how to use gsl with the guile ffi

how to use gsl with the guile ffi

[tantalum]

im getting the error "In procedure dynamic-link: file: "libgsl", 
message: "file not found"" with the following code:

     (import (system foreign))
     (define gsl (dynamic-link "libgsl"))

* gsl (optionally?) depends on libgslcblas, which itself links without 
error, but loading it with (dynamic-link) beforehand did not help
* some libraries work, for example libmagic. libm for example gives the 
same error message
* the file /usr/lib/libgsl.so exists and is a symlink to the regular 
file libgsl.so.23.1.0 whose content begins with ELF>
* similar problem on the mailing list 
https://lists.gnu.org/archive/html/guile-user/2016-05/msg00010.html
* ive tried to set LD_LIBRARY_PATH with export to /usr/lib with no 
apparent effect
* i was going from this manual entry 
https://www.gnu.org/software/guile/manual/html_node/Dynamic-FFI.html
* guile (GNU Guile) 2.2.4

the issue can actually be reproduced with a c program:

     #include <dlfcn.h>
     #include <stdio.h>

     int main () {
       void* a = dlopen("libgsl.so", RTLD_NOW);
       printf("got %p\n", a);
       if (a) printf("ok\n"); else printf("error: %s\n", dlerror());
     }

gcc t.c -ldl && ./a.out

the program only works without error when compiled with -lgslcblas.
so, it could be a more basic issue, but i dont know how to proceed.

Re: how to use gsl with the guile ffi

[Neil Jerram]

tantalum <sph@posteo.eu> writes:

> im getting the error "In procedure dynamic-link: file: "libgsl", 
> message: "file not found"" with the following code:
>
>      (import (system foreign))
>      (define gsl (dynamic-link "libgsl"))
>
> * gsl (optionally?) depends on libgslcblas, which itself links without 
> error, but loading it with (dynamic-link) beforehand did not help
> * some libraries work, for example libmagic. libm for example gives the 
> same error message
> * the file /usr/lib/libgsl.so exists and is a symlink to the regular 
> file libgsl.so.23.1.0 whose content begins with ELF>
> * similar problem on the mailing list 
> https://lists.gnu.org/archive/html/guile-user/2016-05/msg00010.html
> * ive tried to set LD_LIBRARY_PATH with export to /usr/lib with no 
> apparent effect
> * i was going from this manual entry 
> https://www.gnu.org/software/guile/manual/html_node/Dynamic-FFI.html
> * guile (GNU Guile) 2.2.4
>
> the issue can actually be reproduced with a c program:
>
>      #include <dlfcn.h>
>      #include <stdio.h>
>
>      int main () {
>        void* a = dlopen("libgsl.so", RTLD_NOW);
>        printf("got %p\n", a);
>        if (a) printf("ok\n"); else printf("error: %s\n", dlerror());
>      }
>
> gcc t.c -ldl && ./a.out
>
> the program only works without error when compiled with -lgslcblas.
> so, it could be a more basic issue, but i dont know how to proceed.

You could run under strace to confirm which files are being looked for,
and which of those are not found.

Regards,
    Neil

Re: how to use gsl with the guile ffi

[tantalum]

so far i couldnt find the cause with strace.

mmap(NULL, 80013, PROT_READ, MAP_PRIVATE, 
7</usr/lib/guile/2.2/ccache/system/foreign.go>, 0) = 0x7f6a6da6b000
close(7</usr/lib/guile/2.2/ccache/system/foreign.go>)                    
        = 0
mprotect(0x7f6a6da7b000, 8776, PROT_READ|PROT_WRITE)                     
        = 0
openat(AT_FDCWD, "/usr/lib/libgslcblas.la", O_RDONLY)                    
        = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib32/libgslcblas.la", O_RDONLY)                  
        = -1 ENOENT (No such file or directory)
access("/usr/lib/libgslcblas.so", R_OK)                                  
        = 0
futex(0x7f6a73843048, FUTEX_WAKE_PRIVATE, 2147483647)                    
        = 0
openat(AT_FDCWD, "/usr/lib/libgslcblas.so", O_RDONLY|O_CLOEXEC)          
        = 7</usr/lib/libgslcblas.so.0.0.0>
read(7</usr/lib/libgslcblas.so.0.0.0>, 
"\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\240\"\0\0\0\0\0\0@\0\0\0\0\0\0\0\360\340\3\0\0\0\0\0\0\0\0\0@\08\0\7\0@\0\26\0\25\0\1\0\0\0\5\0\0\0\0\0\0\0\0\0\0\0"..., 
832) = 832
fstat(7</usr/lib/libgslcblas.so.0.0.0>, {st_mode=S_IFREG|0755, 
st_size=255600, ...}) = 0
mmap(NULL, 2351120, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 
7</usr/lib/libgslcblas.so.0.0.0>, 0) = 0x7f6a6d82c000
mprotect(0x7f6a6d86a000, 2093056, PROT_NONE)                             
        = 0
mmap(0x7f6a6da69000, 8192, PROT_READ|PROT_WRITE, 
MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 7</usr/lib/libgslcblas.so.0.0.0>, 
0x3d000) = 0x7f6a6da69000
close(7</usr/lib/libgslcblas.so.0.0.0>)                                  
        = 0
mprotect(0x7f6a6da69000, 4096, PROT_READ)                                
        = 0
openat(AT_FDCWD, "/usr/lib/libgsl.la", O_RDONLY)                         
        = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib32/libgsl.la", O_RDONLY)                       
        = -1 ENOENT (No such file or directory)
access("/usr/lib/libgsl.so", R_OK)                                       
        = 0
openat(AT_FDCWD, "/usr/lib/libgsl.so", O_RDONLY|O_CLOEXEC)               
        = 7</usr/lib/libgsl.so.23.1.0>
read(7</usr/lib/libgsl.so.23.1.0>, 
"\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0`l\5\0\0\0\0\0@\0\0\0\0\0\0\0\340+(\0\0\0\0\0\0\0\0\0@\08\0\7\0@\0\27\0\26\0\1\0\0\0\5\0\0\0\0\0\0\0\0\0\0\0"..., 
832) = 832
fstat(7</usr/lib/libgsl.so.23.1.0>, {st_mode=S_IFREG|0755, 
st_size=2634144, ...}) = 0
mmap(NULL, 4730464, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 
7</usr/lib/libgsl.so.23.1.0>, 0) = 0x7f6a6d3a9000
mprotect(0x7f6a6d617000, 2097152, PROT_NONE)                             
        = 0
mmap(0x7f6a6d817000, 86016, PROT_READ|PROT_WRITE, 
MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 7</usr/lib/libgsl.so.23.1.0>, 
0x26e000) = 0x7f6a6d817000
close(7</usr/lib/libgsl.so.23.1.0>)                                      
        = 0
munmap(0x7f6a6d3a9000, 4730464)                                          
        = 0
openat(AT_FDCWD, "/usr/share/locale/en_GB.UTF-8/LC_MESSAGES/libc.mo", 
O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale/en_GB.utf8/LC_MESSAGES/libc.mo", 
O_RDONLY)  = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale/en_GB/LC_MESSAGES/libc.mo", 
O_RDONLY)       = 7</usr/share/locale/en_GB/LC_MESSAGES/libc.mo>
fstat(7</usr/share/locale/en_GB/LC_MESSAGES/libc.mo>, 
{st_mode=S_IFREG|0644, st_size=1474, ...}) = 0
mmap(NULL, 1474, PROT_READ, MAP_PRIVATE, 
7</usr/share/locale/en_GB/LC_MESSAGES/libc.mo>, 0) = 0x7f6a743b8000
close(7</usr/share/locale/en_GB/LC_MESSAGES/libc.mo>)                    
        = 0
openat(AT_FDCWD, "/usr/share/locale/en.UTF-8/LC_MESSAGES/libc.mo", 
O_RDONLY)    = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale/en.utf8/LC_MESSAGES/libc.mo", 
O_RDONLY)     = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale/en/LC_MESSAGES/libc.mo", O_RDONLY)   
        = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/libgsl.la", O_RDONLY)                         
        = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/libgsl.so", O_RDONLY|O_CLOEXEC)               
        = 7</usr/lib/libgsl.so.23.1.0>
read(7</usr/lib/libgsl.so.23.1.0>, 
"\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0`l\5\0\0\0\0\0@\0\0\0\0\0\0\0\340+(\0\0\0\0\0\0\0\0\0@\08\0\7\0@\0\27\0\26\0\1\0\0\0\5\0\0\0\0\0\0\0\0\0\0\0"..., 
832) = 832
fstat(7</usr/lib/libgsl.so.23.1.0>, {st_mode=S_IFREG|0755, 
st_size=2634144, ...}) = 0
mmap(NULL, 4730464, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 
7</usr/lib/libgsl.so.23.1.0>, 0) = 0x7f6a6d3a9000
mprotect(0x7f6a6d617000, 2097152, PROT_NONE)                             
        = 0
mmap(0x7f6a6d817000, 86016, PROT_READ|PROT_WRITE, 
MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 7</usr/lib/libgsl.so.23.1.0>, 
0x26e000) = 0x7f6a6d817000
close(7</usr/lib/libgsl.so.23.1.0>)                                      
        = 0
munmap(0x7f6a6d3a9000, 4730464)                                          
        = 0
openat(AT_FDCWD, "/usr/lib/guile/2.2/extensions/libgsl.la", O_RDONLY)    
        = -1 ENOENT (No such file or directory)

Re: how to use gsl with the guile ffi

[Neil Jerram]

tantalum <sph@posteo.eu> writes:

> so far i couldnt find the cause with strace.

Well I think I'm just stating the obvious here, but clearly
libgslcblas.so is OK -

> openat(AT_FDCWD, "/usr/lib/libgslcblas.so", O_RDONLY|O_CLOEXEC)          
>         = 7</usr/lib/libgslcblas.so.0.0.0>

- and also libgsl.so -

> openat(AT_FDCWD, "/usr/lib/libgsl.so", O_RDONLY|O_CLOEXEC)               
>         = 7</usr/lib/libgsl.so.23.1.0>

- but apparently the system also needs libgsl.la, and that isn't found
at the expected place:

> openat(AT_FDCWD, "/usr/lib/guile/2.2/extensions/libgsl.la", O_RDONLY)    
>         = -1 ENOENT (No such file or directory)

I'm afraid I don't know any more, e.g. about whether libgsl.la _should_
be needed here.

    Neil

Re: how to use gsl with the guile ffi

[Matt Wette]

tantalum <sph@posteo.eu> writes:
>> im getting the error "In procedure dynamic-link: file: "libgsl",
>> message: "file not found"" with the following code:
>>
>>       (import (system foreign))
>>       (define gsl (dynamic-link "libgsl"))
>>
>> * gsl (optionally?) depends on libgslcblas, which itself links without
>> error, but loading it with (dynamic-link) beforehand did not help
>> * some libraries work, for example libmagic. libm for example gives the
>> same error message
>> * the file /usr/lib/libgsl.so exists and is a symlink to the regular
>> file libgsl.so.23.1.0 whose content begins with ELF>
>> * similar problem on the mailing list
>> https://lists.gnu.org/archive/html/guile-user/2016-05/msg00010.html
>> * ive tried to set LD_LIBRARY_PATH with export to /usr/lib with no
>> apparent effect
>> * i was going from this manual entry
>> https://www.gnu.org/software/guile/manual/html_node/Dynamic-FFI.html
>> * guile (GNU Guile) 2.2.4
>>
>> the issue can actually be reproduced with a c program:
>>
>>       #include <dlfcn.h>
>>       #include <stdio.h>
>>
>>       int main () {
>>         void* a = dlopen("libgsl.so", RTLD_NOW);
>>         printf("got %p\n", a);
>>         if (a) printf("ok\n"); else printf("error: %s\n", dlerror());
>>       }
>>
>> gcc t.c -ldl && ./a.out
>>
>> the program only works without error when compiled with -lgslcblas.
>> so, it could be a more basic issue, but i dont know how to proceed.
>

I see this often enough.  It is not a Guile issue.  Your runtime needs to know
where to find the .so file.  Typically you can fix this problem by setting
LD_LIBRARY_PATH prior to "guile".  For HDF5 I need to ...
$ LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/hdf5/serial
$ export LD_LIBRARY_PATH
$ guile hdf5demo.scm
...

Re: how to use gsl with the guile ffi

[tantalum]

only thing is, im not sure yet what i would set LD_LIBRARY_PATH to, as the following are all the library files gsl installs:

gsl /usr/lib/libgsl.so
gsl /usr/lib/libgsl.so.23
gsl /usr/lib/libgsl.so.23.1.0
gsl /usr/lib/libgslcblas.so
gsl /usr/lib/libgslcblas.so.0
gsl /usr/lib/libgslcblas.so.0.0.0

ldd output is
   ldd /usr/lib/libgsl.so
         linux-vdso.so.1 (0x00007ffeb5ded000)
         libm.so.6 => /usr/lib/libm.so.6 (0x00007f804bc32000)
         libc.so.6 => /usr/lib/libc.so.6 (0x00007f804ba6e000)
         /usr/lib64/ld-linux-x86-64.so.2 (0x00007f804c282000)

something that works in my c test program is preloading libgslcblas with RTLD_GLOBAL.

   void* a = dlopen("/usr/lib/libgslcblas.so", RTLD_NOW | RTLD_GLOBAL);
   void* b = dlopen("/usr/lib/libgsl.so", RTLD_NOW);

but guile uses libtool of course. as far as i understand it, libgslcblas is a cblas implementation that can be replaced with other ones, and that is why it is separate.

the RTLD_GLOBAL feature has been referenced in a mailing list post from 2012 "Re: using GSL with cblas via FFI"
https://lists.gnu.org/archive/html/guile-user/2012-06/msg00008.html
https://lists.gnu.org/archive/html/guile-user/2011-03/msg00071.html

what might eventually work is to compile gsl myself with the dependency excluded or statically linked. or using a c extension instead of the ffi.
but it is interesting also how the example from the manual does not work and gives the same error message. (define libm (dynamic-link "libm"))  https://www.gnu.org/software/guile/manual/html_node/Dynamic-FFI.html

it would be interesting to know if it works for others.