Installation issue: [email protected] on MacOSX #19041
Description
After having handed in my thesis (and therefore can risk screwing up my environment again) I tried to upgrade to the up-to-date spack/develop branch. Turns out this breaks building openblas. I'm not sure why, there are at least 3 option that I'm aware of:
- The latest Xcode update (to
[email protected]) is unable to buildopenblas(previously it was[email protected], i.e. my software is older than the clang-rename) - Neither the old, nor the new
gfortranbinary is working with the new system clang (I tried my old one from a[email protected]%[email protected]as well as a new one from[email protected]%[email protected]) - Something broke in the
openblas/package.pyduring the update
I'm using the same environment as before with a couple of not-in-upstream-spack-packages but non of those can interfere (mostly python packages far above blas). Unfortunately I cannot easily recover the old base commit, but the current one is 04771ad9f8 from just now.
Currently I'm trying to set {blas,lapack}: [libvecfort] as suggested in #7803 and it seems to work (at least py-numpy successfully installed). I'm attaching the build log and environment in the hope that someone can point out where I'm just being stupid and that this build normally works... Googling the error message didn't turn up any information, since this (see below) is "just" an Implicit declaration of function 'cggsvp_' is invalid in C99 it may be fine to just patch out the -Werror flag and be done with it but I (at least currently) don't want to fiddle with the build and hope for the libvecfort thing to work.
Pinging a couple of people that work on MacOSX for their comments @adamjstewart @davydden ?
% spack debug report
* **Spack:** 0.15.4-1203-1240db659a
* **Python:** 3.7.4
* **Platform:** darwin-catalina-skylake
spack-build-out.txt
spack-build-env.txt
healther@MacBook-Air-2 spack % spack install
==> Installing environment generalenv
==> Installing openblas
==> No binary for openblas found: installing from source
==> Warning: microarchitecture specific optimizations are not supported yet on mixed compiler toolchains [check [email protected] for further details]
==> Using cached archive: /Users/healther/Documents/git.nosync/spack/var/spack/cache/_source-cache/archive/04/0484d275f87e9b8641ff2eecaa9df2830cbe276ac79ad80494822721de6e1693.tar.gz
==> openblas: Executing phase: 'edit'
==> openblas: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j4' 'CC=/Users/healther/Documents/git.nosync/spack/lib/spack/env/clang/clang' 'FC=/Users/healther/Documents/git.nosync/spack/lib/spack/env/clang/gfortran' 'MAKE_NB_JOBS=0' 'ARCH=x86_64' 'DYNAMIC_ARCH=1' 'USE_OPENMP=0' 'USE_THREAD=0' 'libs' 'netlib' 'shared'
9 errors found in build log:
19707 /Users/healther/Documents/git.nosync/spack/lib/spack/env/clang/clang -O2 -DMAX_STACK_ALLOC=2048 -DEXPRECISION -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DDYNAMIC_ARCH -DNO_WARMUP -DMAX_CPU_NUMBER=4 -DMAX_PARALLEL_NUMBER=1 -DVERSION="0.3.10" -UASMNAME -UASMFNAME
-UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME=_ -DASMFNAME=__ -DNAME=_ -DCNAME= -DCHAR_NAME="_" -DCHAR_CNAME="" -DNO_AFFINITY -I. -DHAVE_LAPACK_CONFIG_H -I../include -c -o lapacke_zupmtr_work.o lapacke_zupmtr_work.c
19708 /Users/healther/Documents/git.nosync/spack/lib/spack/env/clang/clang -O2 -DMAX_STACK_ALLOC=2048 -DEXPRECISION -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DDYNAMIC_ARCH -DNO_WARMUP -DMAX_CPU_NUMBER=4 -DMAX_PARALLEL_NUMBER=1 -DVERSION="0.3.10" -UASMNAME -UASMFNAME
-UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME=_ -DASMFNAME=__ -DNAME=_ -DCNAME= -DCHAR_NAME="_" -DCHAR_CNAME="" -DNO_AFFINITY -I. -DHAVE_LAPACK_CONFIG_H -I../include -c -o lapacke_cggsvp.o lapacke_cggsvp.c
19709 /Users/healther/Documents/git.nosync/spack/lib/spack/env/clang/clang -O2 -DMAX_STACK_ALLOC=2048 -DEXPRECISION -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DDYNAMIC_ARCH -DNO_WARMUP -DMAX_CPU_NUMBER=4 -DMAX_PARALLEL_NUMBER=1 -DVERSION="0.3.10" -UASMNAME -UASMFNAME
-UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME=_ -DASMFNAME=__ -DNAME=_ -DCNAME= -DCHAR_NAME="_" -DCHAR_CNAME="" -DNO_AFFINITY -I. -DHAVE_LAPACK_CONFIG_H -I../include -c -o lapacke_cggsvp_work.o lapacke_cggsvp_work.c
19710 /Users/healther/Documents/git.nosync/spack/lib/spack/env/clang/clang -O2 -DMAX_STACK_ALLOC=2048 -DEXPRECISION -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DDYNAMIC_ARCH -DNO_WARMUP -DMAX_CPU_NUMBER=4 -DMAX_PARALLEL_NUMBER=1 -DVERSION="0.3.10" -UASMNAME -UASMFNAME
-UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME=_ -DASMFNAME=__ -DNAME=_ -DCNAME= -DCHAR_NAME="_" -DCHAR_CNAME="" -DNO_AFFINITY -I. -DHAVE_LAPACK_CONFIG_H -I../include -c -o lapacke_dggsvp.o lapacke_dggsvp.c
19711 /Users/healther/Documents/git.nosync/spack/lib/spack/env/clang/clang -O2 -DMAX_STACK_ALLOC=2048 -DEXPRECISION -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DDYNAMIC_ARCH -DNO_WARMUP -DMAX_CPU_NUMBER=4 -DMAX_PARALLEL_NUMBER=1 -DVERSION="0.3.10" -UASMNAME -UASMFNAME
-UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME=_ -DASMFNAME=__ -DNAME=_ -DCNAME= -DCHAR_NAME="_" -DCHAR_CNAME="" -DNO_AFFINITY -I. -DHAVE_LAPACK_CONFIG_H -I../include -c -o lapacke_dggsvp_work.o lapacke_dggsvp_work.c
19712 /Users/healther/Documents/git.nosync/spack/lib/spack/env/clang/clang -O2 -DMAX_STACK_ALLOC=2048 -DEXPRECISION -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DDYNAMIC_ARCH -DNO_WARMUP -DMAX_CPU_NUMBER=4 -DMAX_PARALLEL_NUMBER=1 -DVERSION="0.3.10" -UASMNAME -UASMFNAME
-UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME=_ -DASMFNAME=__ -DNAME=_ -DCNAME= -DCHAR_NAME="_" -DCHAR_CNAME="" -DNO_AFFINITY -I. -DHAVE_LAPACK_CONFIG_H -I../include -c -o lapacke_sggsvp.o lapacke_sggsvp.c
>> 19713 lapacke_cggsvp_work.c:52:9: error: implicit declaration of function 'cggsvp_' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
19714 LAPACK_cggsvp( &jobu, &jobv, &jobq, &m, &p, &n, a, &lda, b, &ldb, &tola,
19715 ^
19716 ../include/lapack.h:3771:23: note: expanded from macro 'LAPACK_cggsvp'
19717 #define LAPACK_cggsvp LAPACK_GLOBAL(cggsvp,CGGSVP)
19718 ^
19719 ../include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
...
19741 ../include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
19742 #define LAPACK_GLOBAL(lcname,UCNAME) lcname##_
19743 ^
19744 <scratch space>:94:1: note: expanded from here
19745 cggsvp3_
19746 ^
>> 19747 lapacke_cggsvp_work.c:139:9: error: implicit declaration of function 'cggsvp_' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
19748 LAPACK_cggsvp( &jobu, &jobv, &jobq, &m, &p, &n, a_t, &lda_t, b_t,
19749 ^
19750 ../include/lapack.h:3771:23: note: expanded from macro 'LAPACK_cggsvp'
19751 #define LAPACK_cggsvp LAPACK_GLOBAL(cggsvp,CGGSVP)
19752 ^
19753 ../include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
19754 #define LAPACK_GLOBAL(lcname,UCNAME) lcname##_
19755 ^
19756 <scratch space>:229:1: note: expanded from here
19757 cggsvp_
19758 ^
19759 2 errors generated.
>> 19760 make[3]: *** [lapacke_cggsvp_work.o] Error 1
19761 make[3]: *** Waiting for unfinished jobs....
>> 19762 lapacke_dggsvp_work.c:48:9: error: implicit declaration of function 'dggsvp_' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
19763 LAPACK_dggsvp( &jobu, &jobv, &jobq, &m, &p, &n, a, &lda, b, &ldb, &tola,
19764 ^
19765 ../include/lapack.h:3763:23: note: expanded from macro 'LAPACK_dggsvp'
19766 #define LAPACK_dggsvp LAPACK_GLOBAL(dggsvp,DGGSVP)
19767 ^
19768 ../include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
...
19790 ../include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
19791 #define LAPACK_GLOBAL(lcname,UCNAME) lcname##_
19792 ^
19793 <scratch space>:95:1: note: expanded from here
19794 dggsvp3_
19795 ^
>> 19796 lapacke_dggsvp_work.c:127:9: error: implicit declaration of function 'dggsvp_' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
19797 LAPACK_dggsvp( &jobu, &jobv, &jobq, &m, &p, &n, a_t, &lda_t, b_t,
19798 ^
19799 ../include/lapack.h:3763:23: note: expanded from macro 'LAPACK_dggsvp'
19800 #define LAPACK_dggsvp LAPACK_GLOBAL(dggsvp,DGGSVP)
19801 ^
19802 ../include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
19803 #define LAPACK_GLOBAL(lcname,UCNAME) lcname##_
19804 ^
19805 <scratch space>:229:1: note: expanded from here
19806 dggsvp_
19807 ^
19808 2 errors generated.
>> 19809 make[3]: *** [lapacke_dggsvp_work.o] Error 1
>> 19810 make[2]: *** [lapacke] Error 2
>> 19811 make[1]: *** [lapackelib] Error 2
>> 19812 make: *** [netlib] Error 2
See build log for details:
/var/folders/1q/jxx1cgcx3l13d153s6_c1zc00000gn/T/healther/spack-stage/spack-stage-openblas-0.3.10-gkmqerz6bgkp6uw5jdkmeiiadxlwyyhw/spack-build-out.txt
Steps to reproduce the issue
$ spack install openblas
...Information on your system
spack:
# add package specs to the `specs` list
specs: [py-notebook ^[email protected], py-numpy, py-scipy, nest~mpi~optimize~openmp,
py-matplotlib, py-ipython, py-line-profiler, py-memory-profiler, boost, yaml-cpp,
ccache, py-pudb, htop, py-virtualenv, py-sympy, py-scikit-optimize, py-scikit-learn,
py-scikit-image, py-requests, py-flake8, py-black, py-pandas, py-numba, py-tornado,
py-ics, py-xlrd, py-git-review, py-seaborn, openssh, py-pynn, py-sbs]
view: true
config: {}
mirrors: {}
modules:
enable: []
packages: {}
repos: []
upstreams: {}
definitions: []
concretization: together
compilers:
- compiler:
spec: [email protected]
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /Users/healther/Documents/git.nosync/spack/opt/spack/darwin-catalina-x86_64/apple-clang-12.0.0/gcc-10.2.0-j73olo3b5grspw4skyyfkynhtnagj3hd/bin/gfortran
fc: /Users/healther/Documents/git.nosync/spack/opt/spack/darwin-catalina-x86_64/apple-clang-12.0.0/gcc-10.2.0-j73olo3b5grspw4skyyfkynhtnagj3hd/bin/gfortran
flags: {}
operating_system: catalina
target: x86_64
modules: []
environment: {unset: []}
extra_rpaths: []