[package - 132releng-armv7-default][science/gromacs] Failed for gromacs-2024.1 in configure
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Date: Wed, 01 May 2024 01:11:51 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/ampere3/data/132releng-armv7-default/9476d3e04f44/logs/gromacs-2024.1.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=132releng-armv7-default&build=9476d3e04f44
Log:
=>> Building science/gromacs
build started at Wed May 1 01:11:13 UTC 2024
port directory: /usr/ports/science/gromacs
package name: gromacs-2024.1
building for: FreeBSD 132releng-armv7-default-job-10 13.2-RELEASE-p5 FreeBSD 13.2-RELEASE-p5 1302001 arm
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 4398 Apr 11 01:02 /usr/ports/science/gromacs/Makefile
Ports top last git commit: 9476d3e04f4
Ports top unclean checkout: no
Port dir last git commit: 2d3d49352ef
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1302001
Job Id: 10
---Begin Environment---
SHELL=/bin/csh
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---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 gromacs-2024.1:
ATLAS=off: Use ATLAS for BLAS and LAPACK
FLOAT=off: Use single instead of double precision
HWLOC=on: Build with HWLOC2, portable hardware locality package
LEGACY=on: Install legacy API
OPENMP=on: Parallel processing support via OpenMP
SIMD=off: Use CPU-specific optimizations
====> 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
====> Heterogeneous computing via OpenCL: you have to select exactly one of them
OPENCL_NONE=on: No OpenCL
OPENCL_ICD=off: OpenCL via Installable Client Driver
OPENCL_SYCL=off: OpenCL via the OpenSYCL implementation of SYCL
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.9" BLA_VENDOR="Generic" XDG_DATA_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/gromacs/work/.cache HOME=/wrkdirs/usr/ports/science/gromacs/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/gromacs/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/gromacs/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
NINJA_STATUS="[%p %s/%t] " PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/gromacs/work/.cache HOME=/wrkdirs/usr/ports/science/gromacs/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/gromacs/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/gromacs/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 DESTDIR=/wrkdirs/usr/ports/science/gromacs/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -L/usr/local/lib -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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--
ATLAS="@comment " NO_ATLAS="" FLOAT="@comment " NO_FLOAT="" SUFFIX_D="_d" HWLOC="" NO_HWLOC="@comment " LEGACY="" NO_LEGACY="@comment " MPICH="@comment " NO_MPICH="" NOMP="@comment " NO_NOMP="" OPENCL_ICD="@comment " NO_OPENCL_ICD="" OPENCL_NONE="" NO_OPENCL_NONE="@comment " OPENCL_SYCL="@comment " NO_OPENCL_SYCL="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" SIMD="@comment " NO_SIMD="" THREAD_MPI="" NO_THREAD_MPI="@comment " SUFFIX_MPI="" CMAKE_BUILD_TYPE="release" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 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=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=l
ib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 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="@comment " NO_FLOAT="" HWLOC="" NO_HWLOC="@comment " LEGACY="" NO_LEGACY="@comment " MPICH="@comment " NO_MPICH="" NOMP="@comment " NO_NOMP="" OPENCL_ICD="@comment " NO_OPENCL_ICD="" OPENCL_NONE="" NO_OPENCL_NONE="@comment " OPENCL_SYCL="@comment " NO_OPENCL_SYCL="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" SIMD="@comment " NO_SIMD="" THREAD_MPI="" NO_THREAD_MPI="@comment " PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 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/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---
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) 524288
stack size (kbytes, -s) 65536
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 LGPL21 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gromacs-2024.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.2.pkg
[132releng-armv7-default-job-10] Installing pkg-1.21.2...
[132releng-armv7-default-job-10] Extracting pkg-1.21.2: .......... done
===> gromacs-2024.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gromacs-2024.1
===========================================================================
=======================<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 LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2024.1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2024.1 for building
=> SHA256 Checksum OK for gromacs-2024.1.tar.gz.
=> SHA256 Checksum OK for google-googletest-v1.13.0_GH0.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 LGPL21 accepted by the user
===> Fetching all distfiles required by gromacs-2024.1 for building
===> Extracting for gromacs-2024.1
=> SHA256 Checksum OK for gromacs-2024.1.tar.gz.
=> SHA256 Checksum OK for google-googletest-v1.13.0_GH0.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 gromacs-2024.1
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gromacs-2024.1 depends on package: boost-libs>=1.44 - not found
===> Installing existing package /packages/All/boost-libs-1.84.0.pkg
[132releng-armv7-default-job-10] Installing boost-libs-1.84.0...
[132releng-armv7-default-job-10] `-- Installing icu-74.2_1,1...
[132releng-armv7-default-job-10] `-- Extracting icu-74.2_1,1: .......... done
[132releng-armv7-default-job-10] Extracting boost-libs-1.84.0: .......... done
=====
Message from boost-libs-1.84.0:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> gromacs-2024.1 depends on package: boost-libs>=1.44 - found
===> Returning to build of gromacs-2024.1
===> gromacs-2024.1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.28.3.pkg
[132releng-armv7-default-job-10] Installing cmake-core-3.28.3...
[132releng-armv7-default-job-10] `-- Installing expat-2.6.2...
[132releng-armv7-default-job-10] `-- Extracting expat-2.6.2: .......... done
[132releng-armv7-default-job-10] `-- Installing jsoncpp-1.9.5...
[132releng-armv7-default-job-10] `-- Extracting jsoncpp-1.9.5: .......... done
[132releng-armv7-default-job-10] `-- Installing libuv-1.48.0...
[132releng-armv7-default-job-10] `-- Extracting libuv-1.48.0: .......... done
[132releng-armv7-default-job-10] `-- Installing rhash-1.4.4_1...
[132releng-armv7-default-job-10] | `-- Installing gettext-runtime-0.22.5...
[132releng-armv7-default-job-10] | | `-- Installing indexinfo-0.3.1...
[132releng-armv7-default-job-10] | | `-- Extracting indexinfo-0.3.1: .... done
[132releng-armv7-default-job-10] | `-- Extracting gettext-runtime-0.22.5: .......... done
[132releng-armv7-default-job-10] `-- Extracting rhash-1.4.4_1: .......... done
[132releng-armv7-default-job-10] Extracting cmake-core-3.28.3: .......... done
===> gromacs-2024.1 depends on file: /usr/local/bin/cmake - found
===> Returning to build of gromacs-2024.1
===> gromacs-2024.1 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.11.1,2.pkg
[132releng-armv7-default-job-10] Installing ninja-1.11.1,2...
[132releng-armv7-default-job-10] `-- Installing python39-3.9.18_2...
[132releng-armv7-default-job-10] | `-- Installing libffi-3.4.4_1...
[132releng-armv7-default-job-10] | `-- Extracting libffi-3.4.4_1: .......... done
[132releng-armv7-default-job-10] | `-- Installing mpdecimal-4.0.0...
[132releng-armv7-default-job-10] | `-- Extracting mpdecimal-4.0.0: .......... done
[132releng-armv7-default-job-10] | `-- Installing readline-8.2.10...
[132releng-armv7-default-job-10] | `-- Extracting readline-8.2.10: .......... done
[132releng-armv7-default-job-10] `-- Extracting python39-3.9.18_2: .......... done
[132releng-armv7-default-job-10] Extracting ninja-1.11.1,2: ........ done
=====
Message from python39-3.9.18_2:
--
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-2024.1 depends on executable: ninja - found
===> Returning to build of gromacs-2024.1
===> gromacs-2024.1 depends on package: pkgconf>=1.3.0_1 - not found
===> Installing existing package /packages/All/pkgconf-2.2.0,1.pkg
[132releng-armv7-default-job-10] Installing pkgconf-2.2.0,1...
[132releng-armv7-default-job-10] Extracting pkgconf-2.2.0,1: .......... done
===> gromacs-2024.1 depends on package: pkgconf>=1.3.0_1 - found
===> Returning to build of gromacs-2024.1
===> gromacs-2024.1 depends on file: /usr/local/bin/python3.9 - found
===> gromacs-2024.1 depends on package: perl5>=5.36<5.37 - not found
===> Installing existing package /packages/All/perl5-5.36.3_1.pkg
[132releng-armv7-default-job-10] Installing perl5-5.36.3_1...
[132releng-armv7-default-job-10] Extracting perl5-5.36.3_1: .......... done
===> gromacs-2024.1 depends on package: perl5>=5.36<5.37 - found
===> Returning to build of gromacs-2024.1
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gromacs-2024.1 depends on shared library: libfftw3.so - not found
===> Installing existing package /packages/All/fftw3-3.3.10_5.pkg
[132releng-armv7-default-job-10] Installing fftw3-3.3.10_5...
[132releng-armv7-default-job-10] Extracting fftw3-3.3.10_5: .......... done
===> gromacs-2024.1 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so)
===> Returning to build of gromacs-2024.1
===> gromacs-2024.1 depends on shared library: libhwloc.so - not found
===> Installing existing package /packages/All/hwloc2-2.8.0_1.pkg
[132releng-armv7-default-job-10] Installing hwloc2-2.8.0_1...
[132releng-armv7-default-job-10] `-- Installing level-zero-1.16.14...
[132releng-armv7-default-job-10] | `-- Installing libfmt-10.2.1...
[132releng-armv7-default-job-10] | `-- Extracting libfmt-10.2.1: .......... done
[132releng-armv7-default-job-10] | `-- Installing spdlog-1.14.0...
[132releng-armv7-default-job-10] | `-- Extracting spdlog-1.14.0: .......... done
[132releng-armv7-default-job-10] `-- Extracting level-zero-1.16.14: .......... done
[132releng-armv7-default-job-10] `-- Installing libpciaccess-0.18...
[132releng-armv7-default-job-10] `-- Extracting libpciaccess-0.18: ........ done
[132releng-armv7-default-job-10] `-- Installing libxml2-2.11.7...
[132releng-armv7-default-job-10] `-- Extracting libxml2-2.11.7: .......... done
[132releng-armv7-default-job-10] Extracting hwloc2-2.8.0_1: .......... done
===> gromacs-2024.1 depends on shared library: libhwloc.so - found (/usr/local/lib/libhwloc.so)
===> Returning to build of gromacs-2024.1
===> gromacs-2024.1 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so)
===> gromacs-2024.1 depends on shared library: libblas.so - not found
===> Installing existing package /packages/All/blas-3.12.0_1.pkg
[132releng-armv7-default-job-10] Installing blas-3.12.0_1...
[132releng-armv7-default-job-10] `-- Installing gcc13-13.2.0_4...
[132releng-armv7-default-job-10] | `-- Installing binutils-2.40_5,1...
[132releng-armv7-default-job-10] | | `-- Installing zstd-1.5.6...
[132releng-armv7-default-job-10] | | `-- Installing liblz4-1.9.4_1,1...
[132releng-armv7-default-job-10] | | `-- Extracting liblz4-1.9.4_1,1: .......... done
[132releng-armv7-default-job-10] | | `-- Extracting zstd-1.5.6: .......... done
[132releng-armv7-default-job-10] | `-- Extracting binutils-2.40_5,1: .......... done
[132releng-armv7-default-job-10] | `-- Installing gmp-6.3.0...
[132releng-armv7-default-job-10] | `-- Extracting gmp-6.3.0: .......... done
[132releng-armv7-default-job-10] | `-- Installing mpc-1.3.1_1...
[132releng-armv7-default-job-10] | | `-- Installing mpfr-4.2.1,1...
[132releng-armv7-default-job-10] | | `-- Extracting mpfr-4.2.1,1: .......... done
[132releng-armv7-default-job-10] | `-- Extracting mpc-1.3.1_1: ......... done
[132releng-armv7-default-job-10] `-- Extracting gcc13-13.2.0_4: .......... done
[132releng-armv7-default-job-10] Extracting blas-3.12.0_1: ........ done
=====
Message from gcc13-13.2.0_4:
--
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/gcc13
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> gromacs-2024.1 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so)
===> Returning to build of gromacs-2024.1
===> gromacs-2024.1 depends on shared library: liblapack.so - not found
===> Installing existing package /packages/All/lapack-3.12.0_2.pkg
[132releng-armv7-default-job-10] Installing lapack-3.12.0_2...
[132releng-armv7-default-job-10] Extracting lapack-3.12.0_2: .......... done
===> gromacs-2024.1 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so)
===> Returning to build of gromacs-2024.1
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for gromacs-2024.1
===> 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_SIMPLY
-- Performing Test CXX17_COMPILES_SIMPLY - Success
-- Found Python3: /usr/local/bin/python3.9 (found suitable version "3.9.18", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
CMake Error at cmake/gmxManageOpenMP.cmake:50 (message):
The compiler you are using does not support OpenMP parallelism. This might
hurt your performance a lot, in particular with GPUs. Try using a more
recent version, or a different compiler. If you don't want to use OpenMP,
disable it explicitly with -DGMX_OPENMP=OFF
Call Stack (most recent call first):
CMakeLists.txt:421 (include)
-- Configuring incomplete, errors occurred!
*** Error code 1
Stop.
make: stopped in /usr/ports/science/gromacs