[petsc-users] Installation issue of 3.18.* and 3.19.0 on Apple systems

Wed Apr 5 16:09:25 CDT 2023

The documentation does say

  Entries which cannot be determined are set to ''

so I guess we need a guard.

  Matt

On Wed, Apr 5, 2023 at 5:04 PM Kaus, Boris <kaus at uni-mainz.de> wrote:

> That indeed seems to be the issue:
>
> sandbox:${WORKSPACE}/srcdir/petsc-3.18.0 # python3
> Python 3.9.7 (default, Nov 24 2021, 21:15:59)
> [GCC 10.3.1 20211027] on linux
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import platform
> >>> platform.mac_ver()
> ('', ('', '', ''), '')
> >>> platform.mac_ver()[0].split('.')
> ['']
> >>> tuple([int(a) for a in platform.mac_ver()[0].split('.')])
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "<stdin>", line 1, in <listcomp>
> ValueError: invalid literal for int() with base 10: ‘'
>
>
> On 5. Apr 2023, at 23:00, Satish Balay <balay at mcs.anl.gov> wrote:
>
> Sorry, Was looking at the wrong place.
>
>  v = tuple([int(a) for a in platform.mac_ver()[0].split('.')])
>
>
> Can you try:
>
> balay at ypro petsc % python3
> Python 3.9.6 (default, Mar 10 2023, 20:16:38)
> [Clang 14.0.3 (clang-1403.0.22.14.1)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>
> import platform
> platform.mac_ver()
>
> ('13.3', ('', '', ''), 'x86_64')
>
> platform.mac_ver()[0].split('.')
>
> ['13', '3']
>
> tuple([int(a) for a in platform.mac_ver()[0].split('.')])
>
> (13, 3)
>
>
>
>
> Satish
>
>
>
>
> On Wed, 5 Apr 2023, Kaus, Boris wrote:
>
> Don’t think so:
>
> sandbox:${WORKSPACE}/srcdir/petsc-3.18.0 # env
> _=/usr/bin/env
> VERBOSE=true
> BUILD_LD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ld
> OLDPWD=/workspace/srcdir/petsc-3.18.0
> host_libdir=/workspace/x86_64-linux-musl-cxx11/destdir/lib
> nproc=8
> target=aarch64-apple-darwin20
> bindir=/workspace/destdir/bin
> CC=cc
>
> READELF_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-readelf
> host_bindir=/workspace/x86_64-linux-musl-cxx11/destdir/bin
>
> PATH=/opt/bin/aarch64-apple-darwin20-libgfortran5-cxx11-mpi+openmpi:/opt/aarch64-apple-darwin20/bin:/opt/bin/x86_64-linux-musl-cxx11:/opt/x86_64-linux-musl/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/workspace/x86_64-linux-musl-cxx11/destdir/bin:/workspace/destdir/bin
> nbits=64
> BUILD_STRIP=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-strip
> BUILD_OBJDUMP=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-objdump
>
> CMAKE_TARGET_TOOLCHAIN=/opt/toolchains/aarch64-apple-darwin20-libgfortran5-cxx11-mpi+openmpi/target_aarch64-apple-darwin20.cmake
> FC_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-gfortran
> FC=gfortran
> SRC_NAME=PETSc
> RANLIB_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ranlib
> CC_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-gcc
> PS1=\[\]sandbox\[\]:\[\]${PWD//$WORKSPACE/$\{WORKSPACE\}}\[\] \$
> PKG_CONFIG_SYSROOT_DIR=/workspace/destdir
>
> LD_LIBRARY_PATH=/usr/lib/csl-musl-x86_64:/usr/local/lib64:/usr/local/lib:/usr/lib64:/usr/lib:/lib64:/lib:/workspace/x86_64-linux-musl-cxx11/destdir/lib:/opt/x86_64-linux-musl/x86_64-linux-musl/lib64:/opt/x86_64-linux-musl/x86_64-linux-musl/lib:/opt/aarch64-apple-darwin20/aarch64-apple-darwin20/lib:/opt/aarch64-apple-darwin20/lib:/workspace/destdir/lib64:/workspace/destdir/lib
> HOSTOBJCOPY=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-objcopy
> HOSTOBJDUMP=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-objdump
> LIPO_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-lipo
> HOSTSTRIP=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-strip
> BUILD_OBJCOPY=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-objcopy
> ZERO_AR_DATE=1
> dlext=dylib
> HIDDEN_PS1=\[\]sandbox\[\]:\[\]${PWD//$WORKSPACE/$\{WORKSPACE\}}\[\] \$
> CCACHE_COMPILERCHECK=content
> AR_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ar
> HOSTDSYMUTIL=dsymutil
> SHLVL=1
>
> OBJDUMP_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-objdump
> CXX_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-g++
> HOSTCXX=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-g++
> USER=kausb
> BUILD_DSYMUTIL=dsymutil
> CC_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-gcc
>
> OBJCOPY_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-objcopy
> TERM=screen
> LIPO_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-lipo
> BUILD_LIPO=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-lipo
> NM_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-nm
> host_prefix=/workspace/x86_64-linux-musl-cxx11/destdir
> FC_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-gfortran
> AR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ar
> WORKSPACE=/workspace
> STRIP_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-strip
> HOSTRANLIB=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ranlib
> RANLIB_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ranlib
> DSYMUTIL_FOR_BUILD=dsymutil
> HOSTAS=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-as
> HOSTAR=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ar
> BUILD_RANLIB=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ranlib
> NM_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-nm
> LD=/opt/bin/aarch64-apple-darwin20-libgfortran5-cxx11-mpi+openmpi/ld
> HOSTLD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ld
> bb_full_target=aarch64-apple-darwin20-libgfortran5-cxx11-mpi+openmpi
> LLVM_TARGET=aarch64-apple-darwin20
> BUILD_READELF=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-readelf
> CXX_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-g++
> libdir=/workspace/destdir/lib
>
> MESON_TARGET_TOOLCHAIN=/opt/toolchains/aarch64-apple-darwin20-libgfortran5-cxx11-mpi+openmpi/target_aarch64-apple-darwin20.meson
> LLVM_HOST_TARGET=x86_64-linux-musl
> STRIP_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-strip
> AS_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-as
> HISTFILE=/meta/.bash_history
> HOME=/root
> HOSTLIPO=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-lipo
> includedir=/workspace/destdir/include
>
> MESON_HOST_TOOLCHAIN=/opt/toolchains/x86_64-linux-musl-cxx11/host_x86_64-linux-musl.meson
> BUILD_FC=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-gfortran
> V=true
> BUILD_CC=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-gcc
> HOSTCC=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-gcc
> AS_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-as
> CXX=c++
> rust_target=aarch64-apple-darwin
> rust_host=x86_64-unknown-linux-musl
> HOSTFC=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-gfortran
> exeext=
> READELF_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-readelf
> bb_target=aarch64-apple-darwin20
> SOURCE_DATE_EPOCH=0
> PWD=/workspace/srcdir/petsc-3.18.0
> MACOSX_DEPLOYMENT_TARGET=11.0
> proc_family=arm
> BUILD_NM=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-nm
> BUILD_CXX=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-g++
> LD_FOR_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ld
> OBJDUMP_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-objdump
> OBJCOPY_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-objcopy
> HOSTNM=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-nm
> USE_CCACHE=false
> BUILD_AR=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ar
> BUILD_AS=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-as
> prefix=/workspace/destdir
> HOSTNAME=271f88c24b60
> CHARSET=UTF-8
>
> PKG_CONFIG_PATH=/workspace/destdir/lib/pkgconfig:/workspace/destdir/lib64/pkgconfig:/workspace/destdir/share/pkgconfig
> MACHTYPE=x86_64-linux-musl
> HOSTREADELF=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-readelf
> DSYMUTIL_BUILD=dsymutil
> LD_BUILD=/opt/bin/x86_64-linux-musl-cxx11/x86_64-linux-musl-ld
> host_includedir=/workspace/x86_64-linux-musl-cxx11/destdir/include
>
> CMAKE_HOST_TOOLCHAIN=/opt/toolchains/x86_64-linux-musl-cxx11/host_x86_64-linux-musl.cmake
> SHELL=/bin/bash
>
>
> On 5. Apr 2023, at 22:45, Satish Balay <balay at mcs.anl.gov> wrote:
>
> Well this doesn't trigger the error for me. Do you have any env variables
> set with unicode [non-ascii] chars?
>
> Satish
>
> ---
>
> balay at ypro petsc-3.19.0 % sw_vers
> ProductName: macOS
> ProductVersion: 13.3
> BuildVersion: 22E252
> balay at ypro petsc-3.19.0 % ./configure --with-mpi=0
> --prefix=/workspace/destdir/lib/petsc/double_real_Int32/
>
> =============================================================================================
>                        Configuring PETSc to compile on your system
>
> =============================================================================================
>
> =============================================================================================
>                                    ***** WARNING *****
> You have a version of GNU make older than 4.0. It will work, but may not
> support all the
> parallel testing options. You can install the latest GNU make with your
> package manager,
> such as Brew or MacPorts, or use the --download-make option to get the
> latest GNU make
>
> =============================================================================================
> Compilers:
> C Compiler:         gcc  -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas
> -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden
> -g3 -O0
>   Version: Apple clang version 14.0.3 (clang-1403.0.22.14.1)
> ...
> ...
>
>
> On Wed, 5 Apr 2023, Kaus, Boris wrote:
>
> It can be reproduced with this:
> sandbox:${WORKSPACE}/srcdir/petsc-3.18.0 # ./configure
> --prefix=/workspace/destdir/lib/petsc/double_real_Int32/
>
> *******************************************************************************
>   TypeError or ValueError possibly related to ERROR in COMMAND LINE
> ARGUMENT while running ./configure
>
> -------------------------------------------------------------------------------
> invalid literal for int() with base 10: ''
>
> *******************************************************************************
>
>
> File "/workspace/srcdir/petsc-3.18.0/config/configure.py", line 457, in
> petsc_configure
>   framework =
> config.framework.Framework(['--configModules=PETSc.Configure','--optionsModule=config.compilerOptions']+sys.argv[1:],
> loadArgDB = 0)
> File
> "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/framework.py",
> line 101, in __init__
>   self.createChildren()
> File
> "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/framework.py",
> line 338, in createChildren
>   self.getChild(moduleName)
> File
> "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/framework.py",
> line 323, in getChild
>   config.setupDependencies(self)
> File "/workspace/srcdir/petsc-3.18.0/config/PETSc/Configure.py", line 89,
> in setupDependencies
>   self.registerPythonFile(utility,'config.utilities')
> File "/workspace/srcdir/petsc-3.18.0/config/PETSc/Configure.py", line 49,
> in registerPythonFile
>   utilityObj                             =
> self.framework.require(directory+utilityName, self)
> File
> "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/framework.py",
> line 343, in require
>   config = self.getChild(moduleName, keywordArgs)
> File
> "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/framework.py",
> line 317, in getChild
>   config = type(self, *keywordArgs)
> File
> "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/utilities/macosFirewall.py",
> line 12, in __init__
>   self.isDarwin = config.setCompilers.Configure.isDarwin(self.log)
> File
> "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/setCompilers.py",
> line 664, in isDarwin
>   if not isUname_value: config.setCompilers.Configure.isUname(log)
> File
> "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/setCompilers.py",
> line 630, in isUname
>   v = tuple([int(a) for a in platform.mac_ver()[0].split('.')])
> File
> "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/setCompilers.py",
> line 630, in <listcomp>
>   v = tuple([int(a) for a in platform.mac_ver()[0].split('.')])
>
>
> On 5. Apr 2023, at 22:32, Stefano Zampini <stefano.zampini at gmail.com>
> wrote:
>
> It seems there's some typo/error in the configure command that is being
> executed. Can you post it here?
>
> Il giorno mer 5 apr 2023 alle ore 23:18 Kaus, Boris <kaus at uni-mainz.de<
> mailto:kaus at uni-mainz.de <kaus at uni-mainz.de>><mailto:kaus at uni-mainz.de
> <kaus at uni-mainz.de>>> ha scritto:
> Hi everyone,
>
> I’m trying to install precompiled binaries for PETSc 3.18.5 & 3.19.0 using
> the BinaryBuilder cross-compilation:
> https://github.com/JuliaPackaging/Yggdrasil/pull/6533, which mostly works
> fine: https://buildkite.com/julialang/yggdrasil/builds/2093).
>
> Yet, on apple systems I receive a somewhat weird bug during the configure
> step:
>
> [22:08:49]
> *******************************************************************************
> [22:08:49]     TypeError or ValueError possibly related to ERROR in
> COMMAND LINE ARGUMENT while running ./configure
> [22:08:49]
> -------------------------------------------------------------------------------
> [22:08:49] invalid literal for int() with base 10: ''
> [22:08:49]
> *******************************************************************************
> [22:08:49]
> [22:08:49]
> [22:08:49] /workspace/srcdir/petsc-3.18.0/lib/petsc/conf/rules:860:
> /workspace/srcdir/petsc-3.18.0//lib/petsc/conf/petscrules: No such file or
> directory
> [22:08:49] make[1]: *** No rule to make target
> '/workspace/srcdir/petsc-3.18.0//lib/petsc/conf/petscrules'.  Stop.
> [22:08:49] /workspace/srcdir/petsc-3.18.0/lib/petsc/conf/rules:860:
> /workspace/srcdir/petsc-3.18.0//lib/petsc/conf/petscrules: No such file or
> directory
> [22:08:49] make[1]: *** No rule to make target
> '/workspace/srcdir/petsc-3.18.0//lib/petsc/conf/petscrules'.  Stop.
> [22:08:49] make: *** [GNUmakefile:17:
> /workspace/srcdir/petsc-3.18.0//lib/petsc/conf/petscvariables] Error 2
> [22:08:49] make: *** Waiting for unfinished jobs....
> [22:08:49] make: *** [GNUmakefile:17: lib/petsc/conf/petscvariables] Error
> 2
>
> The log file is rather brief:
>
> sandbox:${WORKSPACE}/srcdir/petsc-3.18.0 # more configure.log
> Executing: uname -s
> stdout: Darwin
>
> It works fine for PETSc 3.16.5/3.17.5, and this first occurs in 3.18.0.
> Is there something that changed between 3.17 & 3.18 that could cause this?
>
> The build system seems to use python3.9 (3.4+ as required)
>
> Thanks!
> Boris
>
>
>
>
>
>
> --
> Stefano
>
>
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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