Given this flake
{
inputs = {
nixpkgs.url = "nixpkgs/nixos-23.11";
flake-utils.url = "github:numtide/flake-utils";
zig-overlay.url = "github:mitchellh/zig-overlay";
zls.url = "github:zigtools/zls";
};
outputs = inputs:
let
inherit (inputs) nixpkgs zig-overlay flake-utils zls gsl;
systems = [ "x86_64-linux" ];
in
flake-utils.lib.eachSystem systems (system:
let
pkgs = import nixpkgs { inherit system; };
# zig = zig-overlay.packages.${system}."0.11.0";
zig = zig-overlay.packages.${system}.master;
zls_pkg = zls.packages.${system}.default;
gsl = pkgs.gsl;
blas = pkgs.blas;
pkgconfig = pkgs.pkg-config;
gcc = pkgs.gcc;
in
{
devShells.default = pkgs.mkShell {
packages = [ zig zls_pkg gcc pkgconfig ];
nativeBuildInputs = [ gsl.dev blas pkgconfig ];
buildInputs = [ gsl.dev blas pkgconfig ];
};
});
}
and the C program main-gsl.c
#include <gsl/gsl_cdf.h>
#include <stdio.h>
int main(){
double bottom_tail = gsl_cdf_gaussian_P(-1.96, 1);
printf("Area betweeen [-1.96, 1.96]: %g\n", 1 - 2*bottom_tail);
}
this works: gcc main-gsl.c -lgsl -lblas && ./a.out
Area betweeen [-1.96, 1.96]: 0.950004
but this does not: zig cc main-gsl.c -lgsl -lblas -lc && ./a.out
./a.out: symbol lookup error: /nix/store/0f2jj365fr1z5cfi73bvxzh7sbwg0ns7-gsl-2.7.1/lib/libgsl.so.27: undefined symbol: cblas_ctrmv
ldd a.out gives
linux-vdso.so.1 (0x00007fff78a78000)
libgsl.so.27 => /nix/store/0f2jj365fr1z5cfi73bvxzh7sbwg0ns7-gsl-2.7.1/lib/libgsl.so.27 (0x00007f3184400000)
libc.so.6 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/libc.so.6 (0x00007f3184218000)
libm.so.6 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/libm.so.6 (0x00007f31847af000)
/nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/ld-linux-x86-64.so.2 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib64/ld-linux-x86-64.so.2 (0x00007f3184891000)
My understanding is that the blas libs were not linked explicitly, ld tries to resolve the symbols at run time and fails.
ldd a.out on the gcc’d a.out:
linux-vdso.so.1 (0x00007fcd8c10f000)
libgsl.so.27 => /nix/store/0f2jj365fr1z5cfi73bvxzh7sbwg0ns7-gsl-2.7.1/lib/libgsl.so.27 (0x00007fcd8be00000)
libblas.so.3 => /nix/store/jx5r3fyz26nvrj5zcx2f7fc2yszfalwb-blas-3/lib/libblas.so.3 (0x00007fcd8a380000)
libc.so.6 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/libc.so.6 (0x00007fcd8a198000)
libm.so.6 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/libm.so.6 (0x00007fcd8a0b8000)
libpthread.so.0 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/libpthread.so.0 (0x00007fcd8c102000)
libgfortran.so.5 => /nix/store/4avaj23y8h6hq8wck73250w77y0s6kvi-gfortran-12.3.0-lib/lib/libgfortran.so.5 (0x00007fcd89c00000)
libgomp.so.1 => /nix/store/myw67gkgayf3s2mniij7zwd79lxy8v0k-gcc-12.3.0-lib/lib/libgomp.so.1 (0x00007fcd8a073000)
/nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/ld-linux-x86-64.so.2 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib64/ld-linux-x86-64.so.2 (0x00007fcd8c111000)
libquadmath.so.0 => /nix/store/4avaj23y8h6hq8wck73250w77y0s6kvi-gfortran-12.3.0-lib/lib/libquadmath.so.0 (0x00007fcd8a02c000)
libgcc_s.so.1 => /nix/store/4avaj23y8h6hq8wck73250w77y0s6kvi-gfortran-12.3.0-lib/lib/libgcc_s.so.1 (0x00007fcd8c0e1000)
libdl.so.2 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/libdl.so.2 (0x00007fcd8c0da000)
I am trying to understand why this happens to learn more about Zig and NixOS - I am more familiar with high-level languages in the scientific computing realm, i.e. Python and Julia.
Try with zig cc -target x86_64-linux by default zig applies host specific optimizations so the blas headers might look for different symbols that were compiled in. Nixpkgs are always packaged with -mcpu=baseline to have reproducible output. -target and -Dtarget (for zig build) always use the baseline for that target similar to -mcpu=baseline Exe files not interchangeable among identical Linux systems - #6 by andrewrk
Thanks for taking the time and the explanations!
I tried with zig cc -target x86_64-linux src/main-gsl.c -lgsl -lblas but I get:
error: unable to find Dynamic system library 'gsl' using strategy 'paths_first'. searched paths: none
error: unable to find Dynamic system library 'blas' using strategy 'paths_first'. searched paths: none
You may want to try with $(pkg-config --libs --cflags blas gsl) instead
zig cc -target x86_64-linux $(pkg-config --libs --cflags blas gsl) src/main-gsl.c && ./a.out
bash: ./a.out: cannot execute: required file not found
Most likely BLAS and GSL aren’t in your LD_LIBRARY_PATH, if you run ldd on ./a.out you’ll see entries for “not found”
Ah, I had a similar idea, but I thought LD_LIBRARY_PATH would have been taken care of by the flake.nix…
ldd ./a.out
./a.out: error while loading shared libraries: /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/libc.so: invalid ELF header
Cloudef
February 3, 2024, 10:08am
8
Huh, what does readelf -a say on the a.out?
readelf -a ./a.out
ELF Header:
Magic: 7f 45 4c 46 02 01 01 00 00 00 00 00 00 00 00 00
Class: ELF64
Data: 2's complement, little endian
Version: 1 (current)
OS/ABI: UNIX - System V
ABI Version: 0
Type: EXEC (Executable file)
Machine: Advanced Micro Devices X86-64
Version: 0x1
Entry point address: 0x1001470
Start of program headers: 64 (bytes into file)
Start of section headers: 5192 (bytes into file)
Flags: 0x0
Size of this header: 64 (bytes)
Size of program headers: 56 (bytes)
Number of program headers: 9
Size of section headers: 64 (bytes)
Number of section headers: 28
Section header string table index: 26
Section Headers:
[Nr] Name Type Address Offset
Size EntSize Flags Link Info Align
[ 0] NULL 0000000000000000 00000000
0000000000000000 0000000000000000 0 0 0
[ 1] .interp PROGBITS 0000000001000238 00000238
0000000000000019 0000000000000000 A 0 0 1
[ 2] .dynsym DYNSYM 0000000001000258 00000258
0000000000000090 0000000000000018 A 5 1 8
[ 3] .gnu.hash GNU_HASH 00000000010002e8 000002e8
0000000000000024 0000000000000000 A 2 0 8
[ 4] .hash HASH 000000000100030c 0000030c
0000000000000038 0000000000000004 A 2 0 4
[ 5] .dynstr STRTAB 0000000001000344 00000344
000000000000004e 0000000000000000 A 0 0 1
[ 6] .rela.plt RELA 0000000001000398 00000398
0000000000000048 0000000000000018 AI 2 15 8
[ 7] .rodata PROGBITS 00000000010003e0 000003e0
0000000000000031 0000000000000000 AMS 0 0 8
[ 8] .eh_frame_hdr PROGBITS 0000000001000414 00000414
0000000000000014 0000000000000000 A 0 0 4
[ 9] .eh_frame PROGBITS 0000000001000428 00000428
000000000000003c 0000000000000000 A 0 0 8
[10] .text PROGBITS 0000000001001470 00000470
0000000000000090 0000000000000000 AX 0 0 16
[11] .init PROGBITS 0000000001001500 00000500
0000000000000003 0000000000000000 AX 0 0 1
[12] .fini PROGBITS 0000000001001503 00000503
0000000000000003 0000000000000000 AX 0 0 1
[13] .plt PROGBITS 0000000001001510 00000510
0000000000000040 0000000000000000 AX 0 0 16
[14] .dynamic DYNAMIC 0000000001002550 00000550
0000000000000120 0000000000000010 WA 5 0 8
[15] .got.plt PROGBITS 0000000001002670 00000670
0000000000000030 0000000000000000 WA 0 0 8
[16] .debug_loc PROGBITS 0000000000000000 000006a0
000000000000007f 0000000000000000 0 0 1
[17] .debug_abbrev PROGBITS 0000000000000000 0000071f
000000000000014f 0000000000000000 0 0 1
[18] .debug_info PROGBITS 0000000000000000 0000086e
00000000000003c0 0000000000000000 0 0 1
[19] .debug_str PROGBITS 0000000000000000 00000c2e
0000000000000164 0000000000000001 MS 0 0 1
[20] .comment PROGBITS 0000000000000000 00000d92
000000000000007d 0000000000000001 MS 0 0 1
[21] .debug_frame PROGBITS 0000000000000000 00000e10
0000000000000030 0000000000000000 0 0 8
[22] .debug_line PROGBITS 0000000000000000 00000e40
0000000000000258 0000000000000000 0 0 1
[23] .debug_aranges PROGBITS 0000000000000000 00001098
0000000000000080 0000000000000000 0 0 1
[24] .debug_ranges PROGBITS 0000000000000000 00001118
00000000000000a0 0000000000000000 0 0 1
[25] .symtab SYMTAB 0000000000000000 000011b8
0000000000000120 0000000000000018 27 4 8
[26] .shstrtab STRTAB 0000000000000000 000012d8
0000000000000105 0000000000000000 0 0 1
[27] .strtab STRTAB 0000000000000000 000013dd
0000000000000069 0000000000000000 0 0 1
Key to Flags:
W (write), A (alloc), X (execute), M (merge), S (strings), I (info),
L (link order), O (extra OS processing required), G (group), T (TLS),
C (compressed), x (unknown), o (OS specific), E (exclude),
D (mbind), l (large), p (processor specific)
There are no section groups in this file.
Program Headers:
Type Offset VirtAddr PhysAddr
FileSiz MemSiz Flags Align
PHDR 0x0000000000000040 0x0000000001000040 0x0000000001000040
0x00000000000001f8 0x00000000000001f8 R 0x8
INTERP 0x0000000000000238 0x0000000001000238 0x0000000001000238
0x0000000000000019 0x0000000000000019 R 0x1
[Requesting program interpreter: /lib/ld-musl-x86_64.so.1]
LOAD 0x0000000000000000 0x0000000001000000 0x0000000001000000
0x0000000000000464 0x0000000000000464 R 0x1000
LOAD 0x0000000000000470 0x0000000001001470 0x0000000001001470
0x00000000000000e0 0x00000000000000e0 R E 0x1000
LOAD 0x0000000000000550 0x0000000001002550 0x0000000001002550
0x0000000000000150 0x0000000000000150 RW 0x1000
DYNAMIC 0x0000000000000550 0x0000000001002550 0x0000000001002550
0x0000000000000120 0x0000000000000120 RW 0x8
GNU_RELRO 0x0000000000000550 0x0000000001002550 0x0000000001002550
0x0000000000000150 0x0000000000000ab0 R 0x1
GNU_EH_FRAME 0x0000000000000414 0x0000000001000414 0x0000000001000414
0x0000000000000014 0x0000000000000014 R 0x4
GNU_STACK 0x0000000000000000 0x0000000000000000 0x0000000000000000
0x0000000000000000 0x0000000001000000 RW 0x0
Section to Segment mapping:
Segment Sections...
00
01 .interp
02 .interp .dynsym .gnu.hash .hash .dynstr .rela.plt .rodata .eh_frame_hdr .eh_frame
03 .text .init .fini .plt
04 .dynamic .got.plt
05 .dynamic
06 .dynamic .got.plt
07 .eh_frame_hdr
08
Dynamic section at offset 0x550 contains 18 entries:
Tag Type Name/Value
0x0000000000000001 (NEEDED) Shared library: [libgsl.so.27]
0x0000000000000001 (NEEDED) Shared library: [libc.so]
0x000000000000001e (FLAGS) BIND_NOW
0x000000006ffffffb (FLAGS_1) Flags: NOW
0x0000000000000015 (DEBUG) 0x0
0x0000000000000017 (JMPREL) 0x1000398
0x0000000000000002 (PLTRELSZ) 72 (bytes)
0x0000000000000003 (PLTGOT) 0x1002670
0x0000000000000014 (PLTREL) RELA
0x0000000000000006 (SYMTAB) 0x1000258
0x000000000000000b (SYMENT) 24 (bytes)
0x0000000000000005 (STRTAB) 0x1000344
0x000000000000000a (STRSZ) 78 (bytes)
0x000000006ffffef5 (GNU_HASH) 0x10002e8
0x0000000000000004 (HASH) 0x100030c
0x000000000000000c (INIT) 0x1001500
0x000000000000000d (FINI) 0x1001503
0x0000000000000000 (NULL) 0x0
Relocation section '.rela.plt' at offset 0x398 contains 3 entries:
Offset Info Type Sym. Value Sym. Name + Addend
000001002688 000100000007 R_X86_64_JUMP_SLO 0000000000000000 __libc_start_main + 0
000001002690 000200000007 R_X86_64_JUMP_SLO 0000000000000000 gsl_cdf_gaussian_P + 0
000001002698 000300000007 R_X86_64_JUMP_SLO 0000000000000000 printf + 0
No processor specific unwind information to decode
Symbol table '.dynsym' contains 6 entries:
Num: Value Size Type Bind Vis Ndx Name
0: 0000000000000000 0 NOTYPE LOCAL DEFAULT UND
1: 0000000000000000 0 FUNC GLOBAL DEFAULT UND __libc_start_main
2: 0000000000000000 0 FUNC GLOBAL DEFAULT UND gsl_cdf_gaussian_P
3: 0000000000000000 0 FUNC GLOBAL DEFAULT UND printf
4: 0000000001001500 0 NOTYPE GLOBAL DEFAULT 11 _init
5: 0000000001001503 0 NOTYPE GLOBAL DEFAULT 12 _fini
Symbol table '.symtab' contains 12 entries:
Num: Value Size Type Bind Vis Ndx Name
0: 0000000000000000 0 NOTYPE LOCAL DEFAULT UND
1: 0000000000000000 0 FILE LOCAL DEFAULT ABS crt1.c
2: 0000000000000000 0 FILE LOCAL DEFAULT ABS main-gsl.c
3: 0000000001002550 0 NOTYPE LOCAL HIDDEN 14 _DYNAMIC
4: 0000000001001470 0 NOTYPE GLOBAL DEFAULT 10 _start
5: 0000000001001486 35 FUNC GLOBAL DEFAULT 10 _start_c
6: 00000000010014b0 77 FUNC GLOBAL DEFAULT 10 main
7: 0000000001001500 0 NOTYPE GLOBAL DEFAULT 11 _init
8: 0000000001001503 0 NOTYPE GLOBAL DEFAULT 12 _fini
9: 0000000000000000 0 FUNC GLOBAL DEFAULT UND __libc_start_main
10: 0000000000000000 0 FUNC GLOBAL DEFAULT UND gsl_cdf_gaussian_P
11: 0000000000000000 0 FUNC GLOBAL DEFAULT UND printf
Histogram for bucket list length (total of 6 buckets):
Length Number % of total Coverage
0 2 ( 33.3%)
1 3 ( 50.0%) 60.0%
2 1 ( 16.7%) 100.0%
Histogram for `.gnu.hash' bucket list length (total of 1 bucket):
Length Number % of total Coverage
0 0 ( 0.0%)
1 0 ( 0.0%) 0.0%
2 1 (100.0%) 100.0%
No version information found in this file.
FWIW, $LD_LIBRARY_PATH is empty.
Cloudef
February 3, 2024, 10:35am
11
Ah sorry, try x86_64-linux-gnu, seems like it links to musl by default
zig cc -target x86_64-linux-gnu $(pkg-config --libs --cflags blas gsl) src/main-gsl.c && ./a.out
./a.out: error while loading shared libraries: libgsl.so.27: cannot open shared object file: No such file or directory
ldd ./a.out
linux-vdso.so.1 (0x00007ffd3378a000)
libgsl.so.27 => not found
libc.so.6 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib/libc.so.6 (0x00007f7e9084f000)
/lib64/ld-linux-x86-64.so.2 => /nix/store/qn3ggz5sf3hkjs2c797xf7nan3amdxmp-glibc-2.38-27/lib64/ld-linux-x86-64.so.2 (0x00007f7e90a39000)
Cloudef
February 3, 2024, 10:41am
13
Change gsl.dev to just gsl in your buildinputs
New flake.nix
{
inputs = {
nixpkgs.url = "nixpkgs/nixos-23.11";
flake-utils.url = "github:numtide/flake-utils";
zig-overlay.url = "github:mitchellh/zig-overlay";
zls.url = "github:zigtools/zls";
};
outputs = inputs:
let
inherit (inputs) nixpkgs zig-overlay flake-utils zls;
systems = [ "x86_64-linux" ];
in
flake-utils.lib.eachSystem systems (system:
let
pkgs = import nixpkgs { inherit system; };
# zig = zig-overlay.packages.${system}."0.11.0";
zig = zig-overlay.packages.${system}.master;
zls_pkg = zls.packages.${system}.default;
gsl = pkgs.gsl;
blas = pkgs.blas;
pkgconfig = pkgs.pkg-config;
gcc = pkgs.gcc;
in
{
devShells.default = pkgs.mkShell {
packages = [ zig zls_pkg ];
nativeBuildInputs = [ gcc zig pkgconfig ];
buildInputs = [ gsl blas ];
};
}
);
}
same results as in Zig cc dynamic C lib runtime error on NixOS - #12 by fleimgruber
Cloudef
February 4, 2024, 4:48am
15
I forgot that mkShell does not set the LD_LIBRARY_PATH, you can do it like this:
devShells.default = pkgs.mkShell rec {
nativeBuildInputs = with pkgs; [ gcc zig zls_pkg pkg-config ];
buildInputs = [ gsl blas ];
shellHook = with pkgs.lib; ''
export LD_LIBRARY_PATH="${makeLibraryPath buildInputs}:$LD_LIBRARY_PATH"
'';
}
Slightly funny since it seems to set PKG_CONFIG_PATH though?
Anyhow, you might want to use GitHub - Cloudef/zig2nix: Flake for packaging, building and running Zig projects. that makes all these simpler for you. You can put the packages into zig-env’s customRuntimeDeps and customRuntimeLibs respectively.
@Cloudef edit with actual remaining error.
With your devShells snippet it still does not work for me, zig cc -target x86_64-linux-gnu $(pkg-config --libs --cflags blas gsl) src/main-gsl.c && ./a.out
./a.out: symbol lookup error: /nix/store/9h2wc53zx6x91472d7xwk2k8f9rcq5yb-gsl-2.7.1/lib/libgsl.so.27: undefined symbol: cblas_ctrmv
i.e. the same error as in OP. What’s the full flake.nix that you tested with?
Thanks for recommending zig2nix, it was on my list of projects to look into. About passing packages into zig-env: I am struggling with getting the packages (gsl and blas) into scope to pass them to zig-env via the custom* lists. I looked at your example for mach, where the packages are one of the outputs(?) of zig-env itself AFAIU, see here .
Cloudef
February 5, 2024, 7:21am
17
You can either do what I do there, or use your own nixpkgs input.cblas_ctrmv seems to come from libgslcblas.so which should also be linked by $(pkg-config --libs --cflags blas gsl)
I think I got zig2nix to the point where I see the same results than without it, so I would rather like to understand the cause than using yet another layer. I can share my zig2nix flake.nix if you want to take a look and carry it over the finishing line.
Back to analysis, after your comment I confirmed that libgslcblas.so does show up in the output of pkg-config --libs --cflags blas gsl, but I do not understand why it does not get linked with zig cc (it does get linked with gcc though).
-I/nix/store/bwms0ryhcqf7kyql1bs88a506m3dbvaw-gsl-2.7.1-dev/include -I/nix/store/zd7mm186212ibl659yqbm7nn4miqnrdd-blas-3-dev/include -L/nix/store/9h2wc53zx6x91472d7xwk2k8f9rcq5yb-gsl-2.7.1/lib -L/nix/store/q8fbd9y357n3k6zr2m0gp3hcaj6jwacb-blas-3/lib -lblas -lgsl -lgslcblas -lm
ldd ./a.out
linux-vdso.so.1 (0x00007ffeccb02000)
libgsl.so.27 => /nix/store/0sf6i80ij0s1464qkh965z5piw90v32k-gsl-2.7.1/lib/libgsl.so.27 (0x00007f7513c00000)
libc.so.6 => /nix/store/p3jshbwxiwifm1py0yq544fmdyy98j8a-glibc-2.38-27/lib/libc.so.6 (0x00007f7513a17000)
libm.so.6 => /nix/store/p3jshbwxiwifm1py0yq544fmdyy98j8a-glibc-2.38-27/lib/libm.so.6 (0x00007f7513ef2000)
/lib64/ld-linux-x86-64.so.2 => /nix/store/p3jshbwxiwifm1py0yq544fmdyy98j8a-glibc-2.38-27/lib64/ld-linux-x86-64.so.2 (0x00007f7513fd6000)
Cloudef
February 6, 2024, 5:20am
19
I’m not 100% sure what’s going as I’m not familiar with blas. I wonder if zig has internal blas implementation and simply does not implement that symbol …? Unlike your gcc result, the ldd does not seem to show libblas.so either.
EDIT: Using the Library — GSL 2.8 documentation
AFAICS, zig does not have an internal blas implementation.
It is already in buildInputs, see Zig cc dynamic C lib runtime error on NixOS - #14 by fleimgruber
The GSL documentation says the CBLAS implementation used is libgslblas.so which is present under …-blas-3/lib and is found with pkg-config, see my previous message.