This is looking suspiously like a libatlas bug on Hardy. The
simula-scons tests fail for umfpack and cholmod if libatlas-base-dev is
installed. For plain blas and lapack, I get
>ldd /usr/lib/libblas.so /usr/lib/liblapack.so
libblas.so:
linux-gate.so.1 => (0xb7f97000)
libgfortran.so.2 (0xb7e80000)
libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7d1b000)
libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7cf5000)
/lib/ld-linux.so.2 (0xb7f98000)
liblapack.so:
linux-gate.so.1 => (0xb7fe2000)
libblas.so.3gf (0xb7870000)
libgfortran.so.2 (0xb77d9000)
libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb779d000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7792000)
libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7643000)
/lib/ld-linux.so.2 (0xb7fe3000)
Note that gfortran is present. For atlas (libatlas-base-dev),
>ldd /usr/lib/atlas/libblas.so /usr/lib/atlas/liblapack.so
/usr/lib/atlas/libblas.so:
linux-gate.so.1 => (0xb7f4b000)
libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7a99000)
/lib/ld-linux.so.2 (0xb7f4c000)
/usr/lib/atlas/liblapack.so:
linux-gate.so.1 => (0xb7fc1000)
libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0xb753c000)
libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb73ed000)
/lib/ld-linux.so.2 (0xb7fc2000)
Note that libgfortran is missing. On a Debian machine (lenny), I get
>ldd /usr/lib/atlas/libblas.so /usr/lib/atlas/liblapack.so
/usr/lib/atlas/libblas.so:
linux-gate.so.1 => (0xb7f01000)
libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0xb7abf000)
libm.so.6 => /lib/i686/cmov/libm.so.6 (0xb7a99000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7a8b000)
libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb7930000)
/lib/ld-linux.so.2 (0xb7f02000)
/usr/lib/atlas/liblapack.so:
linux-gate.so.1 => (0xb7f88000)
libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0xb7478000)
libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0xb73c6000)
libm.so.6 => /lib/i686/cmov/libm.so.6 (0xb739f000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7392000)
libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb7237000)
/lib/ld-linux.so.2 (0xb7f89000)
Any idea if this is bug or is it correct behaviour?
Garth
Garth N. Wells wrote:
>
> Johannes Ring wrote:
>> On Thu, August 21, 2008 14:57, Garth N. Wells wrote:
>>> Johannes Ring wrote:
>>>> Should be fixed now. Can you try again?
>>>>
>>> Mixed success. Doesn't work for Hardy, but does work for the alpha
>>> version of Intrepid (inside a VM).
>>>
>>> There is no liblapack.so in /usr/lib/atlas, just liblapack.so.3gf, under
>>> Hardy. There is a liblapack.so in /usr/lib/atlas for Intrepid.
>>>
>>> Somehow I have blas and lapack libs with a suffix "-3",
>>>
>>> /usr/lib/lapack-3.so -> /etc/alternatives/liblapack-3.so
>>> /usr/lib/libblas-3.so -> /etc/alternatives/libblas-3.so
>>>
>>> which pick up the atlas libs via /etc/alternatives/. I don't know what
>>> the '-3' is supposed to mean or why it's there.
>>>
>>> I give up for now trying to use atlas :(.
>> Have you installed the libatlas-base-dev package?
>>
>
> Yes. I see /usr/lib/atlas/liblapack.so now (not sure what happened before).
>
> Back to the cholmod issue, now -lgfortran is also required (see below).
>
> Garth
>
> g++ -I/usr/include/suitesparse cholmod_config_test_include.cpp
> -L/usr/lib/atlas -llapack -L/usr/lib/atlas -lblas -L/usr/lib -lcholmod
> -L/usr/lib -lamd -L/usr/lib -lcolamd
> Failed test program was:
>
> #include <stdio.h>
> #include <cholmod.h>
>
> int main() {
> #ifdef CHOLMOD_MAIN_VERSION
> #ifdef CHOLMOD_SUB_VERSION
> #ifdef CHOLMOD_SUBSUB_VERSION
> printf("%d.%d.%d",
> CHOLMOD_MAIN_VERSION,CHOLMOD_SUB_VERSION,CHOLMOD_SUBSUB_VERSION);
> #else
> printf("%d.%d", CHOLMOD_MAIN_VERSION,CHOLMOD_SUB_VERSION);
> #endif
> #else
> printf("%d", CHOLMOD_MAIN_VERSION);
> #endif
> #endif
> return 0;
> }
>
> Error message:
> /usr/lib/atlas/liblapack.so: undefined reference to
> `_gfortran_concat_string'
> /usr/lib/atlas/liblapack.so: undefined reference to
> `_gfortran_st_write_done'
> /usr/lib/atlas/liblapack.so: undefined reference to
> `_gfortran_transfer_integer'
> /usr/lib/atlas/liblapack.so: undefined reference to `_gfortran_stop_numeric'
> /usr/lib/atlas/liblapack.so: undefined reference to `_gfortran_pow_i4_i4'
> /usr/lib/atlas/liblapack.so: undefined reference to `_gfortran_st_write'
> /usr/lib/atlas/liblapack.so: undefined reference to
> `_gfortran_compare_string'
> /usr/lib/atlas/liblapack.so: undefined reference to `_gfortran_etime'
> /usr/lib/atlas/liblapack.so: undefined reference to `_gfortran_pow_r8_i4'
> /usr/lib/atlas/liblapack.so: undefined reference to
> `_gfortran_transfer_character'
> /usr/lib/atlas/liblapack.so: undefined reference to `_gfortran_pow_r4_i4'
> collect2: ld returned 1 exit status
>
>
>
>> Johannes
>>
>>> Garth
>>>
>>>
>>>> Johannes
>>>>
>>>> On Thu, August 21, 2008 13:42, Garth N. Wells wrote:
>>>>> The test for CHOLMOD fail on my machine when I remove liblapack3fg and
>>>>> use atlas,
>>>>>
>>>>> g++ -I/usr/include/suitesparse cholmod_config_test_include.cpp -L/usr
>>>>> -llapack -L/usr -lblas -L/usr/lib -lcholmod -L/usr/lib -lamd -L/usr/lib
>>>>> -lcolamd
>>>>> Failed test program was:
>>>>>
>>>>> #include <stdio.h>
>>>>> #include <cholmod.h>
>>>>>
>>>>> int main() {
>>>>> #ifdef CHOLMOD_MAIN_VERSION
>>>>> #ifdef CHOLMOD_SUB_VERSION
>>>>> #ifdef CHOLMOD_SUBSUB_VERSION
>>>>> printf("%d.%d.%d",
>>>>> CHOLMOD_MAIN_VERSION,CHOLMOD_SUB_VERSION,CHOLMOD_SUBSUB_VERSION);
>>>>> #else
>>>>> printf("%d.%d", CHOLMOD_MAIN_VERSION,CHOLMOD_SUB_VERSION);
>>>>> #endif
>>>>> #else
>>>>> printf("%d", CHOLMOD_MAIN_VERSION);
>>>>> #endif
>>>>> #endif
>>>>> return 0;
>>>>> }
>>>>>
>>>>> Error message:
>>>>> /usr/bin/ld: cannot find -llapack
>>>>> collect2: ld returned 1 exit status
>>>>>
>>>>> Garth
>>>>>
>>>>> DOLFIN wrote:
>>>>>> One or more new changesets pushed to the primary dolfin repository.
>>>>>> A short summary of the last three changesets is included below.
>>>>>>
>>>>>> changeset: 4599:bcc140c752dceba8fd4cf370997ad457871e3bbe
>>>>>> tag: tip
>>>>>> user: Johannes Ring <[EMAIL PROTECTED]>
>>>>>> date: Mon Aug 18 13:09:15 2008 +0200
>>>>>> files: SConstruct dolfin/scons.cfg
>>>>>> description:
>>>>>> Added CHOLMOD as optional dependency.
>>>>>>
>>>>>>
>>>>>> changeset: 4598:1a2d241d7d00401800fa1dbe2a17aa75287479c8
>>>>>> user: Johannes Ring <[EMAIL PROTECTED]>
>>>>>> date: Mon Aug 18 13:08:37 2008 +0200
>>>>>> files: scons/simula-scons/simula_scons/Customize.py
>>>>>> scons/simula-scons/simula_scons/__init__.py
>>>>>> scons/simula-scons/simula_scons/pkgconfig.py
>>>>>> scons/simula-scons/simula_scons/pkgconfiggenerators/cholmod.py
>>>>>> scons/simula-scons/simula_scons/pkgconfiggenerators/commonPkgConfigUtils.py
>>>>>> description:
>>>>>> simula-scons update.
>>>>>>
>>>>>>
>>>>>> changeset: 4597:52fe4d684f7e7703f285d9dbb5237926e817b73e
>>>>>> parent: 4594:e92305bdc5377cd49f854d1d835b749fadb835b7
>>>>>> parent: 4596:7a229461cb9d1e29f0e4e8c9d98c6d321759d15b
>>>>>> user: "Garth N. Wells <[EMAIL PROTECTED]>"
>>>>>> date: Mon Aug 18 11:03:17 2008 +0100
>>>>>> files:
>>>>>> description:
>>>>>> merge.
>>>>>>
>>>>>> ----------------------------------------------------------------------
>>>>>> For more details, visit http://www.fenics.org/hg/dolfin
>>>>>> _______________________________________________
>>>>>> DOLFIN-dev mailing list
>>>>>> [email protected]
>>>>>> http://www.fenics.org/mailman/listinfo/dolfin-dev
>>>>> _______________________________________________
>>>>> DOLFIN-dev mailing list
>>>>> [email protected]
>>>>> http://www.fenics.org/mailman/listinfo/dolfin-dev
>>>>>
>>>> _______________________________________________
>>>> DOLFIN-dev mailing list
>>>> [email protected]
>>>> http://www.fenics.org/mailman/listinfo/dolfin-dev
>>
>
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