Static build's -fPIC cc::Build flag ineffective?

brainstorm · May 13, 2020, 9:36pm

I'm working on a project that has a bindgen C lib (htslib) dependency, which is wrapped by (rust-htslib) and I'm using a few -sys crates that facilitate static compilation of dependencies, such as xz/lzma:

$ git clone https://github.com/brainstorm/htsget-aws && cd htsget-aws && cargo build

I cannot compile it statically and built against htsget-aws since htslib (the underlying lib that rust-htslib is trying to wrap) has some linker issues:

(...)
" "/home/limsadmin/dev/htsget-
"/home/limsadmin/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-428d15b56101bdc7.rlib" "/home/limsadmin/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-941f7f6bc622e313.rlib" "-Wl,--end-group" "/home/limsadmin/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-e915d31ab7edbbd4.rlib" "-Wl,-Bdynamic" "-lutil" "-ldl" "-lutil" "-ldl" "-lrt" "-lpthread" "-lgcc_s" "-lc" "-lm" "-lrt" "-lpthread" "-lutil" "-ldl" "-lutil"
  = note: /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(bgzf.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(header.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(hfile.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(hfile_net.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(hts.o): relocation R_X86_64_32S against symbol `seq_nt16_table' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(multipart.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(region.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(sam.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(textutils.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(thread_pool.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(cram_decode.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(cram_encode.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(cram_index.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(cram_io.o): relocation R_X86_64_32S against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(cram_samtools.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(cram_stats.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(mFILE.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(open_trace_file.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(rANS_static.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(hfile_libcurl.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(knetfile.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(kstring.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(faidx.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(md5.o): relocation R_X86_64_32S against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
          /usr/bin/ld: /home/limsadmin/dev/htsget-aws/target/debug/deps/libhts_sys-7dace0b999e82069.rlib(cram_codecs.o): relocation R_X86_64_32S against hidden symbol `cram_byte_array_stop_encode_free' can not be used when making a shared object
          /usr/bin/ld: final link failed: Nonrepresentable section on output
          collect2: error: ld returned 1 exit status
          

error: aborting due to previous error

error: could not compile `reads`.

To learn more, run the command again with --verbose.

Even when one of the underlying libs has everything I can imagine pointing and set to static compilation:

https://github.com/brainstorm/rust-htslib/blob/musl_support/hts-sys/build.rs#L34
https://github.com/brainstorm/htsget-aws/blob/master/reads/build.rs#L4
https://github.com/brainstorm/rust-htslib/blob/musl_support/hts-sys/build.rs#L78
https://github.com/brainstorm/rust-htslib/blob/musl_support/hts-sys/build.rs#L93

There seem to be some unresolved symbols on htslib though when looking at the generated libhts.a and its objects when grepping the symbols from the linker errors above:

$ cd ./target/debug/build/hts-sys-76fd95c663d78e71/out
$ ar x libhts.a
$ nm *.o | grep seq_nt16_table
0000000000000640 R seq_nt16_table
                 U seq_nt16_table
                 U seq_nt16_table

That library and symbols seem to have some priors in Debian arm64 builds for packages that depend on it, for instance "segemehl" and "pysam" itself:

http://crossqa.debian.net/build/segemehl_0.3.4-1_arm64_20190306143015.log

So before I dig further on htslib's (static) building logic (and Rust's too), do those unresolved symbol errors sound familiar even when -fPIC cc flags are passed in the aforementioned build.rs files? I've tried with regular CFLAGS="-fPIC" cargo build with same effects, unfortunately

What am I doing wrong? Any pointers/help are highly appreciated!

brainstorm · May 15, 2020, 6:24am

I figured this out (partially) by modifying rust-htslib/hts-sys/build.rs that CFLAGS were not being passed correctly during either autoreconf, configure or make itself:

https://github.com/brainstorm/rust-htslib/commit/1ba12f32430dc3dd1df0e6edcc7fa50ed5615e01

In addition, the -B flag passed to make, also made the build fail to (re)-build reliably (still don't know why):

https://github.com/brainstorm/rust-htslib/commit/7e6ca8d17de74fe2f2baade9258cbe76db391568

Now at least it's just erroring out on undefined references for the symbols that I'm actually using on my own crate, htsget-aws:

htsget-aws]$ cargo build -vvv
(...)
nown-linux-gnu/lib/libcompiler_builtins-e915d31ab7edbbd4.rlib" "-Wl,-Bdynamic" "-lutil" "-ldl" "-lutil" "-ldl" "-lrt" "-lpthread" "-lgcc_s" "-lc" "-lm" "-lrt" "-lpthread" "-lutil" "-ldl" "-lutil"
  = note: /home/limsadmin/dev/htsget-aws/target/debug/deps/librust_htslib-6602f5d5804d9af5.rlib(rust_htslib-6602f5d5804d9af5.2kgc5d1okt3lai62.rcgu.o): In function `rust_htslib::bam::IndexedReader::new::hbccbc07dfdea5d58':
          /home/limsadmin/dev/rust-htslib/src/bam/mod.rs:362: undefined reference to `sam_hdr_read'
          /home/limsadmin/dev/rust-htslib/src/bam/mod.rs:364: undefined reference to `sam_index_load'
          /home/limsadmin/dev/htsget-aws/target/debug/deps/librust_htslib-6602f5d5804d9af5.rlib(rust_htslib-6602f5d5804d9af5.2kgc5d1okt3lai62.rcgu.o): In function `rust_htslib::bam::hts_open::haa5c134654a9c329':
          /home/limsadmin/dev/rust-htslib/src/bam/mod.rs:773: undefined reference to `hts_open'
          /home/limsadmin/dev/htsget-aws/target/debug/deps/librust_htslib-6602f5d5804d9af5.rlib(rust_htslib-6602f5d5804d9af5.32dfbenixrzvd7k8.rcgu.o): In function `_$LT$rust_htslib..bam..IndexedReader$u20$as$u20$core..ops..drop..Drop$GT$::drop::hb5567df68290afc9':
          /home/limsadmin/dev/rust-htslib/src/bam/mod.rs:525: undefined reference to `hts_itr_destroy'
          /home/limsadmin/dev/rust-htslib/src/bam/mod.rs:527: undefined reference to `hts_idx_destroy'
          /home/limsadmin/dev/rust-htslib/src/bam/mod.rs:528: undefined reference to `hts_close'
          /home/limsadmin/dev/htsget-aws/target/debug/deps/librust_htslib-6602f5d5804d9af5.rlib(rust_htslib-6602f5d5804d9af5.32dfbenixrzvd7k8.rcgu.o): In function `_$LT$rust_htslib..bam..HeaderView$u20$as$u20$core..ops..drop..Drop$GT$::drop::h065e2094af67d830':
          /home/limsadmin/dev/rust-htslib/src/bam/mod.rs:934: undefined reference to `sam_hdr_destroy'
          collect2: error: ld returned 1 exit status
          

error: aborting due to previous error

error: could not compile `reads`.

EDIT: A bit more context for the issue:

$ pwd
/home/limsadmin/dev/htsget-aws/target/debug/deps
$ ar x librust_htslib-6602f5d5804d9af5.rlib
$ nm *.o | grep hts_open
                 U hts_open
0000000000000000 t _ZN11rust_htslib3bam8hts_open17haa5c134654a9c329E
                 U hts_open
                 U hts_open

Getting there

berkus · May 15, 2020, 9:10am

If you're building on linux - the linux linker is sensitive to the order of the libraries; check that library containing hts_* functions is linked after the code that references them. If the library architecture is correct, it should solve your missing symbols issue.

brainstorm · May 15, 2020, 1:03pm

Thanks Berkus!

This was all that was needed after the former tweaks!:

https://github.com/brainstorm/rust-htslib/commit/6e587a64634fbad7a451fc45cf50370d1a37c3ce

system · August 13, 2020, 1:03pm

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Static build's -fPIC cc::Build flag ineffective?

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