Fastlib Installation / New way to load data?

[Ivan Caceres]

Alright so it looks like I'm getting close. I tried to build using the
--compiler=gcc flag and attempted to install BLAS and LAPACK using
option 1 for both. Didn't get to record the output successfully but I
think it installed BLAS correctly and the hanged when installing
LAPACK.

The build is almost working though now after I ended the hanging
installation. I figured out that you needed to remove the fx_init()
and the fx_done() from the beginning and end of files but I'm getting
a whole bunch of errors which I think are related to loading data. Is
there a new way to load data rather than:

<code>
const char *test_data_filename = fx_param_str_req(NULL,
"test_data");
Matrix test_data;
data::Load(test_data_filename, &test_data);
</code>

It may be from trying to save data also. I do have some of the
following in my main as well:

<code>
data::Save("file.txt",matrix)
</code>

Here is my output from when I try to build (sorry, don't know how to
attach file):

ivan@teletran-2:/media/media/documents/school/graduate/cse_6740/
final_project/icaceres3$ fl-build cpa --compiler=gcc
*** Building from OUTSIDE build system... cross your fingers!
- I think the build system is here: /media/media/documents/school/
graduate/cse_6740/fastlib/
- This is where you are: /media/media/documents/school/graduate/
cse_6740/final_project/icaceres3/
!!! No ':' is in the target rule name, assuming ':cpa'.
*** Generating Makefile in current directory
*** Target Rule: ':cpa'
... Reading /media/media/documents/school/graduate/cse_6740/
final_project/icaceres3/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/la/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/base/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/col/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/fx/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/file/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/data/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/math/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/tree/build.py
... Reading /media/media/documents/school/graduate/cse_6740/fastlib/
fastlib/par/build.py
*** Running Makefile
... Making /media/media/documents/school/graduate/cse_6740/fastlib/
bin_keep/i686_Linux_COMMON_gcc_COMMON/liblapack.a
... Making bin/i686_Linux_check_gcc_-DDISABLE_DISK_MATRIX/obj/
external_media_media_documents_school_graduate_cse_6740_final_project_icaceres3_cpa_main.o
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h: In member function ‘void DatasetFeature::OT__TraverseObject_
(TVisitor*) [with TVisitor = ot__private::Unstructor]’:
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘void OT__TraverseObject
(DatasetFeature*, TVisitor*) [with TVisitor =
ot__private::Unstructor]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:462: instantiated from
‘ot__private::Unstructor::Unstructor(T*) [with T = DatasetFeature]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from here
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:78: warning: dereferencing type-punned pointer will break
strict-aliasing rules
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘void OT__TraverseObject
(DatasetFeature*, TVisitor*) [with TVisitor =
ot__private::Unstructor]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:462: instantiated from
‘ot__private::Unstructor::Unstructor(T*) [with T = DatasetFeature]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from here
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:78: warning: dereferencing type-punned pointer will break
strict-aliasing rules
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h: In member function ‘void DatasetFeature::OT__TraverseObject_
(TVisitor*) [with TVisitor = ot__private::Destructor<false>]’:
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘void OT__TraverseObject
(DatasetFeature*, TVisitor*) [with TVisitor =
ot__private::Destructor<false>]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:630: instantiated from
‘ot__private::Destructor<t_semi>::Destructor(T*) [with T =
DatasetFeature, bool t_semi = false]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from here
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:78: warning: dereferencing type-punned pointer will break
strict-aliasing rules
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘void OT__TraverseObject
(DatasetFeature*, TVisitor*) [with TVisitor =
ot__private::Destructor<false>]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:630: instantiated from
‘ot__private::Destructor<t_semi>::Destructor(T*) [with T =
DatasetFeature, bool t_semi = false]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from here
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:78: warning: dereferencing type-punned pointer will break
strict-aliasing rules
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h: In member function ‘void DatasetFeature::OT__TraverseObject_
(TVisitor*) [with TVisitor = ot__private::Copier<false>]’:
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘void OT__TraverseObject
(DatasetFeature*, TVisitor*) [with TVisitor =
ot__private::Copier<false>]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:777: instantiated from ‘void
ot__private::Copier<t_thawing>::Obj(T&) [with T = DatasetFeature, bool
t_thawing = false]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:738: instantiated from
‘ot__private::Copier<t_thawing>::Copier(T*, const T*) [with T =
DatasetFeature, bool t_thawing = false]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from here
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:78: warning: dereferencing type-punned pointer will break
strict-aliasing rules
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘void OT__TraverseObject
(DatasetFeature*, TVisitor*) [with TVisitor =
ot__private::Copier<false>]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:777: instantiated from ‘void
ot__private::Copier<t_thawing>::Obj(T&) [with T = DatasetFeature, bool
t_thawing = false]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:738: instantiated from
‘ot__private::Copier<t_thawing>::Copier(T*, const T*) [with T =
DatasetFeature, bool t_thawing = false]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from here
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:78: warning: dereferencing type-punned pointer will break
strict-aliasing rules
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h: In member function ‘void DatasetFeature::OT__TraverseObject_
(TVisitor*) [with TVisitor =
ot__private::Printer<ot::StandardFormat>]’:
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘void OT__TraverseObject
(DatasetFeature*, TVisitor*) [with TVisitor =
ot__private::Printer<ot::StandardFormat>]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:332: instantiated from ‘void
ot__private::Printer<TPrintFormat>::Obj(T&) [with T = DatasetFeature,
TPrintFormat = ot::StandardFormat]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:278: instantiated from
‘ot__private::Printer<TPrintFormat>::Printer(const T&, const char*,
FILE*) [with T = DatasetFeature, TPrintFormat = ot::StandardFormat]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav.h:1494: instantiated from ‘const char* ot::Print(const T&,
const char*, FILE*) [with TPrintFormat = ot::StandardFormat, T =
DatasetFeature]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘const char* DatasetFeature::Print
(const char*, FILE*) [with TPrintFormat = ot::StandardFormat]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from here
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:78: warning: dereferencing type-punned pointer will break
strict-aliasing rules
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘void OT__TraverseObject
(DatasetFeature*, TVisitor*) [with TVisitor =
ot__private::Printer<ot::StandardFormat>]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:332: instantiated from ‘void
ot__private::Printer<TPrintFormat>::Obj(T&) [with T = DatasetFeature,
TPrintFormat = ot::StandardFormat]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav_impl.h:278: instantiated from
‘ot__private::Printer<TPrintFormat>::Printer(const T&, const char*,
FILE*) [with T = DatasetFeature, TPrintFormat = ot::StandardFormat]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/base/
otrav.h:1494: instantiated from ‘const char* ot::Print(const T&,
const char*, FILE*) [with TPrintFormat = ot::StandardFormat, T =
DatasetFeature]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from ‘const char* DatasetFeature::Print
(const char*, FILE*) [with TPrintFormat = ot::StandardFormat]’
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:76: instantiated from here
/media/media/documents/school/graduate/cse_6740/fastlib/fastlib/data/
dataset.h:78: warning: dereferencing type-punned pointer will break
strict-aliasing rules
... Making bin/i686_Linux_check_gcc_-DDISABLE_DISK_MATRIX/
libexternal_media_media_documents_school_graduate_cse_6740_final_project_icaceres3_cpa__auto.a
... Making bin/i686_Linux_check_gcc_-DDISABLE_DISK_MATRIX/external/
media/media/documents/school/graduate/cse_6740/final_project/icaceres3/
cpa
g++: /media/media/documents/school/graduate/cse_6740/fastlib/bin_keep/
i686_Linux_COMMON_gcc_COMMON/liblapack.a: No such file or directory
make: *** [/media/media/documents/school/graduate/cse_6740/fastlib/bin/
i686_Linux_check_gcc_-DDISABLE_DISK_MATRIX/external/media/media/
documents/school/graduate/cse_6740/final_project/icaceres3/cpa] Error
1
ivan@teletran-2:/media/media/documents/school/graduate/cse_6740/
final_project/icaceres3$

Below are my original messages

---------------------------------------------------------------------------------------------
Reply:

fl-build is looking for executables "gcc4" and "g++4" which are not
present on your system (and this isn't a bad thing). To fix this
problem, you can create symlinks to gcc and g++, or you can compile
with

fl-build myprog --compiler=gcc

The reason for this problem is dumb. Recent updates to LAPACK forced
us to move to gfortran and thus to gcc version 4.x.x, but our systems
make that available as "gcc4" (executable "gcc" is version 3.x.x).
Our response was to use the names for the newer version, which works
for us but apparently no one else. We should have corrections made to
the version available from MLOSS shortly.

--Ryan

Original message:

I realized I was still using the old fastlib given to us and wanted to
use the newest version linked here: http://mloss.org/software/view/152/

I downloaded, extracted, and changed my ~/.bashrc to refelect the new
directory.

Upon trying to build a project I got the prompt which asked me to DL
BLAS/LAPACK which I hit 1 for both and got the following error at the
end of installation:

ranlib blas_LINUX.a
make[1]: Leaving directory `/media/media/documents/school/graduate/
cse_6740/fastlib2/bin_keep/i686_Linux_COMMON_gcc4_COMMON/
netlib_workspace1/BLAS'
... Almost done with BLAS...
... Created archive, cleaning up.
*** Done with and BLAS!
... Making bin/i686_Linux_COMMON_gcc4_-DDISABLE_DISK_MATRIX/
libfastlib_base_base.h
... Making bin/i686_Linux_check_gcc4_-DDISABLE_DISK_MATRIX/obj/
fastlib_base_common.o
/bin/sh: gcc4: not found
make: *** [/media/media/documents/school/graduate/cse_6740/fastlib2/
bin/i686_Linux_check_gcc4_-DDISABLE_DISK_MATRIX/obj/
fastlib_base_common.o] Error 127
make: *** Waiting for unfinished jobs....

It just hangs here no matter how long I wait. I do have GCC and
gfortran installed. I reinstalled them to make sure.

When I try and build a project in this state it gives me the following
errors:

Running Makefile
... Making /media/media/documents/school/graduate/cse_6740/fastlib2/
bin_keep/i686_Linux_COMMON_gcc4_COMMON/liblapack.a
... Making bin/i686_Linux_check_gcc4_-DDISABLE_DISK_MATRIX/obj/
fastlib_col_col.o
/bin/sh: g++4: not found
make: *** [/media/media/documents/school/graduate/cse_6740/fastlib2/
bin/i686_Linux_check_gcc4_-DDISABLE_DISK_MATRIX/obj/fastlib_col_col.o]
Error 127
ivan@teletran-2:/media/media/documents/school/graduate/cse_6740/
final_project/icaceres3$

If I change my ~/.bashrc back to point back to the old fastlib it
works fine. My only problem with this is that I'm trying to use the
latest smo.h file in the SVM folder of MLPACK and when I try to use it
I with the old version of FASTLIB I get a ton of errors (mainly
because functions in arraylist.h got changed). I tried copying over
the old arraylist.h with the new one also and that didn't work to well
either.

Here is the GCC and python I'm running.

ivan@teletran-2:~$ /usr/bin/env python
Python 2.5.2 (r252:60911, Jul 31 2008, 17:28:52)
[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()

ivan@teletran-2:/media/media/documents/school/graduate/cse_6740$ cat /
etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=8.04
DISTRIB_CODENAME=hardy
DISTRIB_DESCRIPTION="Ubuntu 8.04.1"

ivan@teletran-2:/media/media/documents/school/graduate/cse_6740$ uname
-a
Linux teletran-2 2.6.24-22-generic #1 SMP Mon Nov 24 18:32:42 UTC 2008
i686 GNU/Linux