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

Kaus, Boris kaus at uni-mainz.de
Wed Apr 5 16:31:14 CDT 2023 

Perhaps python is broken, or perhaps this is because it is not a real Mac OS, but an emulated one.

Seems a similar error now occurs a bit down the line:

---

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 668, in isDarwin
    if not isUname_value: config.setCompilers.Configure.isUname(log)
  File "/workspace/srcdir/petsc-3.18.0/config/BuildSystem/config/setCompilers.py", line 631, 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 631, in <listcomp>
    v = tuple([int(a) for a in platform.mac_ver()[0].split('.')])





On 5. Apr 2023, at 23:11, Satish Balay <balay at mcs.anl.gov> wrote:

Hm - broken python? Either way configure should not fail. Perhaps the following fix:

Satish

---

diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py
index e4d13bea58f..ae53d1e397e 100644
--- a/config/BuildSystem/config/setCompilers.py
+++ b/config/BuildSystem/config/setCompilers.py
@@ -626,10 +626,14 @@ class Configure(config.base.Configure):
        if log: log.write('Detected Darwin')
        isDarwin_value = True
        import platform
-        v = tuple([int(a) for a in platform.mac_ver()[0].split('.')])
-        if v >= (10,15,0):
-          if log: log.write('Detected Darwin/MacOSX Catalina OS\n')
-          isDarwinCatalina_value = True
+        try:
+          v = tuple([int(a) for a in platform.mac_ver()[0].split('.')])
+          if v >= (10,15,0):
+            if log: log.write('Detected Darwin/MacOSX Catalina OS\n')
+            isDarwinCatalina_value = True
+        except RuntimeError:
+          if log: log.write('MacOS version detecton failed!\n')
+          pass
      if output.find('freebsd') >= 0:
        if log: log.write('Detected FreeBSD')
        isFreeBSD_value = True

On Wed, 5 Apr 2023, Kaus, Boris 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><mailto: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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