Moving from mailing lists to discussions

[gtheler]

Hey all. Hopefully all questions, requirements and discussions will take place here, on GitHub discussions (pun).
The wasora mailing list at [email protected] will be transitioned to this place and eventually closed, as this is a better way to stay up to date and to follow improvements and changes in the code.

Welcome to the FeenoX community!

[vitorvas]

Saludos hermano Germán and hello all,

Well, first of all, congrats. Like to see feenox coming into the light.

But let's go to the ugly part. As usual, even not planning to use feenox in the near future, I want to help testing it. And, for my surprise, I got a problem right in the ./configure step:

configure.ac line 327
AC_CHECK_LIB([gsl],[gsl_blas_dgemm], [], AC_MSG_ERROR([GNU Scientific library libgsl-dev not found]))

I decided to check by myself and got this program

#include <stdio.h>
#include <gsl/gsl_blas.h>

int main (void)
{
double a[] = { 0.11, 0.12, 0.13, 0.21, 0.22, 0.23 };
double b[] = { 1011, 1012, 1021, 1022, 1031, 1032 };
double c[] = { 0.00, 0.00, 0.00, 0.00 };

gsl_matrix_view A = gsl_matrix_view_array(a, 2, 3);
gsl_matrix_view B = gsl_matrix_view_array(b, 3, 2);
gsl_matrix_view C = gsl_matrix_view_array(c, 2, 2);

/* Compute C = A B */

gsl_blas_dgemm (CblasNoTrans, CblasNoTrans,
1.0, &A.matrix, &B.matrix,
0.0, &C.matrix);

printf("[ %g, %g\n", c[0], c[1]);
printf(" %g, %g ]\n", c[2], c[3]);

return 0;
}

So, compiling and linking with gcc:

gcc prog.c -o prog -lgsl

and bang!

[vitors@cochon tmp]$ gcc prog.c -o prog -lgsl /bin/ld: /usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/libgsl.so: undefined reference to cblas_ctrmv'
(...)
/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/libgsl.so: undefined reference to cblas_dgemm' /bin/ld: /usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/libgsl.so: undefined reference to cblas_srotmg'
/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/libgsl.so: undefined reference to cblas_dtrsm' /bin/ld: /usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/libgsl.so: undefined reference to cblas_ccopy'
/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/libgsl.so: undefined reference to cblas_zsyrk' /bin/ld: /usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/libgsl.so: undefined reference to cblas_cswap'
/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/libgsl.so: undefined reference to cblas_daxpy' /bin/ld: /usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/libgsl.so: undefined reference to cblas_csyrk'
collect2: error: ld returned 1 exit status`

Linking error. But why, since I'm linking against gsl?

[vitors@cochon tmp]$ gcc prog.c -o prog -lgsl -lcblas
[vitors@cochon tmp]$ ll prog
-rwxrwxr-x. 1 vitors vitors 24456 Sep 1 20:54 prog
[vitors@cochon tmp]$

It works now! What is the problem? I use Fedora (version 34 now) and it seems that when using gsl in Fedora the user also needs to link against cblas library. Yes, really weird. Feel free to follow this quite old discussion.

So, I come with a (dirty) solution:

AC_CHECK_LIB([gsl],[gsl_blas_dgemm], [], AC_MSG_ERROR([GNU Scientific library libgsl-dev not found]), [-lcblas])
gsl_version="from system"
LIBS="$LIBS $LDFLAGS -lcblas"

After changing these lines in configure.ac I got feenox working.

[vitors@cochon feenox]$ ./feenox -V
FeenoX v0.1.34-g6b948b9-dirty
a free no-fee no-X uniX-like finite-element(ish) computational engineering tool

Last commit date : Tue Aug 31 20:07:36 2021 -0300
Build date : Wed Sep 01 20:36:05 2021 -0300
Build architecture : linux-gnu x86_64
Compiler : gcc (GCC) 11.2.1 20210728 (Red Hat 11.2.1-1)
Compiler flags : -ggdb
Builder : vitors@cochon
GSL version : 2.6
SUNDIALS version : 5.6.1
PETSc version : Petsc Release Version 3.14.1, Nov 03, 2020
PETSc arch : arch-linux-c-debug
PETSc options : --with-cc=gcc --with-cxx=g++ --with-fortran-bindings=0 --with-fc=0 --with-mpi=0
SLEPc version : SLEPc Release Version 3.14.0, Sep 30, 2020

You may ask: "Why not to open an issue and patch the fix?". Because it is not a fix. I'm just solving the problem for my Fedora box while ruining the configure.ac file for other distributions. The other obvious reason is that I expect the the gsl problem to get solved by the Fedora staff.

Of course, I'm open to suggestions. If someone knows how to make autotools check for the distribution and add want to live with many if statements to not break the current configure.ac file, I'm here to help. Meanwhile, I just want to share my (dirty) solution with the feenox community.

Regards and glad to share with you,

Vitor

[gtheler]

Hey Vitor! Long time no see! Just a quick answer through the phone, more details tomorrow. Actually it's not a GSL nor Fedora bug, it's a feature. GSL needs and explicit link to gslcblas in case the user wants to use a faster/different blas library (even a non-free one like MKL). The thing is that PETSc already uses (and provides) a blas library which can be used by GSL. So I tried to put a logic in configure.am such that when PETSc is used, the blas provided by PETSc is used by GSL as well and link to gslcblas if there's no PETSc. But I think I failed to do that (or my trick does not work on Fedora). Will investigate tomorrow. Feel free to open an issue so we can track the fix. Thanks!

[vitorvas]

Well, now I feel bad for complaining on Fedora staff! I need to delete that, hahaha. It is just my lack of knowledge of the matter, as usual.
Anyway, I'll wait for you. If you think I should open an issue, I do it.

Regards!

[gtheler]

Moved the thread to another category: #4