Re: [gentoo-science] [sage-on-gentoo] Sage 7.3 crashes

2016-10-18 Thread François Bissey 
I don’t think your situation is possible without mixing stuff
from the main tree (blas) and the science overlay. I didn’t even
realise you could mix, but I don’t think that is sane.
gsl from the science overlay is unfortunately not in a good shape
and I don’t recommend to use it as cblas.

Unless there are particular reasons for not doing so, I would recommend
that you use openblas from the science overlay for both blas and cblas.
The following useflags for openblas are sane:
“int64 threads -openmp”
You’ll want to re-emerge lapack-reference once openblas is eselected.
For sanity.

François

> On 18/10/2016, at 20:43, v...@ukr.net wrote:
> 
> On Tue, 18 Oct 2016 09:11:59 +1300
> François Bissey  wrote:
> 
>> ... If you have
>> "-lreflapack" what blas are you using if not "refblas"?
>> So does /usr/lib64/libgslcblas.so exist on your system?
>> Is /usr/lib64/libblas.so a dangling symlink (point to nothing)?
>> 
> Here is the output:
> 
> $ eselect blas list
> Available providers for blas:
>  [1]   reference *
> 
> $ ls -l /usr/lib64/libgslcblas.so
> lrwxrwxrwx 1 root root 20 бер 28  2016 /usr/lib64/libgslcblas.so -> 
> libgslcblas.so.0.0.0
> $ ls -l /usr/lib64/libgslcblas.so.0.0.0 
> -rwxr-xr-x 1 root root 251720 бер 28  2016 /usr/lib64/libgslcblas.so.0.0.0
> 
> $ ls -l /usr/lib64/libblas.so
> lrwxrwxrwx 1 root root 12 гру 15  2015 /usr/lib64/libblas.so -> libblas.so.3
> $ ls -l /usr/lib64/libblas.so.3
> lrwxrwxrwx 1 root root 16 гру 15  2015 /usr/lib64/libblas.so.3 -> 
> libblas.so.3.6.0
> $ ls -l /usr/lib64/libblas.so.3.6.0 
> -rwxr-xr-x 1 root root 362384 гру 15  2015 /usr/lib64/libblas.so.3.6.0
> 
> 
> So both files do exist.
> As of the GSL, it looks like on my system it is installed from 'science' 
> overlay:
> 
> $ emerge -vp gsl
> [ebuild   R] sci-libs/gsl-2.1:0/19::science  USE="-cblas-external -int64 
> -static-libs" ABI_X86="(64) -32" 0 KiB
> 
> Should I install the GSL from the main Portage tree instead?
>  Vladimir
> - 
> 
>

Re: [gentoo-science] [sage-on-gentoo] Sage 7.3 crashes

2016-10-17 Thread François Bissey 

> On 18/10/2016, at 09:35, Steven Trogdon  wrote:
> 
> On Tue, 18 Oct 2016 09:11:59 +1300
> François Bissey  wrote:
> 
>> On 18/10/16 06:10, v...@ukr.net wrote:
>>>  Hello!
>>> 
>>> On Mon, 17 Oct 2016 21:55:18 +1300
>>> François Bissey  wrote:
>>> 
 OK so I checked on my other machine. liblinbox.so should have been
 linked to (c)blas and so should have matrix_modn_dense_float.so
 independently. Because you didn’t get any complaints from ldd
 on liblinbox.so I’ll assume that it was missing/not properly
 detected when linbox was built. The way matrix_modn_dense_float.so
 is built also suggest that cblas was missing when built.
 
 What does
 pkg-config —libs cblas
 pkg-config —libs blas
 pkg-config —libs lapack
 report?
 
>>> $ pkg-config --libs cblas
>>> -lgsl
>>> 
>>> $ pkg-config --libs blas
>>> -lblas
>>> 
>>> $ pkg-config --libs lapack
>>> -lreflapack -lblas
>>> 
>> 
>> Smells like a system using the main tree blas/lapack rather
>> than the science overlay. I may have to enforce something
>> there. Anyway those are very strange answers nonetheless.
>> I would expect "-lgslcblas" not "-lgsl". If you have
>> "-lreflapack" what blas are you using if not "refblas"?
>> So does /usr/lib64/libgslcblas.so exist on your system?
>> Is /usr/lib64/libblas.so a dangling symlink (point to nothing)?
>> 
>> Francois
>> 
>> 
> 
> OK, the blas does appear to be perhaps dangling, but the the cblas looks like
> what was reported at https://github.com/cschwan/sage-on-gentoo/issues/429.

Good point Steve! I had forgotten about that. And since no one seems 
to care about https://github.com/gentoo-science/sci/pull/638
It is likely to stay that way unless I include it in the sage-on-gentoo
overlay.

Remember folks, gsl from the science overlay is broken.

François

Re: [gentoo-science] [sage-on-gentoo] Sage 7.3 crashes

2016-10-17 Thread François Bissey 

On 18/10/16 06:10, v...@ukr.net wrote:

  Hello!

On Mon, 17 Oct 2016 21:55:18 +1300
François Bissey  wrote:


OK so I checked on my other machine. liblinbox.so should have been
linked to (c)blas and so should have matrix_modn_dense_float.so
independently. Because you didn’t get any complaints from ldd
on liblinbox.so I’ll assume that it was missing/not properly
detected when linbox was built. The way matrix_modn_dense_float.so
is built also suggest that cblas was missing when built.

What does
pkg-config —libs cblas
pkg-config —libs blas
pkg-config —libs lapack
report?


$ pkg-config --libs cblas
-lgsl

$ pkg-config --libs blas
-lblas

$ pkg-config --libs lapack
-lreflapack -lblas



Smells like a system using the main tree blas/lapack rather
than the science overlay. I may have to enforce something
there. Anyway those are very strange answers nonetheless.
I would expect "-lgslcblas" not "-lgsl". If you have
"-lreflapack" what blas are you using if not "refblas"?
So does /usr/lib64/libgslcblas.so exist on your system?
Is /usr/lib64/libblas.so a dangling symlink (point to nothing)?

Francois

Re: [gentoo-science] [sage-on-gentoo] Sage 7.3 crashes

2016-10-17 Thread François Bissey 
OK so I checked on my other machine. liblinbox.so should have been
linked to (c)blas and so should have matrix_modn_dense_float.so
independently. Because you didn’t get any complaints from ldd
on liblinbox.so I’ll assume that it was missing/not properly 
detected when linbox was built. The way matrix_modn_dense_float.so
is built also suggest that cblas was missing when built.

What does 
pkg-config —libs cblas
pkg-config —libs blas
pkg-config —libs lapack
report? 

So First linbox needs to be rebuilt and we have to make sure that
blas is picked up at configuration time and in the final linking.

François

> On 14/10/2016, at 10:00, François Bissey  wrote:
> 
> It is quite strange linbox should be linked to blas and lapack.
> Something didn't work properly when you installed it, or possibly
> fflas-ffpack.
> 
> I'll need to get on my home box where I have a 7.3 install. The combo
> givaro/fflas-ffpack/linbox is locked to particular version sets which
> makes it hard to inspect when it is changing (and it is changing in 7.4
> which the one I have on my dev box here at work).
> 
> Francois
> 
> On 14/10/16 09:48, v...@ukr.net wrote:
>> 
>> On Fri, 14 Oct 2016 07:48:55 +1300
>> "François Bissey"  wrote:
>> 
>>> Sorry, I forgot you are on sage 7.3, so you have an older
>>> version of linbox without a .pc file.
>>> So instead I’ll need
>>> ldd -r /usr/lib64/liblinbox.so.0
>>> readelf -d /usr/lib64/liblinbox.so.0
>>> 
>>  Here is the output:
>> 
>> ldd -r /usr/lib64/liblinbox.so.0
>>  linux-vdso.so.1 (0x7ffcbd902000)
>>  libgivaro.so.0 => /usr/lib64/libgivaro.so.0 (0x7f2b65d26000)
>>  libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.so.6 
>> (0x7f2b65926000)
>>  libc.so.6 => /lib64/libc.so.6 (0x7f2b6558e000)
>>  libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libgcc_s.so.1 
>> (0x7f2b65377000)
>>  libgmpxx.so.4 => /usr/lib64/libgmpxx.so.4 (0x7f2b6517)
>>  libgmp.so.10 => /usr/lib64/libgmp.so.10 (0x7f2b64ef6000)
>>  libm.so.6 => /lib64/libm.so.6 (0x7f2b64bf3000)
>>  /lib64/ld-linux-x86-64.so.2 (0x5627f49a7000)
>> 
>> ===
>> 
>> readelf -d /usr/lib64/liblinbox.so.0
>> 
>> Dynamic section at offset 0x6d40 contains 29 entries:
>>  TagType Name/Value
>> 0x0001 (NEEDED) Shared library: [libgivaro.so.0]
>> 0x0001 (NEEDED) Shared library: [libstdc++.so.6]
>> 0x0001 (NEEDED) Shared library: [libc.so.6]
>> 0x0001 (NEEDED) Shared library: [libgcc_s.so.1]
>> 0x000e (SONAME) Library soname: [liblinbox.so.0]
>> 0x000c (INIT)   0x25b0
>> 0x000d (FINI)   0x525c
>> 0x0019 (INIT_ARRAY) 0x206d08
>> 0x001b (INIT_ARRAYSZ)   40 (bytes)
>> 0x001a (FINI_ARRAY) 0x206d30
>> 0x001c (FINI_ARRAYSZ)   8 (bytes)
>> 0x0004 (HASH)   0x1c8
>> 0x6ef5 (GNU_HASH)   0x618
>> 0x0005 (STRTAB) 0x10b8
>> 0x0006 (SYMTAB) 0x7b8
>> 0x000a (STRSZ)  2847 (bytes)
>> 0x000b (SYMENT) 24 (bytes)
>> 0x0003 (PLTGOT) 0x206fe8
>> 0x0002 (PLTRELSZ)   1344 (bytes)
>> 0x0014 (PLTREL) RELA
>> 0x0017 (JMPREL) 0x2070
>> 0x0007 (RELA)   0x1d58
>> 0x0008 (RELASZ) 792 (bytes)
>> 0x0009 (RELAENT)24 (bytes)
>> 0x6ffe (VERNEED)0x1c98
>> 0x6fff (VERNEEDNUM) 3
>> 0x6ff0 (VERSYM) 0x1bd8
>> 0x6ff9 (RELACOUNT)  13
>> 0x (NULL)   0x0
>> 
>> =
>> 
>> Regards,
>>  Vladimir
>> -
>> 
>> 
> 
>

Re: [gentoo-science] [sage-on-gentoo] Sage 7.3 crashes

2016-10-13 Thread v_2e 

On Fri, 14 Oct 2016 07:48:55 +1300
"François Bissey"  wrote:

> Sorry, I forgot you are on sage 7.3, so you have an older
> version of linbox without a .pc file.
> So instead I’ll need 
> ldd -r /usr/lib64/liblinbox.so.0
> readelf -d /usr/lib64/liblinbox.so.0
> 
  Here is the output:

ldd -r /usr/lib64/liblinbox.so.0
linux-vdso.so.1 (0x7ffcbd902000)
libgivaro.so.0 => /usr/lib64/libgivaro.so.0 (0x7f2b65d26000)
libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.so.6 
(0x7f2b65926000)
libc.so.6 => /lib64/libc.so.6 (0x7f2b6558e000)
libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libgcc_s.so.1 
(0x7f2b65377000)
libgmpxx.so.4 => /usr/lib64/libgmpxx.so.4 (0x7f2b6517)
libgmp.so.10 => /usr/lib64/libgmp.so.10 (0x7f2b64ef6000)
libm.so.6 => /lib64/libm.so.6 (0x7f2b64bf3000)
/lib64/ld-linux-x86-64.so.2 (0x5627f49a7000)

===

 readelf -d /usr/lib64/liblinbox.so.0

Dynamic section at offset 0x6d40 contains 29 entries:
  TagType Name/Value
 0x0001 (NEEDED) Shared library: [libgivaro.so.0]
 0x0001 (NEEDED) Shared library: [libstdc++.so.6]
 0x0001 (NEEDED) Shared library: [libc.so.6]
 0x0001 (NEEDED) Shared library: [libgcc_s.so.1]
 0x000e (SONAME) Library soname: [liblinbox.so.0]
 0x000c (INIT)   0x25b0
 0x000d (FINI)   0x525c
 0x0019 (INIT_ARRAY) 0x206d08
 0x001b (INIT_ARRAYSZ)   40 (bytes)
 0x001a (FINI_ARRAY) 0x206d30
 0x001c (FINI_ARRAYSZ)   8 (bytes)
 0x0004 (HASH)   0x1c8
 0x6ef5 (GNU_HASH)   0x618
 0x0005 (STRTAB) 0x10b8
 0x0006 (SYMTAB) 0x7b8
 0x000a (STRSZ)  2847 (bytes)
 0x000b (SYMENT) 24 (bytes)
 0x0003 (PLTGOT) 0x206fe8
 0x0002 (PLTRELSZ)   1344 (bytes)
 0x0014 (PLTREL) RELA
 0x0017 (JMPREL) 0x2070
 0x0007 (RELA)   0x1d58
 0x0008 (RELASZ) 792 (bytes)
 0x0009 (RELAENT)24 (bytes)
 0x6ffe (VERNEED)0x1c98
 0x6fff (VERNEEDNUM) 3
 0x6ff0 (VERSYM) 0x1bd8
 0x6ff9 (RELACOUNT)  13
 0x (NULL)   0x0

=

Regards,
  Vladimir
-

Re: [gentoo-science] [sage-on-gentoo] Sage 7.3 crashes

2016-10-13 Thread v_2e 
On Thu, 13 Oct 2016 08:54:51 +1300
François Bissey  wrote:

> OK for some reason it wasn't linked to cblas. What does
> pkg-config --libs linbox
> says?
> 
pkg-config --libs linbox

Package linbox was not found in the pkg-config search path.
Perhaps you should add the directory containing `linbox.pc'
to the PKG_CONFIG_PATH environment variable
Package 'linbox', required by 'world', not found


  Vladimir

-

Re: [gentoo-science] [sage-on-gentoo] Sage 7.3 crashes

2016-10-12 Thread François Bissey 

OK for some reason it wasn't linked to cblas. What does
pkg-config --libs linbox
says?

Francois

On 13/10/16 04:11, v...@ukr.net wrote:

On Wed, 12 Oct 2016 07:36:16 +1300
François Bissey  wrote:


ldd
-r /usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so
and readelf
-d /usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so
output please.


ldd
-r /usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so

linux-vdso.so.1 (0x7fffc89f3000)
liblinbox.so.0 => /usr/lib64/liblinbox.so.0 (0x7fa93942a000)
libgivaro.so.0 => /usr/lib64/libgivaro.so.0 (0x7fa9391cb000)
libgmp.so.10 => /usr/lib64/libgmp.so.10 (0x7fa938f51000)
libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libstdc++.so.6 
(0x7fa938b52000)
libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 
(0x7fa938771000)
libm.so.6 => /lib64/libm.so.6 (0x7fa93846d000)
libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/libgcc_s.so.1 
(0x7fa938256000)
libc.so.6 => /lib64/libc.so.6 (0x7fa937ebe000)
libgmpxx.so.4 => /usr/lib64/libgmpxx.so.4 (0x7fa937cb6000)
/lib64/ld-linux-x86-64.so.2 (0x55f9329e7000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x7fa937a99000)
libdl.so.2 => /lib64/libdl.so.2 (0x7fa937895000)
libutil.so.1 => /lib64/libutil.so.1 (0x7fa937691000)
undefined symbol: cblas_dger
(/usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
undefined symbol: cblas_strsm   
(/usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
undefined symbol: cblas_sgemm   
(/usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
undefined symbol: cblas_dgemm   
(/usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
undefined symbol: cblas_sgemv   
(/usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
undefined symbol: cblas_strmm   
(/usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
undefined symbol: cblas_dgemv   
(/usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)


==

readelf -d 
/usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so

Dynamic section at offset 0x75a68 contains 32 entries:
  TagType Name/Value
 0x0001 (NEEDED) Shared library: [liblinbox.so.0]
 0x0001 (NEEDED) Shared library: [libgivaro.so.0]
 0x0001 (NEEDED) Shared library: [libgmp.so.10]
 0x0001 (NEEDED) Shared library: [libstdc++.so.6]
 0x0001 (NEEDED) Shared library: [libpython2.7.so.1.0]
 0x0001 (NEEDED) Shared library: [libm.so.6]
 0x0001 (NEEDED) Shared library: [libgcc_s.so.1]
 0x0001 (NEEDED) Shared library: [libc.so.6]
 0x000c (INIT)   0xe620
 0x000d (FINI)   0x6cbb8
 0x0019 (INIT_ARRAY) 0x275950
 0x001b (INIT_ARRAYSZ)   16 (bytes)
 0x001a (FINI_ARRAY) 0x275960
 0x001c (FINI_ARRAYSZ)   8 (bytes)
 0x0004 (HASH)   0x1c8
 0x6ef5 (GNU_HASH)   0x10d0
 0x0005 (STRTAB) 0x4198
 0x0006 (SYMTAB) 0x1ab0
 0x000a (STRSZ)  22135 (bytes)
 0x000b (SYMENT) 24 (bytes)
 0x0003 (PLTGOT) 0x275fe8
 0x0002 (PLTRELSZ)   6696 (bytes)
 0x0014 (PLTREL) RELA
 0x0017 (JMPREL) 0xcbf8
 0x0007 (RELA)   0x9c70
 0x0008 (RELASZ) 12168 (bytes)
 0x0009 (RELAENT)24 (bytes)
 0x6ffe (VERNEED)0x9b50
 0x6fff (VERNEEDNUM) 4
 0x6ff0 (VERSYM) 0x9810
 0x6ff9 (RELACOUNT)  383
 0x (NULL)   0x0



  Vladimir

-

Re: [gentoo-science] [sage-on-gentoo] Sage 7.3 crashes

2016-10-11 Thread François Bissey 
ldd -r /usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so
and
readelf -d 
/usr/lib64/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so
output please.

François

> On 12/10/2016, at 00:40, v...@ukr.net wrote:
> 
>  Hello!
>  I have recently upgraded to Sage 7.3, but now I cannot start it. 
> It says:
> 
>Oops, Sage crashed. We do our best to make it stable, but...
> 
> and generates the crash report which I put here:
> https://paste.pound-python.org/show/XpqSnolgiEfkYmPMv50v/
> 
> I am not sure if I should report it upstream or Gentoo developers, so I
> decided to start here.
> 
>  Regards,
>Vladimir
> 
> - 
> 
>