8:43 p.m.
Hi,
Trying to install gretl 1.9.5 from source due to the known seg faults
in the downstream ubuntu 11.04 repositories. I have all the
dependencies installed, except my lapack (3.2.2) was built with ATLAS
(3.9.2) with the same version of gcc I have installed. The lapack
stuff seems to be giving me troubles, though I'm not too sure why. It
works fine for numpy/scipy and R.
|2 $ pwd
/home/skipper/built/atlas_files
|3 $ ls lib/
libamd.2.2.1.a libcblas.a liblapack.a libptf77blas.a
libamd.a libcblas.so liblapack.so libptf77blas.so
libatlas.a libf77blas.a libptcblas.a libumfpack.5.5.0.a
libatlas.so libf77blas.so libptcblas.so libumfpack.a
So I change lblas to lcblas in configure. This is my config.log
http://pastebin.com/3GR4yCH6
Any ideas?
Skipper
9:32 p.m.
On Thu, 18 Aug 2011, Skipper Seabold wrote:
Trying to install gretl 1.9.5 from source due to the known seg
faults
in the downstream ubuntu 11.04 repositories. I have all the
dependencies installed, except my lapack (3.2.2) was built with ATLAS
(3.9.2) with the same version of gcc I have installed. The lapack
stuff seems to be giving me troubles, though I'm not too sure why.
No doubt this should be better documented, but if you want to build
gretl against atlas you should use the LAPACK_LIBS environment
variable. For example:
LAPACK_LIBS='-L/your/atlas/lib -llapack -lf77blas -lcblas -latlas' \
./configure <options>
You can't just replace -lblas with -lcblas, because more libraries
are needed with an atlas build, including crucially libatlas.
Also relevant:
http://ricardo.ecn.wfu.edu/~cottrell/tmp/gretl_speed.html
Allin Cottrell
9:35 p.m.
Ahoy Skipper ;)
Can you compile the ATLAS lib locally? And then use the install script. My
solution was to always use standard directories.
See also that the .so files are symbolic links to the .so.3.2.1 libs.
It seems that you are missing a dependency. The FFTW3 is missing.
Here is my listing of libraries:
helio@linux-techno:/usr/lib64> l *lapack*
-rw-r--r-- 1 root root 20018986 Jul 5 2010 liblapack.a
-rw-r--r-- 1 root root 20302074 Jul 5 2010 liblapack_pic.a
lrwxrwxrwx 1 root root 18 Out 4 2010 liblapack.so ->
liblapack.so.3.2.1*
lrwxrwxrwx 1 root root 18 Out 4 2010 liblapack.so.3 ->
liblapack.so.3.2.1*
-rwxr-xr-x 1 root root 5308064 Jul 5 2010 liblapack.so.3.2.1*
helio@linux-techno:/usr/lib64> l *blas*
-rw-r--r-- 1 root root 1471064 Jul 5 2010 libblas.a
-rw-r--r-- 1 root root 1477384 Jul 5 2010 libblas_pic.a
lrwxrwxrwx 1 root root 16 Out 4 2010 libblas.so -> libblas.so.3.2.1*
lrwxrwxrwx 1 root root 16 Out 4 2010 libblas.so.3 ->
libblas.so.3.2.1*
-rwxr-xr-x 1 root root 362648 Jul 5 2010 libblas.so.3.2.1*
lrwxrwxrwx 1 root root 20 Out 4 2010 libgslcblas.so.0 ->
libgslcblas.so.0.0.0*
-rwxr-xr-x 1 root root 215120 Jul 5 2010 libgslcblas.so.0.0.0*
lrwxrwxrwx 1 root root 16 Out 4 2010 liblash.so.2 ->
liblash.so.2.0.0*
-rwxr-xr-x 1 root root 52392 Jul 5 2010 liblash.so.2.0.0*
helio@linux-techno:/usr/lib64> l *fftw*
lrwxrwxrwx 1 root root 18 Out 4 2010 libfftw3f.so ->
libfftw3f.so.3.2.4*
lrwxrwxrwx 1 root root 18 Out 4 2010 libfftw3f.so.3 ->
libfftw3f.so.3.2.4*
-rwxr-xr-x 1 root root 1019824 Jul 5 2010 libfftw3f.so.3.2.4*
lrwxrwxrwx 1 root root 26 Out 4 2010 libfftw3f_threads.so.3 ->
libfftw3f_threads.so.3.2.4*
-rwxr-xr-x 1 root root 27168 Jul 5 2010 libfftw3f_threads.so.3.2.4*
lrwxrwxrwx 1 root root 17 Out 4 2010 libfftw3.so ->
libfftw3.so.3.2.4*
lrwxrwxrwx 1 root root 17 Out 4 2010 libfftw3.so.3 ->
libfftw3.so.3.2.4*
-rwxr-xr-x 1 root root 1048488 Jul 5 2010 libfftw3.so.3.2.4*
lrwxrwxrwx 1 root root 25 Out 4 2010 libfftw3_threads.so.3 ->
libfftw3_threads.so.3.2.4*
-rwxr-xr-x 1 root root 27160 Jul 5 2010 libfftw3_threads.so.3.2.4*
helio@linux-techno:/usr/lib64>
Hope it helped.
(my Linux is OpenSUSE and I am having trouble with gtk/glib, gretl_x11
crashes :( )
Hélio
On Thu, Aug 18, 2011 at 9:43 PM, Skipper Seabold <jsseabold(a)gmail.com>wrote:
Hi,
Trying to install gretl 1.9.5 from source due to the known seg faults
in the downstream ubuntu 11.04 repositories. I have all the
dependencies installed, except my lapack (3.2.2) was built with ATLAS
(3.9.2) with the same version of gcc I have installed. The lapack
stuff seems to be giving me troubles, though I'm not too sure why. It
works fine for numpy/scipy and R.
|2 $ pwd
/home/skipper/built/atlas_files
|3 $ ls lib/
libamd.2.2.1.a libcblas.a liblapack.a libptf77blas.a
libamd.a libcblas.so liblapack.so libptf77blas.so
libatlas.a libf77blas.a libptcblas.a libumfpack.5.5.0.a
libatlas.so libf77blas.so libptcblas.so libumfpack.a
So I change lblas to lcblas in configure. This is my config.log
http://pastebin.com/3GR4yCH6
Any ideas?
Skipper
_______________________________________________
Gretl-users mailing list
Gretl-users(a)lists.wfu.edu
http://lists.wfu.edu/mailman/listinfo/gretl-users
9:49 p.m.
On Thu, Aug 18, 2011 at 5:32 PM, Allin Cottrell <cottrell(a)wfu.edu> wrote:
On Thu, 18 Aug 2011, Skipper Seabold wrote:
> Trying to install gretl 1.9.5 from source due to the known seg faults
> in the downstream ubuntu 11.04 repositories. I have all the
> dependencies installed, except my lapack (3.2.2) was built with ATLAS
> (3.9.2) with the same version of gcc I have installed. The lapack
> stuff seems to be giving me troubles, though I'm not too sure why.
No doubt this should be better documented, but if you want to build
gretl against atlas you should use the LAPACK_LIBS environment
variable. For example:
LAPACK_LIBS='-L/your/atlas/lib -llapack -lf77blas -lcblas -latlas' \
./configure <options>
You can't just replace -lblas with -lcblas, because more libraries
are needed with an atlas build, including crucially libatlas.
Right, I neglected to mention that I also tried to edit configure to link
against atlas, cblas, f77blas, etc. to the same effect about the hidden
symbol.
Are you saying that all I need to do is define LAPACK_LIBS as such and then
run configure, or do I still need the with-lapack-prefix as well?? I tried
the former, and it fails to build, saying it can't find lblas (I changed
back to the original configure file).
|16 $ echo $LAPACK_LIBS
-L/home/skipper/built/atlas_files/lib -llapack -lf77blas -lcblas -latlas
What look to be the relevant lines in config.log are now something like
gcc -o conftest -I./lib/src -msse2 -g -O2 conftest.c -L/usr/lib -llapack
-lblas -lgfortran -lc -lc -lm
Skipper
9:57 p.m.
2011/8/18 Hélio Guilherme <helioxentric(a)gmail.com>
Ahoy Skipper ;)
Can you compile the ATLAS lib locally? And then use the install script. My
solution was to always use standard directories.
See also that the .so files are symbolic links to the .so.3.2.1 libs.
I like to keep them separate so that I can (remember to) back them up easily
and don't have to recompile atlas whenever I upgrade my OS. I suppose I
could make symbolic links in the system directories, but this shouldn't
really be necessary.
It seems that you are missing a dependency. The FFTW3 is missing.
Good catch, I installed the headers for FFTW3, but still have the same
problem.
Skipper
11:13 p.m.
On Thu, 18 Aug 2011, Skipper Seabold wrote:
On Thu, Aug 18, 2011 at 5:32 PM, Allin Cottrell
<cottrell(a)wfu.edu> wrote:
> On Thu, 18 Aug 2011, Skipper Seabold wrote:
>
>> Trying to install gretl 1.9.5 from source due to the known seg faults
>> in the downstream ubuntu 11.04 repositories. I have all the
>> dependencies installed, except my lapack (3.2.2) was built with ATLAS
>> (3.9.2) with the same version of gcc I have installed. The lapack
>> stuff seems to be giving me troubles, though I'm not too sure why.
>
> No doubt this should be better documented, but if you want to build
> gretl against atlas you should use the LAPACK_LIBS environment
> variable. For example:
>
> LAPACK_LIBS='-L/your/atlas/lib -llapack -lf77blas -lcblas -latlas' \
> ./configure <options>
>
> You can't just replace -lblas with -lcblas, because more libraries
> are needed with an atlas build, including crucially libatlas.
Right, I neglected to mention that I also tried to edit configure to link
against atlas, cblas, f77blas, etc. to the same effect about the hidden
symbol.
Are you saying that all I need to do is define LAPACK_LIBS as such and then
run configure, or do I still need the with-lapack-prefix as well??
Just use LAPACK_LIBS; the lapack-prefix thing is only for use where
you have the standard "-llapack -lblas" linkage, but are using a
non-standard installation directory.
[...] it fails to build, saying it can't find lblas
"lblas"? Looks like a typo?
I'll take another look on the host where I'm building against atlas
and report back.
Allin Cottrell
11:23 p.m.
On Thu, Aug 18, 2011 at 7:13 PM, Allin Cottrell <cottrell(a)wfu.edu> wrote:
On Thu, 18 Aug 2011, Skipper Seabold wrote:
> On Thu, Aug 18, 2011 at 5:32 PM, Allin Cottrell <cottrell(a)wfu.edu> wrote:
>> On Thu, 18 Aug 2011, Skipper Seabold wrote:
>>
>>> Trying to install gretl 1.9.5 from source due to the known seg faults
>>> in the downstream ubuntu 11.04 repositories. I have all the
>>> dependencies installed, except my lapack (3.2.2) was built with ATLAS
>>> (3.9.2) with the same version of gcc I have installed. The lapack
>>> stuff seems to be giving me troubles, though I'm not too sure why.
>>
>> No doubt this should be better documented, but if you want to build
>> gretl against atlas you should use the LAPACK_LIBS environment
>> variable. For example:
>>
>> LAPACK_LIBS='-L/your/atlas/lib -llapack -lf77blas -lcblas -latlas' \
>> ./configure <options>
>>
>> You can't just replace -lblas with -lcblas, because more libraries
>> are needed with an atlas build, including crucially libatlas.
>
> Right, I neglected to mention that I also tried to edit configure to link
> against atlas, cblas, f77blas, etc. to the same effect about the hidden
> symbol.
>
> Are you saying that all I need to do is define LAPACK_LIBS as such and then
> run configure, or do I still need the with-lapack-prefix as well??
Just use LAPACK_LIBS; the lapack-prefix thing is only for use where
you have the standard "-llapack -lblas" linkage, but are using a
non-standard installation directory.
That's what I thought. It doesn't look like the LAPACK_LIBS options
are being passed to the compiler, but I haven't gone through the
configure script in great detail.
> [...] it fails to build, saying it can't find lblas
"lblas"? Looks like a typo?
This is why I changed -lblas to -lcblas and tried to add the other
libraries. I have libcblas.*, libf77blas.*, etc. but when I run
configure, it just tries the -llapack -lblas options instead of the
LAPACK_LIBS.
I'll take another look on the host where I'm building against atlas
and report back.
Please do. Thanks,
Skipper
2:08 a.m.
On Thu, 18 Aug 2011, Skipper Seabold wrote:
On Thu, Aug 18, 2011 at 7:13 PM, Allin Cottrell
<cottrell(a)wfu.edu> wrote:
> On Thu, 18 Aug 2011, Skipper Seabold wrote:
>
>> On Thu, Aug 18, 2011 at 5:32 PM, Allin Cottrell <cottrell(a)wfu.edu> wrote:
>>> On Thu, 18 Aug 2011, Skipper Seabold wrote:
>>>
>>>> Trying to install gretl 1.9.5 from source due to the known seg faults
>>>> in the downstream ubuntu 11.04 repositories. I have all the
>>>> dependencies installed, except my lapack (3.2.2) was built with ATLAS
>>>> (3.9.2) with the same version of gcc I have installed. The lapack
>>>> stuff seems to be giving me troubles, though I'm not too sure why.
>>>
>>> No doubt this should be better documented, but if you want to build
>>> gretl against atlas you should use the LAPACK_LIBS environment
>>> variable. For example:
>>>
>>> LAPACK_LIBS='-L/your/atlas/lib -llapack -lf77blas -lcblas -latlas' \
>>> ./configure <options>
>>>
>>> You can't just replace -lblas with -lcblas, because more libraries
>>> are needed with an atlas build, including crucially libatlas.
>>
>> Right, I neglected to mention that I also tried to edit configure to link
>> against atlas, cblas, f77blas, etc. to the same effect about the hidden
>> symbol.
>>
>> Are you saying that all I need to do is define LAPACK_LIBS as such and then
>> run configure, or do I still need the with-lapack-prefix as well??
>
> Just use LAPACK_LIBS; the lapack-prefix thing is only for use where
> you have the standard "-llapack -lblas" linkage, but are using a
> non-standard installation directory.
That's what I thought. It doesn't look like the LAPACK_LIBS options
are being passed to the compiler, but I haven't gone through the
configure script in great detail.
>> [...] it fails to build, saying it can't find lblas
>
> "lblas"? Looks like a typo?
This is why I changed -lblas to -lcblas and tried to add the other
libraries. I have libcblas.*, libf77blas.*, etc. but when I run
configure, it just tries the -llapack -lblas options instead of the
LAPACK_LIBS.
I think that either your atlas installation is broken or you're not
passing the correct LAPACK_LIBS variable.
I just tried here on Ubuntu 10.04, using the latest stable lapack
(3.3.1) plus latest stable atlas (3.8.4), libraries installed into
/opt/atlas/lib. In configuring the gretl build I either pass
LAPACK_LIBS='-L/opt/atlas/lib -llapack_atl -lf77blas \
-lcblas -latlas' [...]
as part of the invocation of gretl's configure script, or else put
the relevant variable into the environment via
export LAPACK_LIBS='-L/opt/atlas/lib -llapack_atl \
-lf77blas -lcblas -latlas'
before invoking ./configure. Either way the gretl build works OK.
And 'grep lapack config.log' shows that what I specified for
LAPACK_LIBS is being respected.
But note: if your atlas libs are built without the correct
dependencies being indicated to the linker, you may need to add
elements to the LAPACK_LIBS variable, for example -lgfortran and
-lgcc_s -- and in that case you may need to add symlinks to your
system to define libgfortran.so and libgcc_s.so.
Building your own atlas BLAS and linking programs against the
relevant libraries is truly an expert option.
Allin Cottrell
2:37 a.m.
On Thu, Aug 18, 2011 at 10:08 PM, Allin Cottrell <cottrell(a)wfu.edu> wrote:
On Thu, 18 Aug 2011, Skipper Seabold wrote:
> On Thu, Aug 18, 2011 at 7:13 PM, Allin Cottrell <cottrell(a)wfu.edu> wrote:
>> On Thu, 18 Aug 2011, Skipper Seabold wrote:
>>
>>> On Thu, Aug 18, 2011 at 5:32 PM, Allin Cottrell <cottrell(a)wfu.edu>
wrote:
>>>> On Thu, 18 Aug 2011, Skipper Seabold wrote:
>>>>
>>>>> Trying to install gretl 1.9.5 from source due to the known seg
faults
>>>>> in the downstream ubuntu 11.04 repositories. I have all the
>>>>> dependencies installed, except my lapack (3.2.2) was built with
ATLAS
>>>>> (3.9.2) with the same version of gcc I have installed. The lapack
>>>>> stuff seems to be giving me troubles, though I'm not too sure
why.
>>>>
>>>> No doubt this should be better documented, but if you want to build
>>>> gretl against atlas you should use the LAPACK_LIBS environment
>>>> variable. For example:
>>>>
>>>> LAPACK_LIBS='-L/your/atlas/lib -llapack -lf77blas -lcblas
-latlas' \
>>>> ./configure <options>
>>>>
>>>> You can't just replace -lblas with -lcblas, because more libraries
>>>> are needed with an atlas build, including crucially libatlas.
>>>
>>> Right, I neglected to mention that I also tried to edit configure to link
>>> against atlas, cblas, f77blas, etc. to the same effect about the hidden
>>> symbol.
>>>
>>> Are you saying that all I need to do is define LAPACK_LIBS as such and then
>>> run configure, or do I still need the with-lapack-prefix as well??
>>
>> Just use LAPACK_LIBS; the lapack-prefix thing is only for use where
>> you have the standard "-llapack -lblas" linkage, but are using a
>> non-standard installation directory.
>
> That's what I thought. It doesn't look like the LAPACK_LIBS options
> are being passed to the compiler, but I haven't gone through the
> configure script in great detail.
>
>>> [...] it fails to build, saying it can't find lblas
>>
>> "lblas"? Looks like a typo?
>
> This is why I changed -lblas to -lcblas and tried to add the other
> libraries. I have libcblas.*, libf77blas.*, etc. but when I run
> configure, it just tries the -llapack -lblas options instead of the
> LAPACK_LIBS.
I think that either your atlas installation is broken or you're not
passing the correct LAPACK_LIBS variable.
All the tests passed when I installed it and I've been doing
numpy/scipy development and using R against it for a while.
I just tried here on Ubuntu 10.04, using the latest stable lapack
(3.3.1) plus latest stable atlas (3.8.4), libraries installed into
/opt/atlas/lib. In configuring the gretl build I either pass
LAPACK_LIBS='-L/opt/atlas/lib -llapack_atl -lf77blas \
-lcblas -latlas' [...]
as part of the invocation of gretl's configure script, or else put
the relevant variable into the environment via
export LAPACK_LIBS='-L/opt/atlas/lib -llapack_atl \
-lf77blas -lcblas -latlas'
before invoking ./configure. Either way the gretl build works OK.
And 'grep lapack config.log' shows that what I specified for
LAPACK_LIBS is being respected.
But note: if your atlas libs are built without the correct
dependencies being indicated to the linker, you may need to add
elements to the LAPACK_LIBS variable, for example -lgfortran and
-lgcc_s -- and in that case you may need to add symlinks to your
system to define libgfortran.so and libgcc_s.so.
Genius. Adding lgcc and lgcc_s worked, though I don't know if the
former was necessary. I have never come across this before, though I
saw one or two similar errors while searching. For posterity here's
the error
/usr/bin/ld: conftest: hidden symbol `__powidf2' in
/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/libgcc.a(_powidf2.o)
is referenced by DSO
and an explanation why
http://stackoverflow.com/questions/4547384/difference-between-lgcc-s-and-gcc
Thanks for sanity checking me.
Cheers,
Skipper
4636
days inactive
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9 comments
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participants (3)
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Allin Cottrell -
Hélio Guilherme -
Skipper Seabold