Suitesparse libs (AMD, ..) issues during configure (Mageia-6)

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Suitesparse libs (AMD, ..) issues during configure (Mageia-6)

PhilipNienhuis
Hi,

I'm trying to build dev octave on Mageia-6 (just released) and run into the
following during configure:

:
configure:42494: checking suitesparse/amd.h usability
configure:42494: gcc -c -g -O2 -pthread -fopenmp   conftest.c >&5
configure:42494: $? = 0
configure:42494: result: yes
configure:42494: checking suitesparse/amd.h presence
configure:42494: gcc -E   conftest.c
configure:42494: $? = 0
configure:42494: result: yes
configure:42494: checking for suitesparse/amd.h
configure:42494: result: yes
configure:42505: checking for amd_postorder in -lamd
configure:42536: gcc -o conftest -g -O2 -pthread -fopenmp     conftest.c
-lamd -lutil -lm   >&5
/usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
undefined reference to `SuiteSparse_config'
/usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
undefined reference to `SuiteSparse_free'
/usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
undefined reference to `SuiteSparse_malloc'
:

Octave builds fine AFAICS but to proceed further and cross-build for
mxe-octave, the dist target needs COLAMD and I suppose AMD / CAMD / CCOLAMD
to build the docs.

How can I get this fixed?

I saw the old bug #43063 but that is quite a while back. Until a few weeks
ago I could build Octave w/o issues on Mageia-6 RC incl suitesparse.

Philip




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Re: Suitesparse libs (AMD, ..) issues during configure (Mageia-6)

John W. Eaton
Administrator
On 09/01/2017 09:18 AM, PhilipNienhuis wrote:

> Hi,
>
> I'm trying to build dev octave on Mageia-6 (just released) and run into the
> following during configure:
>
> :
> configure:42494: checking suitesparse/amd.h usability
> configure:42494: gcc -c -g -O2 -pthread -fopenmp   conftest.c >&5
> configure:42494: $? = 0
> configure:42494: result: yes
> configure:42494: checking suitesparse/amd.h presence
> configure:42494: gcc -E   conftest.c
> configure:42494: $? = 0
> configure:42494: result: yes
> configure:42494: checking for suitesparse/amd.h
> configure:42494: result: yes
> configure:42505: checking for amd_postorder in -lamd
> configure:42536: gcc -o conftest -g -O2 -pthread -fopenmp     conftest.c
> -lamd -lutil -lm   >&5
> /usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
> undefined reference to `SuiteSparse_config'
> /usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
> undefined reference to `SuiteSparse_free'
> /usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
> undefined reference to `SuiteSparse_malloc'
> :
>
> Octave builds fine AFAICS but to proceed further and cross-build for
> mxe-octave, the dist target needs COLAMD and I suppose AMD / CAMD / CCOLAMD
> to build the docs.
>
> How can I get this fixed?
>
> I saw the old bug #43063 but that is quite a while back. Until a few weeks
> ago I could build Octave w/o issues on Mageia-6 RC incl suitesparse.

What does

   ldd /usr/lib64/libamd.so

show you?  Does it include libsuitesparseconfig.so in the list of
libraries that are linked to libamd.so?  If not, then I think maybe this
is a configuration/build/packaging error in your version of suitesparse.

Even though I really think that your suitesparse libraries should be
linked to the config library if they need it, I checked in the following
changeset.  Does it help?

http://hg.savannah.gnu.org/hgweb/octave/rev/6f56efc098bd

jwe

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Re: Suitesparse libs (AMD, ..) issues during configure (Mageia-6)

PhilipNienhuis
John W. Eaton wrote:

> On 09/01/2017 09:18 AM, PhilipNienhuis wrote:
>> Hi,
>>
>> I'm trying to build dev octave on Mageia-6 (just released) and run
>> into the
>> following during configure:
>>
>> :
>> configure:42494: checking suitesparse/amd.h usability
>> configure:42494: gcc -c -g -O2 -pthread -fopenmp   conftest.c >&5
>> configure:42494: $? = 0
>> configure:42494: result: yes
>> configure:42494: checking suitesparse/amd.h presence
>> configure:42494: gcc -E   conftest.c
>> configure:42494: $? = 0
>> configure:42494: result: yes
>> configure:42494: checking for suitesparse/amd.h
>> configure:42494: result: yes
>> configure:42505: checking for amd_postorder in -lamd
>> configure:42536: gcc -o conftest -g -O2 -pthread -fopenmp     conftest.c
>> -lamd -lutil -lm   >&5
>> /usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
>> undefined reference to `SuiteSparse_config'
>> /usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
>> undefined reference to `SuiteSparse_free'
>> /usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
>> undefined reference to `SuiteSparse_malloc'
>> :
>>
>> Octave builds fine AFAICS but to proceed further and cross-build for
>> mxe-octave, the dist target needs COLAMD and I suppose AMD / CAMD /
>> CCOLAMD
>> to build the docs.
>>
>> How can I get this fixed?
>>
>> I saw the old bug #43063 but that is quite a while back. Until a few
>> weeks
>> ago I could build Octave w/o issues on Mageia-6 RC incl suitesparse.
>
> What does
>
>   ldd /usr/lib64/libamd.so
>
> show you?  Does it include libsuitesparseconfig.so in the list of
> libraries that are linked to libamd.so?  If not, then I think maybe this
> is a configuration/build/packaging error in your version of suitesparse.

[philip@DeskPRN octdev]$ ldd /usr/lib64/libamd.so
         linux-vdso.so.1 (0x00007fffa4644000)
         libm.so.6 => /lib64/libm.so.6 (0x00007ffb17e17000)
         libc.so.6 => /lib64/libc.so.6 (0x00007ffb17a64000)
         /lib64/ld-linux-x86-64.so.2 (0x00007ffb18321000)

So no libsuitesparseconfig.so.
According to Mageia's package manager (rpmdrake) I do have it installed
(lib64suitesparseconfig4)

> Even though I really think that your suitesparse libraries should be
> linked to the config library if they need it, I checked in the following
> changeset.  Does it help?

Thanks, I'll check & report back later.
I couldn't find any pkg-config files for suitesparse anywhere, I guess
you're right, but that seems the way Mageia works.

Philip







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Re: Suitesparse libs (AMD, ..) issues during configure (Mageia-6)

PhilipNienhuis
Philip Nienhuis wrote:

> John W. Eaton wrote:
>> On 09/01/2017 09:18 AM, PhilipNienhuis wrote:
>>> Hi,
>>>
>>> I'm trying to build dev octave on Mageia-6 (just released) and run
>>> into the
>>> following during configure:
>>>
>>> :
>>> configure:42494: checking suitesparse/amd.h usability
>>> configure:42494: gcc -c -g -O2 -pthread -fopenmp   conftest.c >&5
>>> configure:42494: $? = 0
>>> configure:42494: result: yes
>>> configure:42494: checking suitesparse/amd.h presence
>>> configure:42494: gcc -E   conftest.c
>>> configure:42494: $? = 0
>>> configure:42494: result: yes
>>> configure:42494: checking for suitesparse/amd.h
>>> configure:42494: result: yes
>>> configure:42505: checking for amd_postorder in -lamd
>>> configure:42536: gcc -o conftest -g -O2 -pthread -fopenmp     conftest.c
>>> -lamd -lutil -lm   >&5
>>> /usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
>>> undefined reference to `SuiteSparse_config'
>>> /usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
>>> undefined reference to `SuiteSparse_free'
>>> /usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/../../../../lib64/libamd.so:
>>> undefined reference to `SuiteSparse_malloc'
>>> :
>>>
>>> Octave builds fine AFAICS but to proceed further and cross-build for
>>> mxe-octave, the dist target needs COLAMD and I suppose AMD / CAMD /
>>> CCOLAMD
>>> to build the docs.
>>>
>>> How can I get this fixed?
>>>
>>> I saw the old bug #43063 but that is quite a while back. Until a few
>>> weeks
>>> ago I could build Octave w/o issues on Mageia-6 RC incl suitesparse.

<snip>

>> Even though I really think that your suitesparse libraries should be
>> linked to the config library if they need it, I checked in the following
>> changeset.  Does it help?
>
> Thanks, I'll check & report back later.

Yep, that helps, I see no more complaints about missing libraies after
./configure.
Thank you very much.

philip