: yes
configure:2649: checking whether to enable maintainer-specific portions of Makefiles
configure:2658: result: no
configure:2672: checking whether make sets $(MAKE)
configure:2694: result: yes
configure:2708: checking build system type
configure:2722: result: x86_64-unknown-linux-gnu
configure:2742: checking host system type
configure:2755: result: x86_64-unknown-linux-gnu
configure:2830: checking for gcc
configure:2846: found /usr/bin/gcc
configure:2857: result: gcc
configure:3086: checking for C compiler version
configure:3095: gcc --version >&5
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:3106: $? = 0
configure:3095: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) 
configure:3106: $? = 0
configure:3095: gcc -V >&5
gcc: error: unrecognized option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3106: $? = 4
configure:3095: gcc -qversion >&5
gcc: error: unrecognized option '-qversion'
gcc: fatal error: no input files
compilation terminated.
configure:3106: $? = 4
configure:3126: checking whether the C compiler works
configure:3148: gcc    conftest.c  >&5
configure:3152: $? = 0
configure:3200: result: yes
configure:3203: checking for C compiler default output file name
configure:3205: result: a.out
configure:3211: checking for suffix of executables
configure:3218: gcc -o conftest    conftest.c  >&5
configure:3222: $? = 0
configure:3244: result: 
configure:3266: checking whether we are cross compiling
configure:3274: gcc -o conftest    conftest.c  >&5
configure:3278: $? = 0
configure:3285: ./conftest
configure:3289: $? = 0
configure:3304: result: no
configure:3309: checking for suffix of object files
configure:3331: gcc -c   conftest.c >&5
configure:3335: $? = 0
configure:3356: result: o
configure:3360: checking whether we are using the GNU C compiler
configure:3379: gcc -c   conftest.c >&5
configure:3379: $? = 0
configure:3388: result: yes
configure:3397: checking whether gcc accepts -g
configure:3417: gcc -c -g  conftest.c >&5
configure:3417: $? = 0
configure:3458: result: yes
configure:3475: checking for gcc option to accept ISO C89
configure:3539: gcc  -c -g -O2  conftest.c >&5
configure:3539: $? = 0
configure:3552: result: none needed
configure:3577: checking how to run the C preprocessor
configure:3608: gcc -E  conftest.c
configure:3608: $? = 0
configure:3622: gcc -E  conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:3622: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "IMa2"
| #define PACKAGE_TARNAME "ima2"
| #define PACKAGE_VERSION "8.27.12"
| #define PACKAGE_STRING "IMa2 8.27.12"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "ima2"
| #define VERSION "8.27.12"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3647: result: gcc -E
configure:3667: gcc -E  conftest.c
configure:3667: $? = 0
configure:3681: gcc -E  conftest.c
conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:3681: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "IMa2"
| #define PACKAGE_TARNAME "ima2"
| #define PACKAGE_VERSION "8.27.12"
| #define PACKAGE_STRING "IMa2 8.27.12"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "ima2"
| #define VERSION "8.27.12"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3710: checking whether ln -s works
configure:3714: result: yes
configure:3722: checking whether gcc and cc understand -c and -o together
configure:3753: gcc -c conftest.cpp -o conftest2.o >&5
configure:3757: $? = 0
configure:3763: gcc -c conftest.cpp -o conftest2.o >&5
configure:3767: $? = 0
configure:3778: cc -c conftest.cpp >&5
configure:3782: $? = 0
configure:3790: cc -c conftest.cpp -o conftest2.o >&5
configure:3794: $? = 0
configure:3800: cc -c conftest.cpp -o conftest2.o >&5
configure:3804: $? = 0
configure:3822: result: yes
configure:3906: checking for g++
configure:3922: found /usr/bin/g++
configure:3933: result: g++
configure:3960: checking for C++ compiler version
configure:3969: g++ --version >&5
g++ (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:3980: $? = 0
configure:3969: g++ -v >&5
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) 
configure:3980: $? = 0
configure:3969: g++ -V >&5
g++: error: unrecognized option '-V'
g++: fatal error: no input files
compilation terminated.
configure:3980: $? = 4
configure:3969: g++ -qversion >&5
g++: error: unrecognized option '-qversion'
g++: fatal error: no input files
compilation terminated.
configure:3980: $? = 4
configure:3984: checking whether we are using the GNU C++ compiler
configure:4003: g++ -c   conftest.cpp >&5
configure:4003: $? = 0
configure:4012: result: yes
configure:4021: checking whether g++ accepts -g
configure:4041: g++ -c -g  conftest.cpp >&5
configure:4041: $? = 0
configure:4082: result: yes
configure:4111: checking how to run the C++ preprocessor
configure:4138: g++ -E  conftest.cpp
configure:4138: $? = 0
configure:4152: g++ -E  conftest.cpp
conftest.cpp:11:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:4152: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "IMa2"
| #define PACKAGE_TARNAME "ima2"
| #define PACKAGE_VERSION "8.27.12"
| #define PACKAGE_STRING "IMa2 8.27.12"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "ima2"
| #define VERSION "8.27.12"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:4177: result: g++ -E
configure:4197: g++ -E  conftest.cpp
configure:4197: $? = 0
configure:4211: g++ -E  conftest.cpp
conftest.cpp:11:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:4211: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "IMa2"
| #define PACKAGE_TARNAME "ima2"
| #define PACKAGE_VERSION "8.27.12"
| #define PACKAGE_STRING "IMa2 8.27.12"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "ima2"
| #define VERSION "8.27.12"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:4240: checking for grep that handles long lines and -e
configure:4298: result: /bin/grep
configure:4303: checking for egrep
configure:4365: result: /bin/grep -E
configure:4370: checking for ANSI C header files
configure:4390: g++ -c -g -O2  conftest.cpp >&5
configure:4390: $? = 0
configure:4463: g++ -o conftest -g -O2   conftest.cpp  >&5
configure:4463: $? = 0
configure:4463: ./conftest
configure:4463: $? = 0
configure:4474: result: yes
configure:4487: checking for sys/types.h
configure:4487: g++ -c -g -O2  conftest.cpp >&5
configure:4487: $? = 0
configure:4487: result: yes
configure:4487: checking for sys/stat.h
configure:4487: g++ -c -g -O2  conftest.cpp >&5
configure:4487: $? = 0
configure:4487: result: yes
configure:4487: checking for stdlib.h
configure:4487: g++ -c -g -O2  conftest.cpp >&5
configure:4487: $? = 0
configure:4487: result: yes
configure:4487: checking for string.h
configure:4487: g++ -c -g -O2  conftest.cpp >&5
configure:4487: $? = 0
configure:4487: result: yes
configure:4487: checking for memory.h
configure:4487: g++ -c -g -O2  conftest.cpp >&5
configure:4487: $? = 0
configure:4487: result: yes
configure:4487: checking for strings.h
configure:4487: g++ -c -g -O2  conftest.cpp >&5
configure:4487: $? = 0
configure:4487: result: yes
configure:4487: checking for inttypes.h
configure:4487: g++ -c -g -O2  conftest.cpp >&5
configure:4487: $? = 0
configure:4487: result: yes
configure:4487: checking for stdint.h
configure:4487: g++ -c -g -O2  conftest.cpp >&5
configure:4487: $? = 0
configure:4487: result: yes
configure:4487: checking for unistd.h
configure:4487: g++ -c -g -O2  conftest.cpp >&5
configure:4487: $? = 0
configure:4487: result: yes
configure:4499: checking for size_t
configure:4499: g++ -c -g -O2  conftest.cpp >&5
configure:4499: $? = 0
configure:4499: g++ -c -g -O2  conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:57:20: error: expected primary-expression before ')' token
configure:4499: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "IMa2"
| #define PACKAGE_TARNAME "ima2"
| #define PACKAGE_VERSION "8.27.12"
| #define PACKAGE_STRING "IMa2 8.27.12"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "ima2"
| #define VERSION "8.27.12"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h.  */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| #  include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| #  include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((size_t)))
|    return 0;
|   ;
|   return 0;
| }
configure:4499: result: yes
configure:4510: checking for working volatile
configure:4529: g++ -c -g -O2  conftest.cpp >&5
configure:4529: $? = 0
configure:4536: result: yes
configure:4544: checking for inline
configure:4560: g++ -c -g -O2  conftest.cpp >&5
configure:4560: $? = 0
configure:4568: result: inline
configure:4586: checking whether char is unsigned
configure:4604: g++ -c -g -O2  conftest.cpp >&5
configure:4604: $? = 0
configure:4611: result: no
configure:4621: checking for vprintf
configure:4621: g++ -o conftest -g -O2   conftest.cpp  >&5
configure:4621: $? = 0
configure:4621: result: yes
configure:4627: checking for _doprnt
configure:4627: g++ -o conftest -g -O2   conftest.cpp  >&5
/tmp/ccIPqxuE.o: In function `main':
/home/ubuntu/ima2/conftest.cpp:56: undefined reference to `_doprnt'
collect2: ld returned 1 exit status
configure:4627: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "IMa2"
| #define PACKAGE_TARNAME "ima2"
| #define PACKAGE_VERSION "8.27.12"
| #define PACKAGE_STRING "IMa2 8.27.12"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "ima2"
| #define VERSION "8.27.12"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_VPRINTF 1
| /* end confdefs.h.  */
| /* Define _doprnt to an innocuous variant, in case <limits.h> declares _doprnt.
|    For example, HP-UX 11i <limits.h> declares gettimeofday.  */
| #define _doprnt innocuous__doprnt
| /* System header to define __stub macros and hopefully few prototypes,
|     which can conflict with char _doprnt (); below.
|     Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
|     <limits.h> exists even on freestanding compilers.  */
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
| #undef _doprnt
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| char _doprnt ();
| /* The GNU C library defines this for functions which it implements
|     to always fail with ENOSYS.  Some functions are actually named
|     something starting with __ and the normal name is an alias.  */
| #if defined __stub__doprnt || defined __stub____doprnt
| choke me
| #endif
| int
| main ()
| {
| return _doprnt ();
|   ;
|   return 0;
| }
configure:4627: result: no
configure:4790: creating ./config.status

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by IMa2 config.status 8.27.12, which was
generated by GNU Autoconf 2.68.  Invocation command line was

  CONFIG_FILES    = 
  CONFIG_HEADERS  = 
  CONFIG_LINKS    = 
  CONFIG_COMMANDS = 
  $ ./config.status 

on ip-10-245-191-114

config.status:857: creating src/Makefile
config.status:857: creating Makefile
config.status:857: creating config.h

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_c_char_unsigned=no
ac_cv_c_compiler_gnu=yes
ac_cv_c_inline=inline
ac_cv_c_volatile=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_func__doprnt=no
ac_cv_func_vprintf=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=mawk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_CXXCPP='g++ -E'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_gcc_c_o=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_type_size_t=yes

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /home/ubuntu/ima2/build-aux/missing --run aclocal-1.10'
AMTAR='${SHELL} /home/ubuntu/ima2/build-aux/missing --run tar'
AUTOCONF='${SHELL} /home/ubuntu/ima2/build-aux/missing --run autoconf'
AUTOHEADER='${SHELL} /home/ubuntu/ima2/build-aux/missing --run autoheader'
AUTOMAKE='${SHELL} /home/ubuntu/ima2/build-aux/missing --run automake-1.10'
AWK='mawk'
CC='gcc'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=''
CXX='g++'
CXXCPP='g++ -E'
CXXFLAGS='-g -O2'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LN_S='ln -s'
LTLIBOBJS=''
MAINT='#'
MAINTAINER_MODE_FALSE=''
MAINTAINER_MODE_TRUE='#'
MAKEINFO='${SHELL} /home/ubuntu/ima2/build-aux/missing --run makeinfo'
MKDIR_P='/bin/mkdir -p'
OBJEXT='o'
PACKAGE='ima2'
PACKAGE_BUGREPORT=''
PACKAGE_NAME='IMa2'
PACKAGE_STRING='IMa2 8.27.12'
PACKAGE_TARNAME='ima2'
PACKAGE_URL=''
PACKAGE_VERSION='8.27.12'
PATH_SEPARATOR=':'
SET_MAKE=''
SHELL='/bin/bash'
STRIP=''
VERSION='8.27.12'
ac_ct_CC='gcc'
ac_ct_CXX='g++'
am__isrc=''
am__leading_dot='.'
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='$(SHELL) /home/ubuntu/ima2/build-aux/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='/bin/mkdir -p'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "IMa2"
#define PACKAGE_TARNAME "ima2"
#define PACKAGE_VERSION "8.27.12"
#define PACKAGE_STRING "IMa2 8.27.12"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#define PACKAGE "ima2"
#define VERSION "8.27.12"
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_VPRINTF 1
#define LINUX 1
#define STRUCTURAMA "/usr/local/bin"

configure: exit 0

/////////////////////////////////

Stéphane Dupas

unread,
Nov 12, 2012, 5:46:24 AM11/12/12
to isolation-wi...@googlegroups.com
Dear Colleagues,

I have just installed IMa2 in my ubuntu 12.04 and have been trying the windows executable as well in an other machine. I always crashes!

I have been trying to run your example file.
./IMa2 -iexample.txt

In linux I obtain a "core dump" message.
In windows, the program crashes as well. "stop functioning message"

In ubuntu 12.04, I have installed from the latest .tar.gz source.
In windows I used the executable available.

I am sorry, I am a new IMa2 user.  But I can't find my error.
thanks in advance,

Stéphane

jhey

unread,
Nov 13, 2012, 11:45:23 AM11/13/12
to Isolation with Migration

is that your actual command line (' ./IMa2 -iexample.txt ')

if so it is not nearly sufficient as you need to provide a bunch of
additional information

jhey

Xiaoli Wu

unread,
Oct 4, 2015, 3:14:57 PM10/4/15
to Isolation with Migration
Can you be specific about what are other information that is needed?
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