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Not compiling on HPC

Open ccbruels opened this issue 1 year ago • 3 comments

Hi Jared, Similar to the previous issue, I have not been able to compile smrest. Do you still plan to release pre-compiled binaries? If not, do you have any suggestions?

Relevant commands:

$ git clone https://github.com/jts/smrest.git $ cd smrest $ module list Currently Loaded Modulefiles:

  1. perl/modules <aL> 3) zlib/1.2.13-gcc-13.1.0-2los5xu <aL>
  2. bioperl/1.6.901(default) 4) openssl/1.1.1t-gcc-13.1.0-hdhinvb
    $ cargo build --release Compiling openssl-sys v0.9.104 Compiling indexmap v1.9.3 Compiling clap_lex v0.2.4 Compiling hashbrown v0.14.5 Compiling clap v2.34.0 Compiling chrono v0.4.38 Compiling longshot v0.4.3 (https://github.com/jts/longshot.git?rev=1174cb6#1174cb61) Compiling nalgebra v0.27.1 Compiling hashbrown v0.11.2 Compiling cached_proc_macro v0.23.0 Compiling error-chain v0.12.4 Compiling smallvec v1.13.2 Compiling textwrap v0.16.1 Compiling fishers_exact v1.0.1 Compiling strsim v0.10.0 Compiling termcolor v1.4.1 Compiling web-time v1.1.0 Compiling cached_proc_macro_types v0.1.1 Compiling cached v0.53.1 Compiling clap v3.2.25 The following warnings were emitted during compilation:

warning: [email protected]: configuring OpenSSL build: 'perl' reported failure with exit status: 127 warning: [email protected]: openssl-src: failed to build OpenSSL from source

error: failed to run custom build command for openssl-sys v0.9.104

Caused by: process didn't exit successfully: /panfs/jay/groups/12/pkang/shared/software/smrest/target/release/build/openssl-sys-d3efc7c330d710d1/build-script-main (exit status: 1) --- stdout cargo:rustc-check-cfg=cfg(osslconf, values("OPENSSL_NO_OCB", "OPENSSL_NO_SM4", "OPENSSL_NO_SEED", "OPENSSL_NO_CHACHA", "OPENSSL_NO_CAST", "OPENSSL_NO_IDEA", "OPENSSL_NO_CAMELLIA", "OPENSSL_NO_RC4", "OPENSSL_NO_BF", "OPENSSL_NO_PSK", "OPENSSL_NO_DEPRECATED_3_0", "OPENSSL_NO_SCRYPT", "OPENSSL_NO_SM3", "OPENSSL_NO_RMD160", "OPENSSL_NO_EC2M", "OPENSSL_NO_OCSP", "OPENSSL_NO_CMS", "OPENSSL_NO_COMP", "OPENSSL_NO_SOCK", "OPENSSL_NO_STDIO", "OPENSSL_NO_EC", "OPENSSL_NO_SSL3_METHOD", "OPENSSL_NO_KRB5", "OPENSSL_NO_TLSEXT", "OPENSSL_NO_SRP", "OPENSSL_NO_RFC3779", "OPENSSL_NO_SHA", "OPENSSL_NO_NEXTPROTONEG", "OPENSSL_NO_ENGINE", "OPENSSL_NO_BUF_FREELISTS")) cargo:rustc-check-cfg=cfg(openssl) cargo:rustc-check-cfg=cfg(libressl) cargo:rustc-check-cfg=cfg(boringssl) cargo:rustc-check-cfg=cfg(libressl250) cargo:rustc-check-cfg=cfg(libressl251) cargo:rustc-check-cfg=cfg(libressl252) cargo:rustc-check-cfg=cfg(libressl261) cargo:rustc-check-cfg=cfg(libressl270) cargo:rustc-check-cfg=cfg(libressl271) cargo:rustc-check-cfg=cfg(libressl273) cargo:rustc-check-cfg=cfg(libressl280) cargo:rustc-check-cfg=cfg(libressl281) cargo:rustc-check-cfg=cfg(libressl291) cargo:rustc-check-cfg=cfg(libressl310) cargo:rustc-check-cfg=cfg(libressl321) cargo:rustc-check-cfg=cfg(libressl332) cargo:rustc-check-cfg=cfg(libressl340) cargo:rustc-check-cfg=cfg(libressl350) cargo:rustc-check-cfg=cfg(libressl360) cargo:rustc-check-cfg=cfg(libressl361) cargo:rustc-check-cfg=cfg(libressl370) cargo:rustc-check-cfg=cfg(libressl380) cargo:rustc-check-cfg=cfg(libressl381) cargo:rustc-check-cfg=cfg(libressl382) cargo:rustc-check-cfg=cfg(libressl390) cargo:rustc-check-cfg=cfg(libressl400) cargo:rustc-check-cfg=cfg(ossl101) cargo:rustc-check-cfg=cfg(ossl102) cargo:rustc-check-cfg=cfg(ossl102f) cargo:rustc-check-cfg=cfg(ossl102h) cargo:rustc-check-cfg=cfg(ossl110) cargo:rustc-check-cfg=cfg(ossl110f) cargo:rustc-check-cfg=cfg(ossl110g) cargo:rustc-check-cfg=cfg(ossl110h) cargo:rustc-check-cfg=cfg(ossl111) cargo:rustc-check-cfg=cfg(ossl111b) cargo:rustc-check-cfg=cfg(ossl111c) cargo:rustc-check-cfg=cfg(ossl111d) cargo:rustc-check-cfg=cfg(ossl300) cargo:rustc-check-cfg=cfg(ossl310) cargo:rustc-check-cfg=cfg(ossl320) cargo:rustc-check-cfg=cfg(ossl330) cargo:rustc-check-cfg=cfg(ossl340) cargo:rerun-if-env-changed=X86_64_UNKNOWN_LINUX_GNU_OPENSSL_NO_VENDOR X86_64_UNKNOWN_LINUX_GNU_OPENSSL_NO_VENDOR unset cargo:rerun-if-env-changed=OPENSSL_NO_VENDOR OPENSSL_NO_VENDOR unset cargo:rerun-if-env-changed=X86_64_UNKNOWN_LINUX_GNU_OPENSSL_CONFIG_DIR X86_64_UNKNOWN_LINUX_GNU_OPENSSL_CONFIG_DIR unset cargo:rerun-if-env-changed=OPENSSL_CONFIG_DIR OPENSSL_CONFIG_DIR unset OUT_DIR = Some(/panfs/jay/groups/12/pkang/shared/software/smrest/target/release/build/openssl-sys-784dd0caf1221102/out) cargo:rerun-if-env-changed=CC_x86_64-unknown-linux-gnu CC_x86_64-unknown-linux-gnu = None cargo:rerun-if-env-changed=CC_x86_64_unknown_linux_gnu CC_x86_64_unknown_linux_gnu = None cargo:rerun-if-env-changed=HOST_CC HOST_CC = None cargo:rerun-if-env-changed=CC CC = None cargo:rerun-if-env-changed=CC_ENABLE_DEBUG_OUTPUT RUSTC_WRAPPER = None cargo:rerun-if-env-changed=CRATE_CC_NO_DEFAULTS CRATE_CC_NO_DEFAULTS = None DEBUG = Some(false) CARGO_CFG_TARGET_FEATURE = Some(fxsr,sse,sse2) cargo:rerun-if-env-changed=CFLAGS_x86_64-unknown-linux-gnu CFLAGS_x86_64-unknown-linux-gnu = None cargo:rerun-if-env-changed=CFLAGS_x86_64_unknown_linux_gnu CFLAGS_x86_64_unknown_linux_gnu = None cargo:rerun-if-env-changed=HOST_CFLAGS HOST_CFLAGS = None cargo:rerun-if-env-changed=CFLAGS CFLAGS = None cargo:rerun-if-env-changed=AR_x86_64-unknown-linux-gnu AR_x86_64-unknown-linux-gnu = None cargo:rerun-if-env-changed=AR_x86_64_unknown_linux_gnu AR_x86_64_unknown_linux_gnu = None cargo:rerun-if-env-changed=HOST_AR HOST_AR = None cargo:rerun-if-env-changed=AR AR = None cargo:rerun-if-env-changed=ARFLAGS_x86_64-unknown-linux-gnu ARFLAGS_x86_64-unknown-linux-gnu = None cargo:rerun-if-env-changed=ARFLAGS_x86_64_unknown_linux_gnu ARFLAGS_x86_64_unknown_linux_gnu = None cargo:rerun-if-env-changed=HOST_ARFLAGS HOST_ARFLAGS = None cargo:rerun-if-env-changed=ARFLAGS ARFLAGS = None cargo:rerun-if-env-changed=RANLIB_x86_64-unknown-linux-gnu RANLIB_x86_64-unknown-linux-gnu = None cargo:rerun-if-env-changed=RANLIB_x86_64_unknown_linux_gnu RANLIB_x86_64_unknown_linux_gnu = None cargo:rerun-if-env-changed=HOST_RANLIB HOST_RANLIB = None cargo:rerun-if-env-changed=RANLIB RANLIB = None cargo:rerun-if-env-changed=RANLIBFLAGS_x86_64-unknown-linux-gnu RANLIBFLAGS_x86_64-unknown-linux-gnu = None cargo:rerun-if-env-changed=RANLIBFLAGS_x86_64_unknown_linux_gnu RANLIBFLAGS_x86_64_unknown_linux_gnu = None cargo:rerun-if-env-changed=HOST_RANLIBFLAGS HOST_RANLIBFLAGS = None cargo:rerun-if-env-changed=RANLIBFLAGS RANLIBFLAGS = None running cd "/panfs/jay/groups/12/pkang/shared/software/smrest/target/release/build/openssl-sys-784dd0caf1221102/out/openssl-build/build/src" && env -u CROSS_COMPILE AR="ar" CC="cc" RANLIB="ranlib" "perl" "./Configure" "--prefix=/panfs/jay/groups/12/pkang/shared/software/smrest/target/release/build/openssl-sys-784dd0caf1221102/out/openssl-build/install" "--openssldir=/usr/local/ssl" "no-shared" "no-ssl3" "no-tests" "no-comp" "no-zlib" "no-zlib-dynamic" "--libdir=lib" "no-md2" "no-rc5" "no-weak-ssl-ciphers" "no-camellia" "no-idea" "no-seed" "linux-x86_64" "-O2" "-ffunction-sections" "-fdata-sections" "-fPIC" "-m64" cargo:warning=configuring OpenSSL build: 'perl' reported failure with exit status: 127 cargo:warning=openssl-src: failed to build OpenSSL from source

--- stderr perl: symbol lookup error: /common/software/install/migrated/perl/modules/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_Istack_sp_ptr

Error configuring OpenSSL build: 'perl' reported failure with exit status: 127 Command failed: cd "/panfs/jay/groups/12/pkang/shared/software/smrest/target/release/build/openssl-sys-784dd0caf1221102/out/openssl-build/build/src" && env -u CROSS_COMPILE AR="ar" CC="cc" RANLIB="ranlib" "perl" "./Configure" "--prefix=/panfs/jay/groups/12/pkang/shared/software/smrest/target/release/build/openssl-sys-784dd0caf1221102/out/openssl-build/install" "--openssldir=/usr/local/ssl" "no-shared" "no-ssl3" "no-tests" "no-comp" "no-zlib" "no-zlib-dynamic" "--libdir=lib" "no-md2" "no-rc5" "no-weak-ssl-ciphers" "no-camellia" "no-idea" "no-seed" "linux-x86_64" "-O2" "-ffunction-sections" "-fdata-sections" "-fPIC" "-m64"

warning: build failed, waiting for other jobs to finish...

ccbruels avatar Oct 23 '24 21:10 ccbruels

Sorry about this, the openssl package in rust seems like a common source of problems. I do intend to provide pre-compiled binaries - I'll put it back on my todo list.

jts avatar Oct 24 '24 14:10 jts

That would be great, thanks! Best, Christine

On Thu, Oct 24, 2024 at 9:16 AM Jared Simpson @.***> wrote:

Sorry about this, the openssl package in rust seems like a common source of problems. I do intend to provide pre-compiled binaries - I'll put it back on my todo list.

— Reply to this email directly, view it on GitHub https://github.com/jts/smrest/issues/2#issuecomment-2435420836, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIZPTZR56BSZGEUKAXDIDHDZ5D6LTAVCNFSM6AAAAABQPYB6ZWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZVGQZDAOBTGY . You are receiving this because you authored the thread.Message ID: @.***>

ccbruels avatar Oct 24 '24 16:10 ccbruels

Hi @ccbruels,

Could you try this binary? https://github.com/jts/smrest/releases/download/0.1.0/smrest-0.1.0

jts avatar Oct 28 '24 16:10 jts