[package - 114amd64-default][science/lammps] Failed for lammps-2020.10.29 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sun Nov 22 21:58:35 UTC 2020
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 at FreeBSD.org
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: head/science/lammps/Makefile 553581 2020-10-29 04:35:35Z yuri $
Log URL: http://beefy9.nyi.freebsd.org/data/114amd64-default/556025/logs/lammps-2020.10.29.log
Build URL: http://beefy9.nyi.freebsd.org/build.html?mastername=114amd64-default&build=556025
Log:
=>> Building science/lammps
build started at Sun Nov 22 21:57:51 UTC 2020
port directory: /usr/ports/science/lammps
package name: lammps-2020.10.29
building for: FreeBSD 114amd64-default-job-05 11.4-RELEASE-p4 FreeBSD 11.4-RELEASE-p4 amd64
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/science/lammps/Makefile 553581 2020-10-29 04:35:35Z yuri $
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1300121
Jail OSVERSION: 1104001
Job Id: 05
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---Begin OPTIONS List---
===> The following configuration options are available for lammps-2020.10.29:
EXCEPTIONS=on: Enable the use of C++ exceptions
FFMPEG=on: FFmpeg support (WMA, AIFF, AC3, APE...)
GZIP=on: Enable GZIP support
JPEG=on: JPEG image format support
PNG=on: PNG image format support
====> Enable parallelizations:
MPI=on: MPI (Message Passing Interface) support
OPENMP=on: Parallel processing support via OpenMP
====> Enable packages:
H5MD=on: USER-H5MD package based on libhdf5
KIM=on: KIM package based on the OpenKim library/repository
KOKKOS=on: kokkos package based on the libkokkos library
LATTE=on: latte package based on the liblatte library
PLUMED=on: plumed package based on the plumed library
VORONOI=on: voro++, Voronoi tessellation package
VTK=off: USER-VTK package based on the external vtk package
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
F77="gfortran9" FC="gfortran9" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc9" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc9" PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/science/lammps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/lammps/work HOME=/wrkdirs/usr/ports/science/lammps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/lammps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
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--MAKE_ENV--
F77="gfortran9" FC="gfortran9" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc9" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc9" XDG_DATA_HOME=/wrkdirs/usr/ports/science/lammps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/lammps/work HOME=/wrkdirs/usr/ports/science/lammps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/lammps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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/objdump" 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 -isystem /usr/local/include -fno-strict-alias
ing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc9 -L/usr/local/lib/gcc9 -B/usr/local/bin -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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--
EXCEPTIONS="" NO_EXCEPTIONS="@comment " FFMPEG="" NO_FFMPEG="@comment " GZIP="" NO_GZIP="@comment " H5MD="" NO_H5MD="@comment " JPEG="" NO_JPEG="@comment " KIM="" NO_KIM="@comment " KOKKOS="" NO_KOKKOS="@comment " LATTE="" NO_LATTE="@comment " MPI="" NO_MPI="@comment " OPENMP="" NO_OPENMP="@comment " PLUMED="" NO_PLUMED="@comment " PNG="" NO_PNG="@comment " VORONOI="" NO_VORONOI="@comment " VTK="@comment " NO_VTK="" CMAKE_BUILD_TYPE="release" OSREL=11.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/lammps" EXAMPLESDIR="share/examples/lammps" DATADIR="share/lammps" WWWDIR="www/lammps" ETCDIR="etc/lammps"
--End PLIST_SUB--
--SUB_LIST--
EXCEPTIONS="" NO_EXCEPTIONS="@comment " FFMPEG="" NO_FFMPEG="@comment " GZIP="" NO_GZIP="@comment " H5MD="" NO_H5MD="@comment " JPEG="" NO_JPEG="@comment " KIM="" NO_KIM="@comment " KOKKOS="" NO_KOKKOS="@comment " LATTE="" NO_LATTE="@comment " MPI="" NO_MPI="@comment " OPENMP="" NO_OPENMP="@comment " PLUMED="" NO_PLUMED="@comment " PNG="" NO_PNG="@comment " VORONOI="" NO_VORONOI="@comment " VTK="@comment " NO_VTK="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/lammps DOCSDIR=/usr/local/share/doc/lammps EXAMPLESDIR=/usr/local/share/examples/lammps WWWDIR=/usr/local/www/lammps ETCDIR=/usr/local/etc/lammps
--End SUB_LIST--
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max memory size (kbytes, -m) unlimited
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swap limit (kbytes, -w) unlimited
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kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> lammps-2020.10.29 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.15.10.txz
[114amd64-default-job-05] Installing pkg-1.15.10...
[114amd64-default-job-05] Extracting pkg-1.15.10: .......... done
===> lammps-2020.10.29 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of lammps-2020.10.29
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by lammps-2020.10.29 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by lammps-2020.10.29 for building
=> SHA256 Checksum OK for lammps-lammps-2020.10.29-patch_29Oct2020_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by lammps-2020.10.29 for building
===> Extracting for lammps-2020.10.29
=> SHA256 Checksum OK for lammps-lammps-2020.10.29-patch_29Oct2020_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for lammps-2020.10.29
===> Applying FreeBSD patches for lammps-2020.10.29 from /usr/ports/science/lammps/files
===========================================================================
=======================<phase: build-depends >============================
===> lammps-2020.10.29 depends on executable: ffmpeg - not found
<snip>
[114amd64-default-job-05] | | `-- Extracting libsysinfo-0.0.3_2: ......... done
[114amd64-default-job-05] | | `-- Installing lua52-5.2.4...
[114amd64-default-job-05] | | `-- Installing libedit-3.1.20191231,1...
[114amd64-default-job-05] | | `-- Extracting libedit-3.1.20191231,1: .......... done
[114amd64-default-job-05] | | `-- Extracting lua52-5.2.4: ......... done
===> Creating groups.
Creating group 'slurm' with gid '468'.
===> Creating users
Creating user 'slurm' with uid '468'.
[114amd64-default-job-05] | `-- Extracting slurm-wlm-20.02.1_2: .......... done
[114amd64-default-job-05] `-- Extracting openmpi-4.0.5: .......... done
[114amd64-default-job-05] Extracting latte-1.2.2: ......... done
===> lammps-2020.10.29 depends on shared library: liblatte.so - found (/usr/local/lib/liblatte.so)
===> Returning to build of lammps-2020.10.29
===> lammps-2020.10.29 depends on shared library: libmpi.so - found (/usr/local/mpi/openmpi/lib/libmpi.so)
===> lammps-2020.10.29 depends on shared library: libplumed.so - not found
===> Installing existing package /packages/All/plumed-2.6.2.txz
[114amd64-default-job-05] Installing plumed-2.6.2...
[114amd64-default-job-05] Extracting plumed-2.6.2: .......... done
===> lammps-2020.10.29 depends on shared library: libplumed.so - found (/usr/local/lib/libplumed.so)
===> Returning to build of lammps-2020.10.29
===> lammps-2020.10.29 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so)
===> lammps-2020.10.29 depends on shared library: libvoro++.so - not found
===> Installing existing package /packages/All/voro++-0.4.6_1.txz
[114amd64-default-job-05] Installing voro++-0.4.6_1...
[114amd64-default-job-05] Extracting voro++-0.4.6_1: .......... done
===> lammps-2020.10.29 depends on shared library: libvoro++.so - found (/usr/local/lib/libvoro++.so)
===> Returning to build of lammps-2020.10.29
===> lammps-2020.10.29 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so)
===> lammps-2020.10.29 depends on shared library: libjpeg.so - found (/usr/local/lib/libjpeg.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for lammps-2020.10.29
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/lammps/work/.build
-- The CXX compiler identification is Clang 10.0.0
-- 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
-- Could NOT find Git (missing: GIT_EXECUTABLE)
-- Running check for auto-generated files from make-based build system
-- Found MPI_CXX: /usr/local/mpi/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Looking for C++ include omp.h
-- Looking for C++ include omp.h - found
-- Found OpenMP_CXX: -fopenmp=libomp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- The C compiler identification is Clang 10.0.0
-- 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
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/local/lib/libopenblas.so
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Found JPEG: /usr/local/lib/libjpeg.so (found version "80")
-- Found PNG: /usr/local/lib/libpng.so (found version "1.6.37+apng")
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.11")
-- Found GZIP: /usr/bin/gzip
-- Found FFMPEG: /usr/local/bin/ffmpeg
-- Found PkgConfig: pkgconf (found version "1.7.3")
-- Checking for module 'fftw3'
-- Found fftw3, version 3.3.8
-- Found FFTW3: /usr/local/lib/libfftw3.so
-- Found VORO: /usr/local/lib/libvoro++.so
-- Checking for module 'plumed'
-- Found plumed, version 2.6.2
-- Found CURL: /usr/local/lib/libcurl.so (found version "7.73.0")
-- Checking for module 'libkim-api>=2.1.3'
-- Found libkim-api, version 2.2.0
-- The Fortran compiler identification is GNU 9.3.0
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/local/bin/gfortran9 - skipped
-- Checking whether /usr/local/bin/gfortran9 supports Fortran 90
-- Checking whether /usr/local/bin/gfortran9 supports Fortran 90 - yes
-- Found MPI_C: /usr/local/mpi/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_Fortran: /usr/local/mpi/openmpi/lib/libmpi_usempi.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found OpenMP_C: -fopenmp=libomp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp=libomp (found version "4.5")
-- Found OpenMP_Fortran: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found OpenMP_C: -fopenmp=libomp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp=libomp (found version "4.5")
-- Found OpenMP_Fortran: -fopenmp (found version "4.5")
-- Checking for module 'libzstd>=1.4'
-- Package 'libzstd', required by 'virtual:world', not found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Found HDF5: /usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so (found version "1.10.6")
-- Enabled Kokkos devices: SERIAL
-- Generating style headers...
-- Generating package headers...
-- Generating lmpinstalledpkgs.h...
-- Found Python: /usr/local/bin/python3.7 (found version "3.7.9") found components: Interpreter
-- The following tools and libraries have been found and configured:
* LAPACK
* BLAS
* JPEG
* PNG
* FFTW3
* VORO
* Eigen3
* CURL
* MPI
* OpenMP
* LATTE (required version >= 1.2.2)
* ZLIB
* PkgConfig
* HDF5
* Kokkos (required version >= 3.2.00)
* Python
-- <<< Build configuration >>>
Operating System: FreeBSD
Build type: Release
Install path: /usr/local
Generator: Unix Makefiles using /usr/bin/make
-- Enabled packages: ASPHERE;BODY;CLASS2;COLLOID;COMPRESS;DIPOLE;GRANULAR;KIM;KOKKOS;KSPACE;LATTE;MANYBODY;MC;MESSAGE;MISC;MOLECULE;MPIIO;PERI;POEMS;QEQ;REPLICA;RIGID;SHOCK;SNAP;SPIN;SRD;USER-ATC;USER-AWPMD;USER-BOCS;USER-CGDNA;USER-CGSDK;USER-COLVARS;USER-DIFFRACTION;USER-DPD;USER-DRUDE;USER-EFF;USER-FEP;USER-H5MD;USER-LB;USER-MANIFOLD;USER-MEAMC;USER-MESODPD;USER-MGPT;USER-MISC;USER-MOFFF;USER-MOLFILE;USER-PHONON;USER-PLUMED;USER-PTM;USER-QMMM;USER-QTB;USER-REACTION;USER-REAXC;USER-SDPD;USER-SMD;USER-SMTBQ;USER-SPH;USER-TALLY;USER-UEF;USER-YAFF;VORONOI
-- <<< Compilers and Flags: >>>
-- C++ Compiler: /usr/bin/c++
Type: Clang
Version: 10.0.0
C++ Flags: -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include
Defines: LAMMPS_SMALLBIG;LAMMPS_MEMALIGN=64;LAMMPS_EXCEPTIONS;LAMMPS_OMP_COMPAT=4;LAMMPS_JPEG;LAMMPS_PNG;LAMMPS_GZIP;LAMMPS_FFMPEG;FFT_FFTW3;LMP_KIM_CURL;LMP_MPIIO;LMP_KOKKOS
-- Fortran Compiler: /usr/local/bin/gfortran9
Type: GNU
Version: 9.3.0
Fortran Flags:-O -Wl,-rpath=/usr/local/lib/gcc9 -O3 -DNDEBUG -O3
-- C compiler: /usr/bin/cc
Type: Clang
Version: 10.0.0
C Flags: -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing
-- <<< Linker flags: >>>
-- Executable name: lmp
-- Executable linker flags: -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc9 -L/usr/local/lib/gcc9 -B/usr/local/bin -fstack-protector-strong -L/usr/local/lib
-- Shared library flags: -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc9 -L/usr/local/lib/gcc9 -B/usr/local/bin -fstack-protector-strong -L/usr/local/lib
-- <<< MPI flags >>>
-- MPI_defines:
-- MPI includes: /usr/local/mpi/openmpi/include
-- MPI libraries: /usr/local/mpi/openmpi/lib/libmpi_cxx.so;/usr/local/mpi/openmpi/lib/libmpi.so;/usr/local/mpi/openmpi/lib/libmpi_usempi.so;/usr/local/mpi/openmpi/lib/libmpi_mpifh.so;/usr/local/mpi/openmpi/lib/libmpi.so
-- Kokkos Arch:
-- <<< FFT settings >>>
-- Primary FFT lib: FFTW3
-- Using double precision FFTs
-- Using non-threaded FFTs
-- Kokkos FFT: FFTW3
-- Configuring done
CMake Error in CMakeLists.txt:
Imported target "PkgConfig::KIM-API" includes non-existent path
"/usr/local/libdata/pkgconfig/../kim-api/mod"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
* The path was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and references files it does not
provide.
CMake Error in CMakeLists.txt:
Imported target "PkgConfig::KIM-API" includes non-existent path
"/usr/local/libdata/pkgconfig/../kim-api/mod"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
* The path was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and references files it does not
provide.
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_MODULE_LINKER_FLAGS
THREADS_HAVE_PTHREAD_ARG
CMake Generate step failed. Build files cannot be regenerated correctly.
*** Error code 1
Stop.
make: stopped in /usr/ports/science/lammps
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