[REL - 83i386-default][science/gromacs] Failed for gromacs-4.6.5_2 in build

pkg-fallout-builder at FreeBSD.org pkg-fallout-builder at FreeBSD.org
Thu Apr 17 08:40:31 UTC 2014


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:     ports at FreeBSD.org
Last committer: gerald at FreeBSD.org
Ident:          $FreeBSD: head/science/gromacs/Makefile 347809 2014-03-10 20:55:20Z gerald $
Log URL:        http://beefy1.isc.freebsd.org/bulk/83i386-default/2014-04-17_00h49m42s/logs/gromacs-4.6.5_2.log
Build URL:      http://beefy1.isc.freebsd.org/bulk/83i386-default/2014-04-17_00h49m42s
Log:

====>> Building science/gromacs
build started at Thu Apr 17 08:39:20 UTC 2014
port directory: /usr/ports/science/gromacs
building for: FreeBSD 83i386-default-job-21 8.3-RELEASE-p15 FreeBSD 8.3-RELEASE-p15 i386
maintained by: ports at FreeBSD.org
Makefile ident:      $FreeBSD: head/science/gromacs/Makefile 347809 2014-03-10 20:55:20Z gerald $
Poudriere version: 3.1-pre
Host OSVERSION: 1100013
Jail OSVERSION: 803000

---Begin Environment---
UNAME_m=i386
UNAME_p=i386
OSVERSION=803000
UNAME_v=FreeBSD 8.3-RELEASE-p15
UNAME_r=8.3-RELEASE-p15
FTP_PASSIVE_MODE=YES
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/build/83i386-default/ref
PKG_EXT=txz
tpid=48818
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNG=1
PKGNAME=gromacs-4.6.5_2
PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f
PKG_ADD=/usr/local/sbin/pkg-static add
OLDPWD=/usr/local/poudriere/data/build/83i386-default/ref/poudriere/rdeps
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---End Environment---

---Begin OPTIONS List---
===> The following configuration options are available for gromacs-4.6.5_2:
     ATLAS=off: Use ATLAS for BLAS and LAPACK
     FLOAT=on: Use single instead of double precision
     GSL=on: Extra analysis using math/gsl
     SIMD=off: Use CPU-specific optimizations
     X11=on: X11 (graphics) support
====> MPI (Message Passing Interface) support: you can only select none or one of them
     MPICH=off: MPI support using net/mpich2
     OMPI=off: MPI support using net/openmpi
===> Use 'make config' to modify these settings
---End OPTIONS List---

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
TMPDIR="/tmp" TMPDIR="/tmp" F77="gfortran47" FC="gfortran47" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc47" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc47" ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PKG_CONFIG=pkgconf SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
TMPDIR="/tmp" TMPDIR="/tmp" F77="gfortran47" FC="gfortran47" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc47" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc47" 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  LIBDIR="/usr/lib"  CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing"  CPP="cpp" CPPFLAGS=""  LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc47  -L/usr/local/lib/gcc47 -B/usr/local/bin"  CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing"  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -o root -g wheel -m 555"  BSD_INSTALL_LIB="install  -s -o root -g wheel -m 444"  BSD_INSTALL_SCRIPT="install  -o root 
 -g wheel -m 555"  BSD_INSTALL_DATA="install  -o root -g wheel -m 444"  BSD_INSTALL_MAN="install  -o root -g wheel -m 444"
--End MAKE_ENV--

--PLIST_SUB--
ATLAS="@comment
"
NO_ATLAS=""
FLOAT=""
NO_FLOAT="@comment
"
GSL=""
NO_GSL="@comment
"
SIMD="@comment
"
NO_SIMD=""
X11=""
NO_X11="@comment
"
MPICH="@comment
"
NO_MPICH=""
OMPI="@comment
"
NO_OMPI=""
SUFFIX_D=""
SUFFIX_MPI=""
CMAKE_BUILD_TYPE="release"
OSREL=8.3
PREFIX=%D
LOCALBASE=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
PORTDATA=""
LIB32DIR=lib
PERL_VERSION=5.16.3
PERL_VER=5.16
PERL_ARCH=mach
PERL5_MAN3=lib/perl5/5.16/man/man3
SITE_PERL=lib/perl5/site_perl/5.16
DOCSDIR="share/doc/gromacs"
EXAMPLESDIR="share/examples/gromacs"
DATADIR="share/gromacs"
WWWDIR="www/gromacs"
ETCDIR="etc/gromacs"
--End PLIST_SUB--

--SUB_LIST--
ATLAS="@comment
"
NO_ATLAS=""
FLOAT=""
NO_FLOAT="@comment
"
GSL=""
NO_GSL="@comment
"
SIMD="@comment
"
NO_SIMD=""
X11=""
NO_X11="@comment
"
MPICH="@comment
"
NO_MPICH=""
OMPI="@comment
"
NO_OMPI=""
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/gromacs
DOCSDIR=/usr/local/share/doc/gromacs
EXAMPLESDIR=/usr/local/share/examples/gromacs
WWWDIR=/usr/local/www/gromacs
ETCDIR=/usr/local/etc/gromacs
--End SUB_LIST--

---Begin make.conf---
ARCH=i386
MACHINE=i386
MACHINE_ARCH=i386
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
===>  Cleaning for gromacs-4.6.5_2
=======================<phase: check-sanity   >============================
===>  License LGPL21 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   gromacs-4.6.5_2 depends on file: /usr/local/sbin/pkg - not found
===>    Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg
===>   Installing existing package /packages/All/pkg-1.2.7_2.txz
Installing pkg-1.2.7_2... done
If you are upgrading from the old package format, first run:

  # pkg2ng
===>   Returning to build of gromacs-4.6.5_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-4.6.5_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-4.6.5_2 for building
=> SHA256 Checksum OK for gromacs-4.6.5.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-4.6.5_2 for building
===>  Extracting for gromacs-4.6.5_2
=> SHA256 Checksum OK for gromacs-4.6.5.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for gromacs-4.6.5_2
===>  Applying FreeBSD patches for gromacs-4.6.5_2
===========================================================================
=======================<phase: build-depends  >============================
===>   gromacs-4.6.5_2 depends on package: fftw3>0 - not found
pkg-static: No package(s) matching fftw3
<snip>
[  4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sighandler.c.o
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cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/ifunc.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/ifunc.c
/usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/CMakeFiles 
[ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/copyrite.c.o
cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/copyrite.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/copyrite.c
/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/copyrite.c: In function 'gmx_print_version_info':
/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/copyrite.c:696: warning: format '%lu' expects type 'long unsigned int', but argument 3 has type 'unsigned int'
/usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/CMakeFiles 
[ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_matrix.c.o
cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/gmx_matrix.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/gmx_matrix.c
/usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/CMakeFiles 
[ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trnio.c.o
cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/trnio.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/trnio.c
/usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/CMakeFiles 
[ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrnb.c.o
cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/nrnb.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/nrnb.c
/usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/CMakeFiles 22
[ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md_logging.c.o
cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/md_logging.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/md_logging.c
/usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/CMakeFiles 
[ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ewald_util.c.o
cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/ewald_util.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/ewald_util.c
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[ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/invblock.c.o
cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/invblock.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/invblock.c
/usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/CMakeFiles 
[ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mvdata.c.o
cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/mvdata.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/mvdata.c
/usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/CMakeFiles 
[ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_cyclecounter.c.o
cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib && /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -Dgmx_EXPORTS -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -O2 -pipe -fno-strict-aliasing -fomit-frame-pointer -funroll-all-loops  -O2 -pipe -fno-strict-aliasing -fPIC -I/usr/local/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib    -fopenmp -o CMakeFiles/gmx.dir/gmx_cyclecounter.c.o   -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5/src/gmxlib/gmx_cyclecounter.c
{standard input}: Assembler messages:
{standard input}:28: Error: no such instruction: `rdtscp'
{standard input}:99: Error: no such instruction: `rdtscp'
*** Error code 1

Stop in /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5.
*** Error code 1

Stop in /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5.
*** Error code 1

Stop in /wrkdirs/usr/ports/science/gromacs/work/gromacs-4.6.5.
*** Error code 1

Stop in /usr/ports/science/gromacs.
===>  Cleaning for gromacs-4.6.5_2


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