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

Kaus, Boris kaus at uni-mainz.de
Wed Apr 5 15:59:09 CDT 2023 

In case anyone wants to reproduce this:

$julia build_tarballs.jl --debug --verbose aarch64-apple-darwin-libgfortran5-mpi+openmpi

Here build_tarballs.jl is given here:

https://github.com/JuliaPackaging/Yggdrasil/blob/46a609970e3236610804a66903936ea1d6fa3759/P/PETSc/build_tarballs.jl

It requires Julia, BinaryBuilder and a system that allows Docker.

Boris

On 5. Apr 2023, at 22:49, Kaus, Boris <kaus at uni-mainz.de> 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><mailto: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


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