reinh-bader / fgsl Goto Github PK

Hello,

I get the following error on compilation :

gfortran -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -c -o fgsl.o fgsl.F90
api/spmatrix.finc:75.36:
Included at fgsl.F90:1939:

fgsl_fit_wmul = gsl_fit_wmul(c_loc(x), xstride, c_loc(w), wstride, &
                                   1

fgsl_fit_mul = gsl_fit_mul(c_loc(x), xstride, c_loc(y), ystride, n, c1, &
                                 1

fgsl_fit_wlinear = gsl_fit_wlinear(c_loc(x), xstride, c_loc(w), wstride, &
                                         1

fgsl_fit_linear = gsl_fit_linear(c_loc(x), xstride, c_loc(y), ystride, n, c
                                       1

fgsl_dht_apply = gsl_dht_apply(t%gsl_dht, c_loc(f_in), c_loc(f_out))
                                                1

     gsl_wavelet2d_nstransform_inverse(w%gsl_wavelet, c_loc(data), &
                                                            1

     gsl_wavelet2d_nstransform_forward(w%gsl_wavelet, c_loc(data), &
                                                            1

     gsl_wavelet2d_transform_inverse(w%gsl_wavelet, c_loc(data), &
                                                          1

     gsl_wavelet2d_transform_forward(w%gsl_wavelet, c_loc(data), &
                                                          1

fgsl_wavelet_transform = gsl_wavelet_transform(w%gsl_wavelet, c_loc(data), &
                                                                    1

     t, t1, h, c_loc(y))
                     1

     c_loc(y0), c_loc(yerr), c_loc(dydt), c_loc(h))
           1

     c_loc(scale_abs), size(scale_abs, kind=fgsl_size_t))
           1

c_loc(y), c_loc(yerr), &
      1

     dydt%gsl_odeiv2_system, t, h0, c_loc(y))
                                          1

     t, t1, h, c_loc(y))
                     1

     c%gsl_odeiv2_control, s%gsl_odeiv2_step, c_loc(y), c_loc(yerr), c_loc(
                                                    1

     c_loc(scale_abs), size(scale_abs, kind=fgsl_size_t))
           1

c_loc(y), c_loc(yerr), c_loc(dydt_in), c_loc(dydt_out), dydt%gsl_odeiv2_sys
      1

        gsl_ntuple_open(c_loc(lname), data, size)
                              1

Error: CHARACTER argument 'lname' to 'c_loc' at (1) must have a length of 1
Fatal Error: Error count reached limit of 25.
make: *** [fgsl.o] Erreur 1


I tried with both the latest stable release (1.1.0) and the git master, same error.

gsl is version 2.1, compiled from the sources.

Please let me know if any other information is useful...

build with ifx causes one test in linalg (fgsl_linalg_qrpt_lssolve2:x) to fail

Intel(R) Fortran Compiler for applications running on Intel(R) 64, Version 2024.0.2 Build 20231213
OS: Ubuntu 20.04.6 LTS / executing under WSL 2

I suggest adding topics such as gsl, gsl-library in the About section at https://github.com/reinh-bader/fgsl

Hello, I am trying to use the fgsl linear algebra solver. I am running into issues with CPU usage when I run my program. I have used the example docs on your page to make the Fortran script linked below.
Issue: When I uncomment to solver section in the main script (lines 104 to 116 in main.F90) and run the program the CPU usage reaches astronomical levels! I am using “fgsl_splinalg_itersolve_iterate()” to solve the equation Au=f, where A is a 25920 by 25920 matrix and both u and f are 25920 length vectors. This equation is solved for each time step. I was just wondering if anyone else experienced similar issues with CPU usage when using fgsl/ is there a fix?
Minimal reproducible example found at: https://github.com/exoclim/ulmo/tree/main/MRE_fgsl/src

The following error occurs when building against recent GSL versions:
make -j3 -j1
make all-recursive
make[1]: Entering directory '/var/tmp/paludis/build/sci-libs-fgsl-1.0.0-r1/work/fgsl-1.0.0'
Making all in .
make[2]: Entering directory '/var/tmp/paludis/build/sci-libs-fgsl-1.0.0-r1/work/fgsl-1.0.0'
/bin/sh ./libtool --tag=FC --mode=compile x86_64-pc-linux-gnu-gfortran -DHAVE_CONFIG_H -I. -I. -I. -pipe -O2 -march=native -g -O2 -c -o fgsl.lo fgsl.F90
libtool: compile: x86_64-pc-linux-gnu-gfortran -DHAVE_CONFIG_H -I. -I. -I. -pipe -O2 -march=native -g -O2 -c fgsl.F90 -fPIC -o .libs/fgsl.o
libtool: compile: x86_64-pc-linux-gnu-gfortran -DHAVE_CONFIG_H -I. -I. -I. -pipe -O2 -march=native -g -O2 -c fgsl.F90 -o fgsl.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-cc -DHAVE_CONFIG_H -I. -I. -I. -pipe -O2 -march=native -pipe -O2 -march=native -c -o libfgsl_la-fgsl_utils.lo test -f 'fgsl_utils.c' || echo './'fgsl_utils.c
libtool: compile: x86_64-pc-linux-gnu-cc -DHAVE_CONFIG_H -I. -I. -I. -pipe -O2 -march=native -pipe -O2 -march=native -c fgsl_utils.c -fPIC -DPIC -o .libs/libfgsl_la-fgsl_utils.o
fgsl_utils.c:1090:13: error: conflicting types for 'gsl_multifit_fdfsolver_jac'
gsl_matrix gsl_multifit_fdfsolver_jac(gsl_multifit_fdfsolver s) {
^
In file included from fgsl_utils.c:21:0:
/usr/x86_64-pc-linux-gnu/include/gsl/gsl_multifit_nlin.h:177:5: note: previous declaration of 'gsl_multifit_fdfsolver_jac' was here
int gsl_multifit_fdfsolver_jac (gsl_multifit_fdfsolver * s,
^
fgsl_utils.c: In function 'gsl_multifit_fdfsolver_jac':
fgsl_utils.c:1091:13: error: 'gsl_multifit_fdfsolver' has no member named 'J'
return s->J;
^
Makefile:397: recipe for target 'libfgsl_la-fgsl_utils.lo' failed
make[2]: [libfgsl_la-fgsl_utils.lo] Error 1
make[2]: Leaving directory '/var/tmp/paludis/build/sci-libs-fgsl-1.0.0-r1/work/fgsl-1.0.0'
Makefile:449: recipe for target 'all-recursive' failed
make[1]: [all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/paludis/build/sci-libs-fgsl-1.0.0-r1/work/fgsl-1.0.0'
Makefile:266: recipe for target 'all' failed
make: *** [all] Error 2

Someone else install FGSL on my desktop, I can use FGSL in such an easy way:

gfortran -I/usr/include/fgsl bessel.f90 -lfgsl

However I installed FGSL on my Laptop, the same test does not work properly.

chen@jesuslovesme:~/Documents/numerical/fortran/fgsl$ gfortran -I/usr/include/fgsl bessel.f90 -lfgsl

Errors:
/usr/bin/ld: /tmp/cceiCL9M.o: in function MAIN__': bessel.f90:(.text+0x1d): undefined reference to gsl_sf_bessel_Kn'
/usr/bin/ld: bessel.f90:(.text+0xc3): undefined reference to `gsl_sf_bessel_Knu'
collect2: error: ld returned 1 exit status

The method I install is like this, doese there any problem?

export FC=gfortran
export PKG_CONFIG_PATH=/usr/include/gsl/lib/pkgconfig
export gsl_LIBS=/usr/include/gsl
[ -f ./fgsl.tar.gz ] && echo "No need to download fgsl" || wget https://github.com/reinh-bader/fgsl/archive/v1.3.0.tar.gz -O fgsl.tar.gz
mkdir -p fgsl_build
cd fgsl_build
tar -xzf ../fgsl.tar.gz --strip 1
autoreconf -fi
./configure CFLAGS="-Wall" FCFLAGS="-Wall" --prefix=${gsl_LIBS}
make
make check
make install
cd ..
rm -rf fgsl_build

... and will need support in FGSL in order to use the new features.

As far as I can tell, it is still possible to compile the current FGSL release against GSL 2.2.1, as the API was not broken.

Anyone interested in writing some code for this? I won't have time until the christmas holidays for this unfortunately....

Dear Sir,

Primarily, I am an opensuse user, so it would be nice to have a fgsl package specific for that (compiling from source did nor work for me).
As a contouring, I have a Kubuntu (virutal)Machine , version 20.04.4.
Unfortunately, for me the ubuntu instructions did not work.
I issue:
"
iulek@iulek-VirtualBox:/usr/local$ sudo curl http://lvserver.ugent.be/apt/xmi.packages.key | sudo apt-key add -
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 6439 100 6439 0 0 13613 0 --:--:-- --:--:-- --:--:-- 13584
OK
iulek@iulek-VirtualBox:/usr/local$
"
Then I add:
"
deb [arch=amd64] http://lvserver.ugent.be/apt/ubuntu wily stable
deb-src http://lvserver.ugent.be/apt/ubuntu wily stable
"
to /etc/apt/sources.list
(or, even if I change "wily" to "focal")
But then I get:
"
iulek@iulek-VirtualBox:/usr/local$ sudo apt-get update
Hit:1 http://br.archive.ubuntu.com/ubuntu focal InRelease
Hit:2 http://br.archive.ubuntu.com/ubuntu focal-updates InRelease
Hit:3 http://br.archive.ubuntu.com/ubuntu focal-backports InRelease
Hit:4 http://archive.canonical.com/ubuntu focal InRelease
Get:5 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]
Hit:6 http://lvserver.ugent.be/apt/ubuntu focal InRelease
Get:7 http://lvserver.ugent.be/apt/ubuntu wily InRelease [2.343 B]
Err:7 http://lvserver.ugent.be/apt/ubuntu wily InRelease
The following signatures were invalid: CB66CB1174623729C9A3AC4F1CA7FDC8856B2D18
Reading package lists... Done
W: GPG error: http://lvserver.ugent.be/apt/ubuntu wily InRelease: The following signatures were invalid: CB66CB1174623729C9A3AC4F1CA7FDC8856B2D18
E: The repository 'http://lvserver.ugent.be/apt/ubuntu wily InRelease' is not signed.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration details.
iulek@iulek-VirtualBox:/usr/local$
"
and so it says to me it cannot find packages libfgsl0, etc.

Is there a work around for that?
Thank you,

Jorge

The distribution specific builds do not seem to be available anymore. LRZ points out to install packages from http://lvserver.ugent.be/ - but this Server does not exist. Any other package repo? Or is the only way to install selfcompiling?

I tried to compile FGSL with PGI's fortran compiler and got the following error messages:

PGF90-S-0034-Syntax error at or near VALUE (./interface/ode.finc: 141)
PGF90-S-0034-Syntax error at or near VALUE (./interface/spmatrix.finc: 61)
  0 inform,   0 warnings,   2 severes, 0 fatal for fgsl

Apparently pgfortran does not like value statements. After replacing the statements by attributes the code compiled but two tests failed:

FAIL: spmatrix
FAIL: splinalg

There are also two XFAILs but I think they are expected:

XFAIL: error
XFAIL: error_1

Please refer to the attached files for details.

• fgsl-pgi.txt
• error.txt
• error_1.txt
• splinalg.txt
• spmatrix.txt

Hello, is it possible for fgsl to support fortran-lang/fpm, which is a package manager and build system for Fortran?
(Also see fortran-lang/fpm#445)

and introduces a couple of new features which will need support in FGSL...

Hello. I'm a beginner for programing.
I installed fgsl through Macbrew. And I made a file with "use fgsl".
But I can't compile it.
How do you compile using gfortran.
Please tell me ....

For some build scenarios, __FILE__ turns into a very long string, which then results in "Line truncated" error messages. While this can generally be worked around with the appropriate (compiler-dependent) compile flags, it would be better if __FILE__ were replaced with the corresponding hardcoded string so as to keep the build process simple.

i linked this against gfortran-5.3, gfortran-6-latest and gfortran-6-dev with gsl 1.16 all report following

  1 =============================================
  2    fgsl 1.0.0: doc/examples/test-suite.log
  3 =============================================
  4 
  5 # TOTAL: 45
  6 # PASS:  44
  7 # SKIP:  0
  8 # XFAIL: 1
  9 # FAIL:  0
 10 # XPASS: 0
 11 # ERROR: 0
 12 
 13 .. contents:: :depth: 2
 14 
 15 XFAIL: error_1
 16 ==============
 17 
 18 gsl: gamma.c:1264: ERROR: domain error
 19 Default GSL error handler invoked.
 20 
 21 Program received signal SIGABRT: Process abort signal.
 22 
 23 Backtrace for this error:
 24 #0  0x10ce17354
 25 #1  0x10ce16b44
 26 #2  0x7fff8d591ea9
 27 XFAIL error_1 (exit status: 134)

When I run make check, I get lots of undefined reference messages like this:

/usr/lib/libgsl.so: undefined reference to `cblas_*'

I even tried the env: export gsl_LIBS=/usr/lib/libgsl.so:/usr/lib/libgslcblas.so

i ran ./configure and make under "/home/segtovichisv/Desktop/workspace-fortran+steroids/1. gsl/3. fortran fgsl/setup fgsl/fgsl-1.1.0"

.configure and make did not raise errors
make check did
by looking at test-suite.log (renamed to test-suite.log.txt in the attachment) i believe spaces in the working directory path were the problem. (i found nothing about spaces in the README)

i moved the whole dir with source and build instructions to ~/Desktop and re-ran make clean, ./configure, make and make check and then all tests passed

the error said Please report to [email protected]
and the site said Users of FGSL are encouraged to send bug reports via the Github ticket system.

i couldn't test on the latest release because i am testing stuff on the default "apt install gsl" which is the 2.1

So i guess by creating this issue, if it is not something already fixed in the latest release, some warning about spaces might be added in the README file, and maybe some next version scripts would be able to deal with spaces.

thanks for your consideration

test-suite.log.txt

There is also a parallel build issue in the testsuite that I noticed. If you cannot replicate it I can attach another log. The following is from the compilation phase.

When compiling with make -j4:
make all-recursive
make[1]: Entering directory '/home/thomas/Downloads/fgsl-1.0.0'
Making all in .
make[2]: Entering directory '/home/thomas/Downloads/fgsl-1.0.0'
/bin/sh ./libtool --tag=FC --mode=compile gfortran -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -c -o fgsl.lo fgsl.F90
/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT libfgsl_la-fgsl_utils.lo -MD -MP -MF .deps/libfgsl_la-fgsl_utils.Tpo -c -o libfgsl_la-fgsl_utils.lo test -f 'fgsl_utils.c' || echo './'fgsl_utils.c
gfortran -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -c -o fgsl.o fgsl.F90
libtool: compile: gfortran -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -c fgsl.F90 -fPIC -o .libs/fgsl.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT libfgsl_la-fgsl_utils.lo -MD -MP -MF .deps/libfgsl_la-fgsl_utils.Tpo -c fgsl_utils.c -fPIC -DPIC -o .libs/libfgsl_la-fgsl_utils.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT libfgsl_la-fgsl_utils.lo -MD -MP -MF .deps/libfgsl_la-fgsl_utils.Tpo -c fgsl_utils.c -o libfgsl_la-fgsl_utils.o >/dev/null 2>&1
Fatal Error: Can't rename module file 'fgsl.mod0' to 'fgsl.mod': No such file or directory
Makefile:542: recipe for target 'fgsl.o' failed
make[2]: [fgsl.o] Error 1
make[2]: Waiting for unfinished jobs....

Hello,
I copied and paste the example program multiroot.f90. I tried to compile it using
gfortran -I/usr/local/include/fgsl -I/home/sara/fgsl_build/tests prova_multiroot.f -lfgsl -lgsl -lgslcblas -lm but i get the following message /tmp/cccwLMcu.o: In function MAIN__': prova_multiroot.f:(.text+0x676): undefined reference to __mod_unit_MOD_unit_init'
prova_multiroot.f:(.text+0x7e5): undefined reference to __mod_unit_MOD_unit_assert_equal_string' prova_multiroot.f:(.text+0x8e2): undefined reference to __mod_unit_MOD_unit_assert_equal_integer'
prova_multiroot.f:(.text+0x96d): undefined reference to __mod_unit_MOD_unit_assert_true' prova_multiroot.f:(.text+0xb5c): undefined reference to __mod_unit_MOD_unit_assert_equal_integer'
prova_multiroot.f:(.text+0xbc4): undefined reference to __mod_unit_MOD_unit_assert_equal_within_double_array' prova_multiroot.f:(.text+0xd47): undefined reference to __mod_unit_MOD_unit_assert_equal_string'
prova_multiroot.f:(.text+0xe51): undefined reference to __mod_unit_MOD_unit_assert_equal_integer' prova_multiroot.f:(.text+0xedc): undefined reference to __mod_unit_MOD_unit_assert_true'
prova_multiroot.f:(.text+0x10cb): undefined reference to __mod_unit_MOD_unit_assert_equal_integer' prova_multiroot.f:(.text+0x1133): undefined reference to __mod_unit_MOD_unit_assert_equal_within_double_array'
prova_multiroot.f:(.text+0x114c): undefined reference to `__mod_unit_MOD_unit_finalize'
collect2: error: ld returned 1 exit status
Can you help me?

ps: removing the instruction I/home/sara/fgsl_build/tests, that is the the path wher I found mod_unit.mod, I got use mod_unit
1
Fatal Error: Can't open module file ‘mod_unit.mod’ for reading at (1): No such file or directory
compilation terminated.

Thank you in advance,
Sara

It would appear that gsl_spmatrix_compare_idx was removed in 2.6, which is causing linker trouble on Windows.

/bin/sh ./libtool  --tag=FC   --mode=compile gfortran -DHAVE_CONFIG_H -I.  -I. -I.   -g -O2 -c -o fgsl.lo fgsl.F90
libtool: compile:  gfortran -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -c fgsl.F90  -DDLL_EXPORT -o .libs/fgsl.o
/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -I. -I.   -g -O2 -MT libfgsl_la-fgsl_utils.lo -MD -MP -MF .deps/libfgsl_la-fgsl_utils.Tpo -c -o libfgsl_la-fgsl_utils.lo `test -f 'fgsl_utils.c' || echo './'`fgsl_utils.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT libfgsl_la-fgsl_utils.lo -MD -MP -MF .deps/libfgsl_la-fgsl_utils.Tpo -c fgsl_utils.c  -DDLL_EXPORT -DPIC -o .libs/libfgsl_la-fgsl_utils.o
mv -f .deps/libfgsl_la-fgsl_utils.Tpo .deps/libfgsl_la-fgsl_utils.Plo
/bin/sh ./libtool  --tag=FC   --mode=link gfortran  -g -O2 -version-info 1:0:0 -no-undefined  -o libfgsl.la -rpath /home/VssAdministrator/install/lib fgsl.lo libfgsl_la-fgsl_utils.lo  -lgsl -lgslcblas -lm 
libtool: link: gfortran -shared  .libs/fgsl.o .libs/libfgsl_la-fgsl_utils.o   -lgsl -lgslcblas  -O2   -o .libs/libfgsl-1.dll -Wl,--enable-auto-image-base -Xlinker --out-implib -Xlinker .libs/libfgsl.dll.a
C:/msys64/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/9.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: .libs/fgsl.o: in function `__fgsl_MOD_fgsl_spmatrix_compare_idx':
D:\a\1\s\fgsl-1.1.0/api/spmatrix.finc:42: undefined reference to `gsl_spmatrix_compare_idx'
collect2.exe: error: ld returned 1 exit status

Example program doc/example/nlfit4 crashes with a segfault.

Compiler: nvfortran 24.3-0 64-bit target on x86-64 Linux -tp icelake-server
OS: Ubuntu 20.04.6 LTS / executing under WSL 2