lapackpp-devel — Discussion of Lapack++ development

Re: [Lapackpp-devel] assert(cI.end() >= 0) (was: Interesting crash in QR solve)

[Christian S. <sti...@tu...>]

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Dear Michael,

thank you for your nice feedback. I'd happily try to fix these bugs,
although I probably need some assistance to track them down. I'll reply
to both bugs in individual posts; first this one:

Michael Price schrieb:
> situations: printing out matrices, and linear systems solution.  (I 
> don't remember seeing the problem when using LU, only QR and SVD.)  
> First, sometimes the assertion
> 
>     assert(cI.end() >= 0); (mtmpl.h, line 279)
> 
> fails.

This assertion should only be reached when you used negative increments
for a submatrix index; do you really use negative increments? I would
certainly agree that several functions have never been tested with
negative increments, only with positive ones, so there can very well be
a bug in there. The assertion is perfectly valid and if it fails then it
means that probably somewhere else some code is wrong if the increments
are negative (instead of positive). Could you submit a code snippet that
 crashes with that assertion? Thanks.

Christian
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[Lapackpp-devel] Interesting crash in QR solve

[Michael P. <mr...@cm...>]

Dear Christian and others,

I am thankful for this library to avoid calling LAPACK functions 
directly, but I'm having trouble from memory corruption in two 
situations: printing out matrices, and linear systems solution.  (I 
don't remember seeing the problem when using LU, only QR and SVD.)  
First, sometimes the assertion

    assert(cI.end() >= 0); (mtmpl.h, line 279)

fails.   The main issue is a strange crash, which I was able to track 
down in valgrind (since the stack in GDB is messed up):

==16581== Invalid write of size 4
==16581==    at 0x40635D7: dgels_ (in /usr/local/lib/liblapackpp.so.1.13.0)
==16581==    by 0x4031EA1: LaQRLinearSolveIP(LaGenMatDouble&, 
LaGenMatDouble&, L aGenMatDouble const&) (linslv.cc:220)
==16581==    by 0x4032141: LaQRLinearSolve(LaGenMatDouble const&, 
LaGenMatDouble &, LaGenMatDouble const&) (linslv.cc:160)
==16581==    by 0x4032BD7: LaLinearSolve(LaGenMatDouble const&, 
LaGenMatDouble&,  LaGenMatDouble const&) (linslv.cc:56)
==16581==    by 0x805385D: Patch::solve() (in 
/home/mrprice/student_projects/IAV /segmenter/segmenter)
==16581==    by 0x8054388: SurfaceFit::solve() (in 
/home/mrprice/student_project s/IAV/segmenter/segmenter)
==16581==    by 0x804AE39: Segmenter::surfacefit() (segmenter.cpp:935)
==16581==    by 0x804A480: main (main.cpp:133)
==16581==  Address 0x6DC5C10 is 0 bytes after a block of size 16 alloc'd
==16581==    at 0x40057E9: operator new[](unsigned) 
(vg_replace_malloc.c:195)
==16581==    by 0x4052287: VectorDouble::VectorDouble(unsigned) (vd.h:46)
==16581==    by 0x403701F: LaGenMatDouble::LaGenMatDouble(int, int) 
(gmd.cc:62)
==16581==    by 0x4042954: LaGenMatDouble::resize(int, int) (mtmpl.h:189)
==16581==    by 0x4042C2D: LaGenMatDouble::resize(LaGenMatDouble const&) 
(gmtmpl .cc:113)
==16581==    by 0x4044A1B: LaGenMatDouble::copy(LaGenMatDouble const&) 
(mtmpl.h: 210)
==16581==    by 0x4031E0D: LaQRLinearSolveIP(LaGenMatDouble&, 
LaGenMatDouble&, L aGenMatDouble const&) (gmd.h:665)
==16581==    by 0x4032141: LaQRLinearSolve(LaGenMatDouble const&, 
LaGenMatDouble &, LaGenMatDouble const&) (linslv.cc:160)
==16581==    by 0x4032BD7: LaLinearSolve(LaGenMatDouble const&, 
LaGenMatDouble&,  LaGenMatDouble const&) (linslv.cc:56)
==16581==    by 0x805385D: Patch::solve() (in 
/home/mrprice/student_projects/IAV /segmenter/segmenter)
==16581==    by 0x8054388: SurfaceFit::solve() (in 
/home/mrprice/student_project s/IAV/segmenter/segmenter)
==16581==    by 0x804AE39: Segmenter::surfacefit() (segmenter.cpp:935)
==16581==
==16581== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- y
starting debugger
==16581== starting debugger with cmd: /usr/bin/gdb -nw 
/proc/16618/fd/1014 16618
GNU gdb Red Hat Linux (6.3.0.0-1.122rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain 
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "i386-redhat-linux-gnu"...Using host 
libthread_db lib rary "/lib/libthread_db.so.1".

Attaching to program: /proc/16618/fd/1014, process 16618
Reading symbols from shared object read from target memory...done.
Loaded system supplied DSO at 0x37fff000
`shared object read from target memory' has disappeared; keeping its 
symbols.
0x040635d7 in ?? ()
(gdb) bt
#0  0x040635d7 in ?? ()
#1  0xbef53da4 in ?? ()
#2  0xbef53d6c in ?? ()
#3  0x00000001 in ?? ()
#4  0x00929300 in ?? ()
#5  0x00000000 in ?? ()

Here's the code in question, it's just a variable-order polynomial least 
squares fit function.  I have checked (using valgrind) and found no 
memory leaks or other issues up to this point.

void Patch::solve()
{
    int i = 0;
    int j = 0;
    surfcoord x = 0, y = 0, z = 0;
    int eq_size = PATCH_EQ_LENGTH;
    switch (MAX_ORDER)
    {
    case 1: eq_size = 3;    break;
    case 2: eq_size = 6;    break;
    case 3: eq_size = 10;    break;
    case 4: eq_size = 15;    break;
    }
    //    Every patch makes a 15x15 square in the matrix AtA
    LaGenMatDouble A(num_points, eq_size);
    LaVectorDouble b(num_points);
    LaVectorDouble eq(eq_size);
       
    for (j = 0; j < num_points; j++)
    {
        x = points[j * 3];
        y = points[j * 3 + 1];
        z = points[j * 3 + 2];
   
        A(j, 0) = 1;                   
        A(j, 1) = x;           
        A(j, 2) = y;   

        if (MAX_ORDER >= 2)
        {
            A(j, 3) = x * x;
            A(j, 4) = x * y;
            A(j, 5) = y * y;
        }
        if (MAX_ORDER >= 3)
        {
            A(j, 6) = A(j, 3) * x;
            A(j, 7) = A(j, 3) * y;
            A(j, 8) = A(j, 5) * x;
            A(j, 9) = A(j, 5) * y;
        }
        if (MAX_ORDER >= 4)
        {
            A(j, 10) = A(j, 6) * x;
            A(j, 11) = A(j, 6) * y;
            A(j, 12) = A(j, 3) * A(j, 5);
            A(j, 13) = A(j, 9) * x;
            A(j, 14) = A(j, 9) * y;
        }

        b(j) = z;
    }
  
    LaLinearSolve(A, eq, b);

    for (j = 0; j < eq_size; j++)
    {
        equation[j] = eq2(j);
    }

}

I don't know the workings of Lapack++ too well, but it sounds like the 
workspace of the Fortran function may not have been allocated correctly 
in LaQRLinearSolveIP().  Have you seen this problem before, or know how 
to fix it?

Thanks
Michael

[Lapackpp-devel] many thanks

[Do bi <mrc...@ya...>]

I appreciate the genius work of the Lapackpp group. Maybe very soon I will get much better in C++ and software, so that I may be able to contribute some code. I thank Christian Stimming, and I will be following his ansers to my last question shortly.
  Regards
  Donald

 		
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Re: [Lapackpp-devel] almost succeded

[Christian S. <sti...@tu...>]

Am Samstag, 1. Juli 2006 01:17 schrieb Do bi:
> In compiling lapackpp.vcproj, I encounter this:
>   LINK : fatal error LNK1181: cannot open input file 'liblapack32.lib'

The linker library file "liblapack32.lib" (without the "pp") is needed 
together with "liblapack32.dll", and both are contained in the setup.exe 
package of lapackpp-2.4.10. In order for the compiler/linker to find the file 
"liblapack32.lib", you need to specify the directory where it is located in 
the setting "Linker -> General -> Input directories" (or similar). If you 
installed the setup.exe into c:\Lapackpp, then the respective directory would 
be c:\Lapackpp\lib . This is where libblas32.lib and liblapack32.lib is 
located.

Christian

[Lapackpp-devel] gcc compilet

[Do bi <mrc...@ya...>]

Dear Christian, in a previous message (2005) to a fellow member, you wrote " The only alternative would be to try to compile lapack++ from its source 
 code with the vc6 compiler. However, I have never done this and I 
 believe this requires a lot of work. In other words, on windows you can 
 use lapack++ only for the gcc compiler."
   
  Given that I use VC++ :net, and not the gcc compiler, do you mean I cannot use Lapackpp?
 


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[Lapackpp-devel] almost succeded

[Do bi <mrc...@ya...>]

In compiling lapackpp.vcproj, I encounter this:
  LINK : fatal error LNK1181: cannot open input file 'liblapack32.lib'
   
  Please help. Thanks

 		
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[Lapackpp-devel] 'lapackpp.lib'

[Do bi <mrc...@ya...>]

  Although you did not mention 'lapackpp.lib' I have an error about it.
  LINK : fatal error LNK1181: cannot open input file 'lapackpp.lib'
  Where can I find 'lapackpp.lib' in lapackpp.vcproj? What should I do?

 		
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Re: [Lapackpp-devel] almost succeeded

[Do bi <mrc...@ya...>]

  After coping and pasting the lapackpp.lib.intermedtiate.manifest into my project directory, I try to invoke LaGenMatDouble (8,8); and this is what I get. I have included all the necessary files.
   
  trixTest.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall LaGenMatDouble::~LaGenMatDouble(void)" (__imp_??1LaGenMatDouble@@UAE@XZ) referenced in function _wmain
   
  MatrixTest.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall LaGenMatDouble::LaGenMatDouble(int,int)" (__imp_??0LaGenMatDouble@@QAE@HH@Z) referenced in function _wmain
  C:\Documents and Settings\dbesong\My Documents\Visual Studio 2005
   
  \Projects\MatrixTest\Debug\MatrixTest.exe : fatal error LNK1120: 2 unresolved external
   
Do bi <mrc...@ya...> wrote:
    Hi there. I followed all the instructions for lapack. Compiling lapackp.vcproj, I got one error:
   
  LINK : fatal error LNK1181: cannot open input file 'liblapack32.lib'
   
   and 19 warnings of this sort: 
   
  warning C4275: non dll-interface class 'std::runtime_error' used as base for dll-interface class 'LaException'
  C:\Program Files (x86)\Microsoft Visual Studio 8\VC\include\stdexcept(149) : see declaration of 'std::runtime_error'
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Re: [Lapackpp-devel] almost succeeded

[Do bi <mrc...@ya...>]

Yes, i think I got it, but instead of having the lapackpp.dll I have lapackpp.dll.manifest
  Wht do I do? Change the name?

Do bi <mrc...@ya...> wrote:
    Hi there. I followed all the instructions for lapack. Compiling lapackp.vcproj, I got one error:
   
  LINK : fatal error LNK1181: cannot open input file 'liblapack32.lib'
   
   and 19 warnings of this sort: 
   
  warning C4275: non dll-interface class 'std::runtime_error' used as base for dll-interface class 'LaException'
  C:\Program Files (x86)\Microsoft Visual Studio 8\VC\include\stdexcept(149) : see declaration of 'std::runtime_error'
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[Lapackpp-devel] almost succeeded

[Do bi <mrc...@ya...>]

Hi there. I followed all the instructions for lapack. Compiling lapackp.vcproj, I got one error:
   
  LINK : fatal error LNK1181: cannot open input file 'liblapack32.lib'
   
   and 19 warnings of this sort: 
   
  warning C4275: non dll-interface class 'std::runtime_error' used as base for dll-interface class 'LaException'
  C:\Program Files (x86)\Microsoft Visual Studio 8\VC\include\stdexcept(149) : see declaration of 'std::runtime_error'

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Re: [Lapackpp-devel] vc++ and lapackpp

[Do bi <mrc...@ya...>]

sorry 2.0x is the version numbers of my .Net framework. The number of my VC is 8.0x

Christian Stimming <sti...@tu...> wrote:  -----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

General answer to your questions: You need to compile the lapackpp
library (DLL) yourself in order to use it. Obviously you are not very
familiar with the process of compiling a DLL. I can help a little bit,
but I'm neither willing nor able to give you a full-fledged introduction
into how to use a compiler. You might want to consider using a different
tool for completing your homework if you're in a hurry here and if
you're not willing or able to work with your compiler yourself.

Here are quick answers:

Do bi schrieb:
> I am using Microsoft Visual Studio version 2.0.50727

Are you really sure this is the only version number and it is the
version number of your compiler? I know of "Microsoft Visual Studio"
versions 6.x, 7.0.x, 7.1.x and maybe higher (8.x?), but *not* 2.0.x.
Additionally, the "About" box will show you the version number of the
"Microsoft .NET Framework", which is 1.1.x here, but that doesn't matter
for a C++ project. If you are really using MSVC version 2.x, then this
is way too old and lapackpp will not compile with this. You need at
least 6.0.

> 1. Install the .exe setup package( *I did this* )
> but it does not contain any auxiliary libraries BLAS32.DLL and others;

Yes it does. Where did you look for BLAS32.DLL? It installs BLAS32.DLL
into your c:\windows, and BLAS32.LIB into c:\program-files\lapackpp\lib
(or whatever directory prefix you have chosen).

> 2. Unpack the tar.gz package with the source code:
> *do you mean unzipping the lapackpp-2.4.10.tar file?*

http://sourceforge.net/project/showfiles.php?group_id=99696 says there
is exactly one file ending with "tar.gz".

> *What do you mean "with the source code", where is it?

In the directories extracted from that package?

> 3. compile the source code using the provided
> lapackpp.vcproj MSVC project file, which will also
> compile two small test programs. You might have to adapt the
> linker input directories (Project Properties -> Linker -> Input)
> so that the BLAS32.DLL library can be found.
> 
> *I saw the lapackpp.vcproj, but how do I compile the soucecode with it?*

Like, opening it with your MSVC compiler? And clicking Compile -> Build All?

> *When I do "Project Properties -> Linker -> Input" what should i do, add
> a file, which file or directory? *

If you don't know what I mean, then just ignore it. You will encounter
the respective error message early enough.

> 4. After successfully compiling the DLL, you need to copy the
> LAPACKPP.DLL file to whatever location you consider
> appropriate. This can either be your c:\WINNT directory, or the
> working directory of your actual application that should use
> lapackpp.
> 
> *Do you mean copying Lapackpp.ddl or addin it through project->properties*

By "copy the LAPACKPP.DLL file" I indeed mean "copying lapackpp.dll", yes.

Christian
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Re: [Lapackpp-devel] vc++ and lapackpp

[Christian S. <sti...@tu...>]

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Hash: SHA1

General answer to your questions: You need to compile the lapackpp
library (DLL) yourself in order to use it. Obviously you are not very
familiar with the process of compiling a DLL. I can help a little bit,
but I'm neither willing nor able to give you a full-fledged introduction
into how to use a compiler. You might want to consider using a different
tool for completing your homework if you're in a hurry here and if
you're not willing or able to work with your compiler yourself.

Here are quick answers:

Do bi schrieb:
> I am using Microsoft Visual Studio version 2.0.50727

Are you really sure this is the only version number and it is the
version number of your compiler? I know of "Microsoft Visual Studio"
versions 6.x, 7.0.x, 7.1.x and maybe higher (8.x?), but *not* 2.0.x.
Additionally, the "About" box will show you the version number of the
"Microsoft .NET Framework", which is 1.1.x here, but that doesn't matter
for a C++ project. If you are really using MSVC version 2.x, then this
is way too old and lapackpp will not compile with this. You need at
least 6.0.

> 1. Install the .exe setup package( *I did this* )
> but it does not contain any auxiliary libraries BLAS32.DLL and others;

Yes it does. Where did you look for BLAS32.DLL? It installs BLAS32.DLL
into your c:\windows, and BLAS32.LIB into c:\program-files\lapackpp\lib
(or whatever directory prefix you have chosen).

> 2. Unpack the tar.gz package with the source code:
> *do you mean unzipping the lapackpp-2.4.10.tar file?*

http://sourceforge.net/project/showfiles.php?group_id=99696 says there
is exactly one file ending with "tar.gz".

> *What do you mean "with the source code", where is it?

In the directories extracted from that package?

>  3. compile the source code using the provided
> lapackpp.vcproj MSVC project file, which will also
> compile two small test programs. You might have to adapt the
> linker input directories (Project Properties -> Linker -> Input)
> so that the BLAS32.DLL library can be found.
>  
> *I saw the lapackpp.vcproj, but how do I compile the soucecode with it?*

Like, opening it with your MSVC compiler? And clicking Compile -> Build All?

> *When I do "Project Properties -> Linker -> Input" what should i do, add
> a file, which file or directory? *

If you don't know what I mean, then just ignore it. You will encounter
the respective error message early enough.

>  4. After successfully compiling the DLL, you need to copy the
> LAPACKPP.DLL file to whatever location you consider
> appropriate. This can either be your c:\WINNT directory, or the
> working directory of your actual application that should use
> lapackpp.
>  
> *Do you mean copying Lapackpp.ddl or addin it through project->properties*

By "copy the LAPACKPP.DLL file" I indeed mean "copying lapackpp.dll", yes.

Christian
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[Lapackpp-devel] vc++ and lapackpp

[Do bi <mrc...@ya...>]

I am using Microsoft Visual Studio version 2.0.50727
  Please help me because this is homework and I need todo it to take my exams. Please. I have inserted my questions into the instructions Christian Stimming sent to me:
   
  For compiling on Windows with MSVC compiler:

 1. Install the .exe setup package( I did this )
  but it does not contain any auxiliary libraries BLAS32.DLL and others;

 2. Unpack the tar.gz package with the source code:
  do you mean unzipping the lapackpp-2.4.10.tar file?
  What do you mean "with the source code", where is it?

 3. compile the source code using the provided
 lapackpp.vcproj MSVC project file, which will also
 compile two small test programs. You might have to adapt the
 linker input directories (Project Properties -> Linker -> Input)
 so that the BLAS32.DLL library can be found.
   
  I saw the lapackpp.vcproj, but how do I compile the soucecode with it?
  When I do "Project Properties -> Linker -> Input" what should i do, add a file, which file or directory?

 4. After successfully compiling the DLL, you need to copy the
 LAPACKPP.DLL file to whatever location you consider
 appropriate. This can either be your c:\WINNT directory, or the
 working directory of your actual application that should use
 lapackpp.
   
  Do you mean copying Lapackpp.ddl or addin it through project->properties


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Re: [Lapackpp-devel] lapack++ in c++.Net

[Christian S. <sti...@tu...>]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Do bi schrieb:
>  I have downloaded lapack. I am using C++.Net. I have incuded the .h
> files, and LaGenMatDouble A() works, but LaGenMatDouble A(8,8) does not
> work. The problem might be that I do not have the ddl's, because I
> looked in the directories and there is none. How do I generate the
> necessary DDL's. More precisely, can you summarise the instructions for
> installing and using Lapack? The instructions on the site are a bit
> ambiguous to me.

Compilation and installation depends on the C++ compiler you are using.
You say "C++.Net", which I guess means you use the "Microsoft Visual
Studio .NET" (MSVC) -- however, you would have to say the version number
as well. (In the compiler, click Help->About, then it says the version
number.)

For compiling on Windows with MSVC compiler:

 1. Install the .exe setup package because it contains the
 auxiliary libraries BLAS32.DLL and others;

 2. Unpack the tar.gz package with the source code, and

 3. compile the source code using the provided
 lapackpp.vcproj MSVC project file, which will also
 compile two small test programs. You might have to adapt the
 linker input directories (Project Properties -> Linker -> Input)
 so that the BLAS32.DLL library can be found.

 4. After successfully compiling the DLL, you need to copy the
 LAPACKPP.DLL file to whatever location you consider
 appropriate. This can either be your c:\WINNT directory, or the
 working directory of your actual application that should use
 lapackpp.

Christian
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[Lapackpp-devel] lapack++ in c++.Net

[Do bi <mrc...@ya...>]

Dear computer devils!!
   I have downloaded lapack. I am using C++.Net. I have incuded the .h files, and LaGenMatDouble A() works, but LaGenMatDouble A(8,8) does not work. The problem might be that I do not have the ddl's, because I looked in the directories and there is none. How do I generate the necessary DDL's. More precisely, can you summarise the instructions for installing and using Lapack? The instructions on the site are a bit ambiguous to me.
Thanks

 		
---------------------------------
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Re: [Lapackpp-devel] Reusing LU Factorization in LAPACK++

[Christian S. <sti...@tu...>]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi,

Bill Woessner schrieb:
>> > According to the project page, the mailing lists are down.
> 
>> Are down? They shouldn't be - where did you read this?
> 
> I misspoke.  The web page says that the archives are disabled.  In
> case you're still wondering, here's the web page in question:
> 
> http://sourceforge.net/mail/?group_id=99696

I see. Yes, that's a temporary problem of sourceforge - I hope they have
this resolved within 2-3 days.

>> Yea, look into the LAPACK++ User's Manual, use the functions from the
>> fmd.h
>> header which will use a class from the gfd.h header but you don't have to
>> care about that class, apart from passing it to the function.
> 
> Sounds like a plan.  I just wanted to make sure this functionality
> wasn't already provided.  Since I'm already familiar with LAPACK and
> calling it from C, this shouldn't be a big problem.

Right. None of this functionality is already being provided by a tested
and verified and documented class in lapackpp. But the code in fmd.h and
gfd.h still exists and if you use it as if you were using the C LAPACK
then everything should be fine.

If it does work correctly, I would be glad to hear about that, because
then I would add the appropriate documentation.

Christian
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Re: [Lapackpp-devel] Reusing LU Factorization in LAPACK++

[Christian S. <sti...@tu...>]

Hi,

Am Mittwoch, 21. Juni 2006 18:31 schrieb Bill Woessner:
> Hi.  I just downloaded and am playing with LAPACK++.  I apologize for
> emailing you directly.  According to the project page, the mailing
> lists are down.

Are down? They shouldn't be - where did you read this?

> I'm looking at the web page
>
> http://lapackpp.sourceforge.net/html/laslv_8h.html
>
> And I have a question.  I can use the function LUFactorizeIP to
> compute the LU factorization of a matrix (presumably by calling
> DGETRF).  But how do I then use the factorization to solve the system
> with a given right hand side?

This particular function obviously cannot do this. Currently there is no C++ 
function available, but:

> The LAPACK routine I want to call is DGETRS.  I searched for it in the
> source base.  It appears in fmd.h and gfd.h.  But neither of those
> files appear in the documentation.

The header files are the correct location. You need to look into the header 
files directly, then you will see in gfd.h that I added a comment that says 
this code is neither tested nor verified and might very well be broken. The 
explanation for this is as follows: I never needed the LU factorization all 
the time since I took over lapack++, so that part was never reviewed and 
verified by me. What I *did* need was a QR factorization, and that's why the 
class LaGenQRFactComplex exists. I just never came around to add a similar 
class for the LU decomposition.

Hm... looking at fmd.h, it seems to me this header file might actually work. 
If you already know DGETRF and DGETRS, then you will find exactly these two 
functions in the fmd.h header file. If I recall correctly, then this is even 
mentioned in that very old "LAPACK++ User's Manual " as mentioned on 
http://lapackpp.sourceforge.net/html/index.html

> Alternatively, I can use the function LaLUInverseIP to explicitly
> compute the inverse.  But that's almost never a good idea.

Right. I didn't like this InverseIP function as well -- maybe I should add 
such a comment to that.

> Can you point me in the right direction, here?

Yea, look into the LAPACK++ User's Manual, use the functions from the fmd.h 
header which will use a class from the gfd.h header but you don't have to 
care about that class, apart from passing it to the function.

Christian

Re: [Lapackpp-devel] lapack++ using mkl?

[Christian S. <sti...@tu...>]

Hi,

Am Montag, 5. Juni 2006 21:37 schrieb Jacob Graham:
> Hi, is it possible to compile lapack++ using the blas/lapack libraries
> within Intel's MKL (Math Kernel Library)? 

I think this should be possible. If I understand correctly, the MKL implements 
the BLAS functions (but in Intel's way) but the function signatures should be 
unchanged? If that is the case, then this will probably be picked up 
correctly during lapackpp's ./configure (you might want to use 
--with-blas=... and --with-lapack=... options for the corresponding library 
names to use).

> Also, is it possible to use the 
> intel compilers icc and ifort? 

In principle this would be possible, but in practice I guess the Intel 
compiler will complain about various gcc-specific c++ features that have been 
used in lapackpp. You would need to fix those one by one (or report them 
here). I think this is not too difficult, but it would require some work 
nevertheless.

> If it's not possible or untested, I suppose 
> I can just go back to good ol' gcc and compile blas/lapack from source....

Sure. That should work anyway.

Christian

[Lapackpp-devel] lapack++ using mkl?

[Jacob G. <gam...@ya...>]

Hi, is it possible to compile lapack++ using the blas/lapack libraries within Intel's MKL (Math Kernel Library)? Also, is it possible to use the intel compilers icc and ifort? If it's not possible or untested, I suppose I can just go back to good ol' gcc and compile blas/lapack from source....

 __________________________________________________
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Re: [Lapackpp-devel] How to solve this compiling error on Compaq Tru64 UNIX

[Christian S. <sti...@tu...>]

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Hash: SHA1

Hi,

I'm sorry, your compiler and stdc++ environment is so different from
what I have that I actually can't help you here. Lapackpp uses the
<iosfwd> include file, which is part of a "normal" standard c++ library,
but if your system has a "non-normal" c++ library, then you have to
figure out the differences for yourself. Same for std::ostringstream.

Maybe instead of <iosfwd> you can include <ostream> or <istream>,
whichever is needed.

Maybe instead of std::ostringstream, the class might be called
std::ostrstream on your system.

Christian

Cheng Guo schrieb:
> It solved the problem, thank you!
> 
> However I encountered  another three kinds of error which I think is
> related. The first kind is like  this:
> _______________________________________________________________________________________
> 
> cxx: Error: ../../include/vd.h, line 119: namespace "std" has no member
>          "ostream"
>    friend std::ostream&   operator<<(std::ostream&, const VectorDouble&);
> ----------------^
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> Deleting all the "std::" in the source file can solve this problem
> thought it's not a very easy task.
> 
> Second problem is:
> _______________________________________________________________________________________
> 
> cxx: Error: /usr/lib/cmplrs/cxx/V6.5-014/include/cxx/iosfwd, line 58:
> #error
>          directive: "cannot include iosfwd -- define __USE_STD_IOSTREAM to
>          override default - see section 7.1.2 of the C++ Using Guide"
> #error "cannot include iosfwd -- define __USE_STD_IOSTREAM to override
> default - see section 7.1.2 of the C++ Using Guide"
> -^
> cxx: Error: /usr/lib/cmplrs/cxx/V6.5-014/include/cxx/sstream, line 58:
> #error
>          directive: "cannot include sstream -- define __USE_STD_IOSTREAM to
>          override default - see section 7.1.2 of the C++ Using Guide"
> #error "cannot include sstream -- define __USE_STD_IOSTREAM to override
> default - see section 7.1.2 of the C++ Using Guide"
> -^
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> The third error is:
> __________________________________________________________________________________________
> 
> cxx: Error: ../../include/lacomplex, line 487: identifier
> "ostringstream" is
>          undefined
>          detected during instantiation of "ostream
> &la::operator<<(ostream &,
>                    const la::complex<_Tp> &) [with _Tp=double]"
>      ostringstream __s;
> ------^
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> I don't know how to get rid of them.
> 
> 
> 
> Cheng
> 
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Re: [Lapackpp-devel] undefined reference problem

[Christian S. <sti...@tu...>]

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Hash: SHA1

Hi,

Andrew Oh schrieb:
> 
> I added -lblas -lg2c and -llapack to the linker flags and my errors
> have been reduced to this:
> 
> /usr/local/apps/intel/compiler8/lib/libimf.so.6: warning: log2l is not
> implemented and will always fail
> /usr/local/apps/intel/compiler8/lib/libimf.so.6: warning: exp2l is not
> implemented and will always fail
^^^^ those can be ignored

> /usr/lib/liblapack.so: undefined reference to `f_cpstr'
> /usr/lib/libblas.so: undefined reference to `f_iob'
> /usr/lib/liblapack.so: undefined reference to `f_cpystr'
> /usr/lib/liblapack.so: undefined reference to `f_concat'
> /usr/lib/libblas.so: undefined reference to `f_stop'
> 
> Is there anyway I can find out which linker flags I need to add so
> that the undefined references go away? I'm really sorry but I don't
> know how to use automake, autoconfig or libtool... I guess I should
> start reading up on tutorials =[.

Sigh... obviously you also need to link against some fortran library,
but I can't tell the name as this depends on your system. Hm... have you
been able to compile the lapackpp tarball completely? Can you also run
"make check" in the tarball? The command "make check" will compile
several executables, e. g. in the testing/ directory. During "make
check", you can look at the commands and see which additional linker
flags are being used. Or in the file ./config.status, look for the line
that contains @FLIBS@ and this should tell you the library flags as well.

Christian

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Re: [Lapackpp-devel] undefined reference problem

[Andrew O. <end...@gm...>]

Hey

I added -lblas -lg2c and -llapack to the linker flags and my errors
have been reduced to this:

/usr/local/apps/intel/compiler8/lib/libimf.so.6: warning: log2l is not
implemented and will always fail
/usr/local/apps/intel/compiler8/lib/libimf.so.6: warning: exp2l is not
implemented and will always fail
/usr/lib/liblapack.so: undefined reference to `f_cpstr'
/usr/lib/libblas.so: undefined reference to `f_iob'
/usr/lib/liblapack.so: undefined reference to `f_cpystr'
/usr/lib/liblapack.so: undefined reference to `f_concat'
/usr/lib/libblas.so: undefined reference to `f_stop'

Is there anyway I can find out which linker flags I need to add so
that the undefined references go away? I'm really sorry but I don't
know how to use automake, autoconfig or libtool... I guess I should
start reading up on tutorials =[.

This is specs for machine I am trying to build on

http://www.sdsc.edu/user_services/ia64/tech-summary.html

Andy

On 5/23/06, Christian Stimming <sti...@tu...> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Your commands look fine, but they will work only in the simple case. You
> specify "-llapackpp" on the gcc line so that your test.cc links against
> liblapackpp.so. Obviously liblapackpp.so needs to link against more
> libraries, which is why liblapack.so (without the pp) is linked in. This
> one in turn needs to link against yet more libraries - on my system it
> requires -lblas and -lg2c; maybe you should add these arguments to gcc
> as well.
>
> I don't specify the gcc line directly in my programs; instead, I let
> libtool/automake generate that for me, and this will usually find the
> appropriate linker flags automatically from the lib*.la files. In your
> case the problem only is that some linker flags are missing but which
> are required for your liblapack.so library.
>
> BTW for future bugreports please remember to specify your compiler
> version number and your OS (linux? bsd? amd64?).
>
> Christian
>
> Andrew Oh schrieb:
> > Hey
> >
> >
> > I tried compiling a simple "hello world" program and I get these errors:
> >
> >
> > tg-login1 /users/aoh> g++ test.cc -I/usr/local/apps/mpich-gm/include
> > -L/usr/local/apps/mpich-gm/lib -lmpich
> > -I/usr/local/apps/lapackpp-2.4.8/include/lapackpp
> > -L/usr/local/apps/lapackpp-2.4.8/lib -llapackpp
> > -I/users/aoh/random/include
> >
> > In file included from /usr/include/g++/backward/iostream.h:31,
> >                 from test.cc:7:
> > /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> > This file includes at least one deprecated or antiquated header.
> > Please consider using one of the 32 headers found in section 17.4.1.2
> > of the C++ standard. Examples include substituting the <X> header for
> > the <X.h> header for C++ includes, or <sstream> instead of the
> > deprecated header <strstream.h>. To disable this warning use
> > -Wno-deprecated.
> > /usr/local/apps/intel/compiler8/lib/libimf.so.6: warning: log2l is not
> > implemented and will always fail
> > /usr/local/apps/intel/compiler8/lib/libimf.so.6: warning: exp2l is not
> > implemented and will always fail
> > /usr/local/apps/intel/compiler8/lib/libcxa.so.6: undefined reference
> > to `__ashldi3'
> > /usr/lib/liblapack.so.3: undefined reference to `z_abs'
> > /usr/lib/liblapack.so.3: undefined reference to `c_sqrt'
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Re: [Lapackpp-devel] How to solve this compiling error on Compaq Tru64 UNIX

[Christian S. <sti...@tu...>]

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Hash: SHA1

Hi,

there's a problem with a defined macro in the compiler command. This
happens because your system name is quite unusual. You can fix this as
follows:

After you have run ./configure, open the file ./config.status with a
text editor. Search for the line with the string all_includes. At the
end this line contains the string "-DOS_osf5.1a". Remove the decimal
point there, i.e. replace that with "-DOS_osf51a". Then call

  ./config.status

and then "make" should work.

Christian

Cheng Guo schrieb:
> Hi,
> 
> I want to install lapackpp on a HP parallel supercomputer(HP-SC45). The
> OS is Compaq Tru64 UNIX V5.1A. Configuration succeeded.However, when I
> tried to make I got the following error:
> ____________________________________________________________________________
> 
> sigma-x0> make
> No suffix list.
> make  all-recursive
> No suffix list.
> Making all in include
> No suffix list.
> make  all-am
> No suffix list.
> Making all in blaspp
> No suffix list.
> Making all in src
> source='blas1pp.cc' object='blas1pp.lo' libtool=yes  DEPDIR=.deps
> depmode=tru64 /bin/ksh ../../depcomp  /bin/ksh ../../libtool --tag=CXX
> --mode=compile cxx -DHAVE_CONFIG_H  -I. -I. -I../.. -I../../include
> -I../../include -DLA_COMPLEX_SUPPORT -DHAVE_CONFIG_H -DOS_osf5.1a -g  -c
> -o blas1pp.lo blas1pp.cc
>  "cxx" "-DHAVE_CONFIG_H" "-I." "-I." "-I../.." "-I../../include"
> "-I../../include" "-DLA_COMPLEX_SUPPORT" "-DHAVE_CONFIG_H"
> "-DOS_osf5.1a" "-g" "-c" "-MD" blas1pp.cc  -DPIC -o .libs/blas1pp.o
> cxx: Severe: invalid macro definition: OS_osf5.1a
> cxx: Info: 1 catastrophic error detected in the compilation of
> "blas1pp.cc".
> cxx: Info: Compilation terminated.
> *** Exit 1
> Stop.
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
> 
> The output of configuration is:
> __________________________________________________________________________________
> 
> checking build system type... alphaev68-dec-osf5.1a
> checking host system type... alphaev68-dec-osf5.1a

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[Lapackpp-devel] How to solve this compiling error on Compaq Tru64 UNIX

[Cheng G. <cg...@it...>]

Hi,

I want to install lapackpp on a HP parallel supercomputer(HP-SC45). The 
OS is Compaq Tru64 UNIX V5.1A. Configuration succeeded.However, when I 
tried to make I got the following error:
____________________________________________________________________________
sigma-x0> make
No suffix list.
make  all-recursive
No suffix list.
Making all in include
No suffix list.
make  all-am
No suffix list.
Making all in blaspp
No suffix list.
Making all in src
source='blas1pp.cc' object='blas1pp.lo' libtool=yes  DEPDIR=.deps 
depmode=tru64 /bin/ksh ../../depcomp  /bin/ksh ../../libtool --tag=CXX 
--mode=compile cxx -DHAVE_CONFIG_H  -I. -I. -I../.. -I../../include 
-I../../include -DLA_COMPLEX_SUPPORT -DHAVE_CONFIG_H -DOS_osf5.1a 
-g  -c -o blas1pp.lo blas1pp.cc
  "cxx" "-DHAVE_CONFIG_H" "-I." "-I." "-I../.." "-I../../include" 
"-I../../include" "-DLA_COMPLEX_SUPPORT" "-DHAVE_CONFIG_H" 
"-DOS_osf5.1a" "-g" "-c" "-MD" blas1pp.cc  -DPIC -o .libs/blas1pp.o
cxx: Severe: invalid macro definition: OS_osf5.1a
cxx: Info: 1 catastrophic error detected in the compilation of "blas1pp.cc".
cxx: Info: Compilation terminated.
*** Exit 1
Stop.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



The output of configuration is:
__________________________________________________________________________________
checking build system type... alphaev68-dec-osf5.1a
checking host system type... alphaev68-dec-osf5.1a
checking target system type... alphaev68-dec-osf5.1a
checking for a BSD-compatible install... ./install-sh -c
checking whether build environment is sane... yes
checking for gawk... nawk
checking whether make sets $(MAKE)... yes
checking whether make sets $(MAKE)... (cached) yes
checking whether build environment is sane... yes
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... cxx
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... no
checking whether cxx accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of cxx... tru64
checking for gcc... no
checking for cc... cc
checking whether we are using the GNU C compiler... no
checking whether cc accepts -g... yes
checking for cc option to accept ANSI C... none needed
checking dependency style of cc... tru64
checking how to run the C preprocessor... cc -E
checking for a BSD-compatible install... ./install-sh -c
checking for sed... /bin/sed
checking for a sed that does not truncate output... /bin/sed
checking for egrep... grep -E
checking for non-GNU ld... /bin/ld
checking if the linker (/bin/ld) is GNU ld... no
checking for /bin/ld option to reload object files... -r
checking for BSD-compatible nm... /bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... no
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... cxx -E
checking for g77... no
checking for f77... f77
checking whether we are using the GNU Fortran 77 compiler... no
checking whether f77 accepts -g... yes
checking the maximum length of command line arguments... 16384
checking command to parse /bin/nm -B output from cc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if cc static flag  works... yes
checking for cc option to produce PIC...
checking if cc supports -c -o file.o... yes
checking whether the cc linker (/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... osf5.1a ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
configure: creating libtool
appending configuration tag "CXX" to libtool
checking whether the cxx linker (/bin/ld) supports shared libraries... yes
checking for cxx option to produce PIC...
checking if cxx supports -c -o file.o... yes
checking whether the cxx linker (/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... osf5.1a ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for f77 option to produce PIC...
checking if f77 supports -c -o file.o... yes
checking whether the f77 linker (/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... osf5.1a ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
checking for an ANSI C-conforming const... yes
checking for ANSI C header files... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking bits/cpp_type_traits.h usability... no
checking bits/cpp_type_traits.h presence... no
checking for bits/cpp_type_traits.h... no
checking whether the compiler implements namespaces... yes
checking how to get verbose linking output from f77... -v
checking for Fortran libraries of f77...  -lUfor -lfor -lFutil -lm -lots 
-lm_c32 -lmld -lexc
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no 
extra underscore
checking for sgemm_... no
checking if ATLAS should be used... yes
checking for ATLAS library... checking for f77blas library... configure: 
WARNING: not found
checking for cblas library... configure: WARNING: not found
checking whether ATLAS is usable... configure: WARNING: no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... yes
checking for cheev_... yes
checking for f95... f95
checking whether we are using the GNU Fortran compiler... no
checking whether f95 accepts -g... yes
checking how to get verbose linking output from f95... -v
checking for Fortran libraries of f95...  -lUfor -lfor -lFutil -lm -lots 
-lm_c32 -lmld -lexc
checking for dummy main to link with Fortran libraries... none
checking for system type... "OS_osf5.1a"
checking for compiler arguments... -g
configure: creating ./config.status
config.status: creating Makefile
config.status: creating lapackpp.iss
config.status: creating mainpage.doxygen
config.status: creating lapackpp.spec
config.status: creating lapackpp.pc
config.status: creating src/ressource.rc
config.status: creating blaspp/Makefile
config.status: creating blaspp/src/Makefile
config.status: creating blaspp/testing/Makefile
config.status: creating contrib/Makefile
config.status: creating include/Makefile
config.status: creating include/lacomplex.h
config.status: creating include/laversion.h
config.status: creating macros/Makefile
config.status: creating matrix/Makefile
config.status: creating matrix/src/Makefile
config.status: creating matrix/testing/Makefile
config.status: creating src/Makefile
config.status: creating testing/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

How can I solve this problem?


Cheng

Re: [Lapackpp-devel] undefined reference problem

[Christian S. <sti...@tu...>]

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Your commands look fine, but they will work only in the simple case. You
specify "-llapackpp" on the gcc line so that your test.cc links against
liblapackpp.so. Obviously liblapackpp.so needs to link against more
libraries, which is why liblapack.so (without the pp) is linked in. This
one in turn needs to link against yet more libraries - on my system it
requires -lblas and -lg2c; maybe you should add these arguments to gcc
as well.

I don't specify the gcc line directly in my programs; instead, I let
libtool/automake generate that for me, and this will usually find the
appropriate linker flags automatically from the lib*.la files. In your
case the problem only is that some linker flags are missing but which
are required for your liblapack.so library.

BTW for future bugreports please remember to specify your compiler
version number and your OS (linux? bsd? amd64?).

Christian

Andrew Oh schrieb:
> Hey
> 
> 
> I tried compiling a simple "hello world" program and I get these errors:
> 
> 
> tg-login1 /users/aoh> g++ test.cc -I/usr/local/apps/mpich-gm/include
> -L/usr/local/apps/mpich-gm/lib -lmpich
> -I/usr/local/apps/lapackpp-2.4.8/include/lapackpp
> -L/usr/local/apps/lapackpp-2.4.8/lib -llapackpp
> -I/users/aoh/random/include
> 
> In file included from /usr/include/g++/backward/iostream.h:31,
>                 from test.cc:7:
> /usr/include/g++/backward/backward_warning.h:32:2: warning: #warning
> This file includes at least one deprecated or antiquated header.
> Please consider using one of the 32 headers found in section 17.4.1.2
> of the C++ standard. Examples include substituting the <X> header for
> the <X.h> header for C++ includes, or <sstream> instead of the
> deprecated header <strstream.h>. To disable this warning use
> -Wno-deprecated.
> /usr/local/apps/intel/compiler8/lib/libimf.so.6: warning: log2l is not
> implemented and will always fail
> /usr/local/apps/intel/compiler8/lib/libimf.so.6: warning: exp2l is not
> implemented and will always fail
> /usr/local/apps/intel/compiler8/lib/libcxa.so.6: undefined reference
> to `__ashldi3'
> /usr/lib/liblapack.so.3: undefined reference to `z_abs'
> /usr/lib/liblapack.so.3: undefined reference to `c_sqrt'
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