[package - main-amd64-default][science/PETSc] Failed for PETSc-3.20.2 in configure
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Date: Sat, 23 Dec 2023 04:53:54 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p471524a16046_sdac33a65b9/logs/PETSc-3.20.2.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p471524a16046_sdac33a65b9
Log:
=>> Building science/PETSc
build started at Sat Dec 23 04:52:02 UTC 2023
port directory: /usr/ports/science/PETSc
package name: PETSc-3.20.2
building for: FreeBSD main-amd64-default-job-02 15.0-CURRENT FreeBSD 15.0-CURRENT 1500007 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 2686 Dec 14 01:01 /usr/ports/science/PETSc/Makefile
Ports top last git commit: 471524a1604
Ports top unclean checkout: no
Port dir last git commit: ae14ec9905d
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.0
Host OSVERSION: 1500006
Jail OSVERSION: 1500007
Job Id: 02
!!! Jail is newer than host. (Jail: 1500007, Host: 1500006) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500007
UNAME_v=FreeBSD 15.0-CURRENT 1500007
UNAME_r=15.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.0
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-amd64-default/02/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=main-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.0
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for PETSc-3.20.2:
METIS=on: Enable metis support for graph partitioning algorithms
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--with-64-bit-indices --with-metis=1 --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" MAKE=gmake PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/science/PETSc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/PETSc/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/PETSc/work/.cache HOME=/wrkdirs/usr/ports/science/PETSc/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/PETSc/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/PETSc/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/u
sr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" XDG_DATA_HOME=/wrkdirs/usr/ports/science/PETSc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/PETSc/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/PETSc/work/.cache HOME=/wrkdirs/usr/ports/science/PETSc/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/PETSc/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/PETSc/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/ob
jdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" /usr/local/lib/libmpi.so -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
SHLIB=3.20.2 SHL=3.20 PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/PETSc" EXAMPLESDIR="share/examples/PETSc" DATADIR="share/petsc" WWWDIR="www/PETSc" ETCDIR="etc/PETSc"
--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/petsc DOCSDIR=/usr/local/share/doc/PETSc EXAMPLESDIR=/usr/local/share/examples/PETSc WWWDIR=/usr/local/www/PETSc ETCDIR=/usr/local/etc/PETSc
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> PETSc-3.20.2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9.pkg
[main-amd64-default-job-02] Installing pkg-1.20.9...
[main-amd64-default-job-02] Extracting pkg-1.20.9: .......... done
===> PETSc-3.20.2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of PETSc-3.20.2
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
=> petsc-3.20.2.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch http://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.20.2.tar.gz
petsc-3.20.2.tar.gz 16 MB 78 MBps 00s
===> Fetching all distfiles required by PETSc-3.20.2 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by PETSc-3.20.2 for building
=> SHA256 Checksum OK for petsc-3.20.2.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by PETSc-3.20.2 for building
===> Extracting for PETSc-3.20.2
=> SHA256 Checksum OK for petsc-3.20.2.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for PETSc-3.20.2
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> PETSc-3.20.2 depends on executable: cmake - not found
===> Installing existing package /packages/All/cmake-core-3.27.9.pkg
[main-amd64-default-job-02] Installing cmake-core-3.27.9...
[main-amd64-default-job-02] `-- Installing expat-2.5.0...
[main-amd64-default-job-02] `-- Extracting expat-2.5.0: .......... done
[main-amd64-default-job-02] `-- Installing jsoncpp-1.9.5...
[main-amd64-default-job-02] `-- Extracting jsoncpp-1.9.5: .......... done
[main-amd64-default-job-02] `-- Installing libuv-1.47.0...
[main-amd64-default-job-02] `-- Extracting libuv-1.47.0: .......... done
[main-amd64-default-job-02] `-- Installing rhash-1.4.4...
[main-amd64-default-job-02] | `-- Installing gettext-runtime-0.22.3...
<snip>
On compute nodes, run:
torque-config compute
For further information, see
http://www.adaptivecomputing.com/products/open-source/torque/
--
===> NOTICE:
The torque port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
--
===> NOTICE:
This port is deprecated; you may wish to reconsider installing it:
unfetchable, upstream no longer open source.
It is scheduled to be removed on or after 2023-12-31.
=====
Message from mpich-4.1.2_1:
--
===> NOTICE:
The mpich port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> PETSc-3.20.2 depends on shared library: libmpich.so - found (/usr/local/lib/libmpich.so)
===> Returning to build of PETSc-3.20.2
===> PETSc-3.20.2 depends on shared library: libmetis.so - not found
===> Installing existing package /packages/All/metis-5.1.0_9.pkg
[main-amd64-default-job-02] Installing metis-5.1.0_9...
[main-amd64-default-job-02] Extracting metis-5.1.0_9: .......... done
=====
Message from metis-5.1.0_9:
--
===> NOTICE:
The metis port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> PETSc-3.20.2 depends on shared library: libmetis.so - found (/usr/local/lib/libmetis.so)
===> Returning to build of PETSc-3.20.2
===> PETSc-3.20.2 depends on shared library: libblas.so - not found
===> Installing existing package /packages/All/blas-3.11.0_1.pkg
[main-amd64-default-job-02] Installing blas-3.11.0_1...
[main-amd64-default-job-02] Extracting blas-3.11.0_1: ........ done
===> PETSc-3.20.2 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so)
===> Returning to build of PETSc-3.20.2
===> PETSc-3.20.2 depends on shared library: liblapack.so - not found
===> Installing existing package /packages/All/lapack-3.11.0_1.pkg
[main-amd64-default-job-02] Installing lapack-3.11.0_1...
[main-amd64-default-job-02] Extracting lapack-3.11.0_1: .......... done
===> PETSc-3.20.2 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so)
===> Returning to build of PETSc-3.20.2
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for PETSc-3.20.2
=============================================================================================
Configuring PETSc to compile on your system
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: CC=cc. Ignoring it! Use "./configure CC=$CC" if you really
want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: CXX=c++. Ignoring it! Use "./configure CXX=$CXX" if you
really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: FC=gfortran12. Ignoring it! Use "./configure FC=$FC" if you
really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: F77=gfortran12. Ignoring it! Use "./configure F77=$F77" if
you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: F90=gfortran12. Ignoring it! Use "./configure F90=$F90" if
you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: CFLAGS=-O2 -pipe -fstack-protector-strong
-fno-strict-aliasing . Ignoring it! Use "./configure CFLAGS=$CFLAGS" if you really want
to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: CXXFLAGS=-O2 -pipe -fstack-protector-strong
-fno-strict-aliasing . Ignoring it! Use "./configure CXXFLAGS=$CXXFLAGS" if you really
want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: FCFLAGS=-Wl,-rpath=/usr/local/lib/gcc12. Ignoring it! Use
"./configure FCFLAGS=$FCFLAGS" if you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: FFLAGS=-O -Wl,-rpath=/usr/local/lib/gcc12. Ignoring it! Use
"./configure FFLAGS=$FFLAGS" if you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: F90FLAGS=-O -Wl,-rpath=/usr/local/lib/gcc12. Ignoring it! Use
"./configure F90FLAGS=$F90FLAGS" if you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: CPP=cpp. Ignoring it! Use "./configure CPP=$CPP" if you
really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: CPPFLAGS=. Ignoring it! Use "./configure CPPFLAGS=$CPPFLAGS"
if you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: LDFLAGS= /usr/local/lib/libmpi.so -L/usr/local/lib
-Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -fstack-protector-strong .
Ignoring it! Use "./configure LDFLAGS=$LDFLAGS" if you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: LIBS=. Ignoring it! Use "./configure LIBS=$LIBS" if you
really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: MAKEFLAGS= ARCH=amd64 CONFIGURE_MAX_CMD_LEN=524288
HAVE_COMPAT_IA32_KERN=YES OPSYS=FreeBSD OSREL=15.0 OSVERSION=1500007
PYTHONBASE=/usr/local _OSRELEASE=15.0-CURRENT. Ignoring it! Use "./configure
MAKEFLAGS=$MAKEFLAGS" if you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: AR=/usr/local/bin/ar. Ignoring it! Use "./configure AR=$AR"
if you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
Found environment variable: RANLIB=/usr/local/bin/ranlib. Ignoring it! Use "./configure
RANLIB=$RANLIB" if you really want to use this value
=============================================================================================
=============================================================================================
***** WARNING *****
mpiexec may not work on your system due to network issues. Perhaps you have VPN running
whose network settings may not work with mpiexec or your network is misconfigured
=============================================================================================
*********************************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
---------------------------------------------------------------------------------------------
Unable to find metis in default locations!
Perhaps you can specify with --with-metis-dir=<directory>
If you do not want metis, then give --with-metis=0
You might also consider using --download-metis instead
*********************************************************************************************
===> Script "configure" failed unexpectedly.
Please report the problem to yuri@FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/science/PETSc/work/petsc-3.20.2/configure.log" including
the output of the failure of your make command. Also, it might be a good idea
to provide an overview of all packages installed on your system (e.g. a
/usr/local/sbin/pkg-static info -g -Ea).
*** Error code 1
Stop.
make: stopped in /usr/ports/science/PETSc