[package - main-armv7-default][science/gromacs] Failed for gromacs-2022.4 in configure
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Date: Sat, 18 Feb 2023 18:04:21 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/ampere2/data/main-armv7-default/p909032bc6729_s8147104965/logs/gromacs-2022.4.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p909032bc6729_s8147104965
Log:
=>> Building science/gromacs
build started at Sat Feb 18 18:03:49 UTC 2023
port directory: /usr/ports/science/gromacs
package name: gromacs-2022.4
building for: FreeBSD main-armv7-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400078 arm
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400078
Job Id: 05
!!! Jail is newer than host. (Jail: 1400078, Host: 1400073) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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---Begin OPTIONS List---
===> The following configuration options are available for gromacs-2022.4:
ATLAS=off: Use ATLAS for BLAS and LAPACK
FLOAT=off: Use single instead of double precision
LEGACY=on: Install legacy API
OPENCL=off: Heterogeneous computing via OpenCL
OPENMP=on: Parallel processing support via OpenMP
SIMD=off: Use CPU-specific optimizations
X11=on: X11 (graphics) support
====> Multiprocessing: you have to select exactly one of them
NOMP=off: No multiprocessing support
MPICH=off: Parallel processing support via MPICH 3
OPENMPI=off: Parallel processing support via Open MPI
THREAD_MPI=on: Build a thread-MPI-based multithreaded version of GROMACS
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
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--End CONFIGURE_ARGS--
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R="share/doc/gromacs" EXAMPLESDIR="share/examples/gromacs" DATADIR="share/gromacs" WWWDIR="www/gromacs" ETCDIR="etc/gromacs"
--End PLIST_SUB--
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--End resource limits--
=======================<phase: check-sanity >============================
===> License LGPL21 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> gromacs-2022.4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1.pkg
[main-armv7-default-job-05] Installing pkg-1.19.1...
[main-armv7-default-job-05] Extracting pkg-1.19.1: .......... done
===> gromacs-2022.4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gromacs-2022.4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2022.4 for building
===========================================================================
=======================<phase: checksum >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2022.4 for building
=> SHA256 Checksum OK for gromacs-2022.4.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2022.4 for building
===> Extracting for gromacs-2022.4
<snip>
=====
Message from boost-libs-1.81.0:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> gromacs-2022.4 depends on package: boost-libs>=1.44 - found
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.25.1.pkg
[main-armv7-default-job-05] Installing cmake-core-3.25.1...
[main-armv7-default-job-05] `-- Installing expat-2.5.0...
[main-armv7-default-job-05] `-- Extracting expat-2.5.0: .......... done
[main-armv7-default-job-05] `-- Installing jsoncpp-1.9.5...
[main-armv7-default-job-05] `-- Extracting jsoncpp-1.9.5: .......... done
[main-armv7-default-job-05] `-- Installing libuv-1.44.2...
[main-armv7-default-job-05] `-- Extracting libuv-1.44.2: .......... done
[main-armv7-default-job-05] `-- Installing rhash-1.4.3...
[main-armv7-default-job-05] | `-- Installing gettext-runtime-0.21.1...
[main-armv7-default-job-05] | | `-- Installing indexinfo-0.3.1...
[main-armv7-default-job-05] | | `-- Extracting indexinfo-0.3.1: .... done
[main-armv7-default-job-05] | `-- Extracting gettext-runtime-0.21.1: .......... done
[main-armv7-default-job-05] `-- Extracting rhash-1.4.3: .......... done
[main-armv7-default-job-05] Extracting cmake-core-3.25.1: .......... done
===> gromacs-2022.4 depends on file: /usr/local/bin/cmake - found
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on executable: gfortran12 - not found
===> Installing existing package /packages/All/gcc12-12.2.0_5.pkg
[main-armv7-default-job-05] Installing gcc12-12.2.0_5...
[main-armv7-default-job-05] `-- Installing binutils-2.39,1...
[main-armv7-default-job-05] `-- Extracting binutils-2.39,1: .......... done
[main-armv7-default-job-05] `-- Installing gmp-6.2.1...
[main-armv7-default-job-05] `-- Extracting gmp-6.2.1: .......... done
[main-armv7-default-job-05] `-- Installing mpc-1.2.1...
[main-armv7-default-job-05] | `-- Installing mpfr-4.2.0,1...
[main-armv7-default-job-05] | `-- Extracting mpfr-4.2.0,1: .......... done
[main-armv7-default-job-05] `-- Extracting mpc-1.2.1: ......... done
[main-armv7-default-job-05] Extracting gcc12-12.2.0_5: .......... done
=====
Message from gcc12-12.2.0_5:
--
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc12
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> gromacs-2022.4 depends on executable: gfortran12 - found
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on package: pkgconf>=1.3.0_1 - not found
===> Installing existing package /packages/All/pkgconf-1.8.1,1.pkg
[main-armv7-default-job-05] Installing pkgconf-1.8.1,1...
[main-armv7-default-job-05] Extracting pkgconf-1.8.1,1: .......... done
===> gromacs-2022.4 depends on package: pkgconf>=1.3.0_1 - found
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on file: /usr/local/bin/python3.9 - not found
===> Installing existing package /packages/All/python39-3.9.16.pkg
[main-armv7-default-job-05] Installing python39-3.9.16...
[main-armv7-default-job-05] `-- Installing libffi-3.4.4...
[main-armv7-default-job-05] `-- Extracting libffi-3.4.4: .......... done
[main-armv7-default-job-05] `-- Installing mpdecimal-2.5.1...
[main-armv7-default-job-05] `-- Extracting mpdecimal-2.5.1: .......... done
[main-armv7-default-job-05] `-- Installing readline-8.2.0...
[main-armv7-default-job-05] `-- Extracting readline-8.2.0: .......... done
[main-armv7-default-job-05] Extracting python39-3.9.16: .......... done
=====
Message from python39-3.9.16:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> gromacs-2022.4 depends on file: /usr/local/bin/python3.9 - found
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on file: /usr/local/bin/as - found
===> gromacs-2022.4 depends on package: perl5>=5.32.r0<5.33 - not found
===> Installing existing package /packages/All/perl5-5.32.1_3.pkg
[main-armv7-default-job-05] Installing perl5-5.32.1_3...
[main-armv7-default-job-05] Extracting perl5-5.32.1_3: .......... done
===> gromacs-2022.4 depends on package: perl5>=5.32.r0<5.33 - found
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on file: /usr/local/libdata/pkgconfig/ice.pc - not found
===> Installing existing package /packages/All/libICE-1.1.0_1,1.pkg
[main-armv7-default-job-05] Installing libICE-1.1.0_1,1...
[main-armv7-default-job-05] Extracting libICE-1.1.0_1,1: .......... done
===> gromacs-2022.4 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on file: /usr/local/libdata/pkgconfig/sm.pc - not found
===> Installing existing package /packages/All/libSM-1.2.3,1.pkg
[main-armv7-default-job-05] Installing libSM-1.2.3,1...
[main-armv7-default-job-05] Extracting libSM-1.2.3,1: .......... done
===> gromacs-2022.4 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on file: /usr/local/libdata/pkgconfig/xext.pc - not found
===> Installing existing package /packages/All/libXext-1.3.4,1.pkg
[main-armv7-default-job-05] Installing libXext-1.3.4,1...
[main-armv7-default-job-05] `-- Installing libX11-1.7.2,1...
[main-armv7-default-job-05] | `-- Installing libxcb-1.15...
[main-armv7-default-job-05] | | `-- Installing libXau-1.0.9...
[main-armv7-default-job-05] | | `-- Extracting libXau-1.0.9: .......... done
[main-armv7-default-job-05] | | `-- Installing libXdmcp-1.1.3...
[main-armv7-default-job-05] | | `-- Installing xorgproto-2022.1...
[main-armv7-default-job-05] | | `-- Extracting xorgproto-2022.1: .......... done
[main-armv7-default-job-05] | | `-- Extracting libXdmcp-1.1.3: ......... done
[main-armv7-default-job-05] | | `-- Installing libpthread-stubs-0.4...
[main-armv7-default-job-05] | | `-- Extracting libpthread-stubs-0.4: .... done
[main-armv7-default-job-05] | `-- Extracting libxcb-1.15: .......... done
[main-armv7-default-job-05] `-- Extracting libX11-1.7.2,1: .......... done
[main-armv7-default-job-05] Extracting libXext-1.3.4,1: .......... done
===> gromacs-2022.4 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found
===========================================================================
=======================<phase: lib-depends >============================
===> gromacs-2022.4 depends on shared library: libhwloc.so - not found
===> Installing existing package /packages/All/hwloc2-2.8.0.pkg
[main-armv7-default-job-05] Installing hwloc2-2.8.0...
[main-armv7-default-job-05] `-- Installing level-zero-1.9.4...
[main-armv7-default-job-05] `-- Extracting level-zero-1.9.4: .......... done
[main-armv7-default-job-05] `-- Installing libpciaccess-0.16...
[main-armv7-default-job-05] | `-- Installing pciids-20230126...
[main-armv7-default-job-05] | `-- Extracting pciids-20230126: ..... done
[main-armv7-default-job-05] `-- Extracting libpciaccess-0.16: ......... done
[main-armv7-default-job-05] `-- Installing libxml2-2.10.3_1...
[main-armv7-default-job-05] `-- Extracting libxml2-2.10.3_1: .......... done
[main-armv7-default-job-05] Extracting hwloc2-2.8.0: .......... done
===> gromacs-2022.4 depends on shared library: libhwloc.so - found (/usr/local/lib/libhwloc.so)
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on shared library: libfftw3.so - not found
===> Installing existing package /packages/All/fftw3-3.3.10_2.pkg
[main-armv7-default-job-05] Installing fftw3-3.3.10_2...
[main-armv7-default-job-05] Extracting fftw3-3.3.10_2: .......... done
===> gromacs-2022.4 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so)
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so)
===> gromacs-2022.4 depends on shared library: libblas.so - not found
===> Installing existing package /packages/All/blas-3.11.0.pkg
[main-armv7-default-job-05] Installing blas-3.11.0...
[main-armv7-default-job-05] Extracting blas-3.11.0: ........ done
===> gromacs-2022.4 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so)
===> Returning to build of gromacs-2022.4
===> gromacs-2022.4 depends on shared library: liblapack.so - not found
===> Installing existing package /packages/All/lapack-3.11.0.pkg
[main-armv7-default-job-05] Installing lapack-3.11.0...
[main-armv7-default-job-05] Extracting lapack-3.11.0: .......... done
===> gromacs-2022.4 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so)
===> Returning to build of gromacs-2022.4
===========================================================================
=======================<phase: configure >============================
===> Configuring for gromacs-2022.4
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/gromacs/work/.build
-- The C compiler identification is Clang 14.0.5
-- The CXX compiler identification is Clang 14.0.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CXX17_COMPILES
-- Performing Test CXX17_COMPILES - Success
CMake Warning at cmake/gmxPythonDiscovery.cmake:51 (message):
Specifying FindPython3 artifacts may complicate consistent Python detection
in projects bundled with GROMACS. See
https://cmake.org/cmake/help/latest/module/FindPython3.html#artifacts-specification
Call Stack (most recent call first):
CMakeLists.txt:72 (include)
-- Found Python3: /usr/local/bin/python3.9 (found suitable version "3.9.16", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed
CMake Error at /wrkdirs/usr/ports/science/gromacs/work/.build/CMakeFiles/CMakeTmp/CMakeLists.txt:16 (add_executable):
No SOURCES given to target: cmTC_2ba3c
CMake Error at /usr/local/share/cmake/Modules/FindOpenMP.cmake:261 (try_compile):
Failed to generate test project build system.
Call Stack (most recent call first):
/usr/local/share/cmake/Modules/FindOpenMP.cmake:537 (_OPENMP_GET_FLAGS)
cmake/gmxManageOpenMP.cmake:41 (find_package)
CMakeLists.txt:295 (include)
-- Configuring incomplete, errors occurred!
See also "/wrkdirs/usr/ports/science/gromacs/work/.build/CMakeFiles/CMakeOutput.log".
*** Error code 1
Stop.
make: stopped in /usr/ports/science/gromacs