[gmx-users] gromacs 4.6.7 plumed -Segmentation fault
Mark Abraham
mark.j.abraham at gmail.com
Fri Oct 23 22:17:36 CEST 2015
Hi,
http://manual.gromacs.org/documentation/5.1/index.html
On Fri, Oct 23, 2015 at 9:39 PM Ana Marija <sokovic.anamarija at gmail.com>
wrote:
> I tried installing gromacs 5.1 and this is what I got:
>
> ams at login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake ../
> -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build
> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
> -DCMAKE_SKIP_RPATH=ON -DBUILD_SHARED_EXE=OFF -DGMX_BUILD_SHARED_EXE=OFF
> -- The C compiler identification is GNU 4.9.2
> -- The CXX compiler identification is GNU 4.9.2
> -- Check for working C compiler: /opt/cray/craype/2.4.0/bin/cc
> -- Check for working C compiler: /opt/cray/craype/2.4.0/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /opt/cray/craype/2.4.0/bin/CC
> -- Check for working CXX compiler: /opt/cray/craype/2.4.0/bin/CC -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> CMake Error at CMakeLists.txt:61 (message):
> GROMACS cannot be installed into the build tree, choose a different
> location for CMAKE_INSTALL_PREFIX
>
>
> -- Configuring incomplete, errors occurred!
>
> Can you please advise
>
I don't know to be more specific than "choose a different location for
CMAKE_INSTALL_PREFIX." You chose something that won't work.
Mark
>
> On Fri, Oct 23, 2015 at 2:06 PM, Ana Marija <sokovic.anamarija at gmail.com>
> wrote:
>
>> is there is anywhere installation instruction page for gromacs 5.1? like
>> there is for gromacs 5.0
>>
>> and did any of the basic flags for cmake changed?
>>
>> On Fri, Oct 23, 2015 at 1:44 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> On Fri, Oct 23, 2015 at 7:52 PM Ana Marija <sokovic.anamarija at gmail.com>
>>> wrote:
>>>
>>>> after cmake step I got this:
>>>> CMake Warning:
>>>> Manually-specified variables were not used by the project:
>>>>
>>>> BUILD_SHARED_EXE
>>>>
>>>
>>> This doesn't exist, don't use it.
>>>
>>>
>>>> GMX_BUILD_SHARED_EXE
>>>>
>>>
>>> This doesn't exist in 5.0.4, because we added it after then. That's
>>> awkward because PLUMED only claims to support 5.0.4. Probably later 5.0.x
>>> are fine if one was to make a frankenstein, but since PLUMED 2.2 supports
>>> 5.1, use that.
>>>
>>>
>>>> GMX_FORCE_CXX
>>>>
>>>
>>> This was only present in GROMACS 4.6, as it is no longer useful in 5.x.
>>>
>>>
>>>> MPI_LIBRARY
>>>>
>>>
>>> This is not useful at all - that's what cray's MPI wrapper compilers are
>>> for.
>>>
>>> Mark
>>>
>>>
>>>> my cmake was this:
>>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>>>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>>>> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
>>>> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
>>>> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
>>>> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4/build
>>>> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
>>>> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
>>>> -DCMAKE_SKIP_RPATH=ON -DBUILD_SHARED_EXE=OFF -DGMX_BUILD_SHARED_EXE=OFF
>>>>
>>>> can you please let me know what I am doing wrong?
>>>>
>>>> On Fri, Oct 23, 2015 at 12:06 PM, Mark Abraham <
>>>> mark.j.abraham at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I don't know what's going to work. Every machine is precious
>>>>> individual snowflake. Try it :-)
>>>>>
>>>>> Mark
>>>>>
>>>>> On Fri, Oct 23, 2015 at 7:04 PM Ana Marija <
>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>
>>>>>> thanks, I do I need to set?
>>>>>>
>>>>>> export CFLAGS="-static"
>>>>>> export CXXFLAGS="-static"
>>>>>>
>>>>>> before cmake step?
>>>>>>
>>>>>> On Fri, Oct 23, 2015 at 12:03 PM, Mark Abraham <
>>>>>> mark.j.abraham at gmail.com> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I think -DGMX_BUILD_SHARED_EXE=off is supposed to handle this - see
>>>>>>> http://www.gromacs.org/Documentation/Installation_Instructions_5.0#static-linking.
>>>>>>> Or there are environment variables you can set that force the Cray tools to
>>>>>>> do dynamic vs static linking - check your local docs.
>>>>>>>
>>>>>>> As you can see on that Redmine, we're trying to get Cray to be
>>>>>>> useful solving these problems in a general way, but progress is slow :-(
>>>>>>>
>>>>>>> Mark
>>>>>>>
>>>>>>> On Fri, Oct 23, 2015 at 6:17 PM Ana Marija <
>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>
>>>>>>>> or should I do just this before cmake step?
>>>>>>>>
>>>>>>>> export CFLAGS="-static"
>>>>>>>> export CXXFLAGS="-static"
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Oct 23, 2015 at 11:12 AM, Ana Marija <
>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> the above was reported here as a bug, but I am not sure where and
>>>>>>>>> how should I put this flag: CFLAGS=CXXFLAGS=-static
>>>>>>>>>
>>>>>>>>> http://redmine.gromacs.org/issues/1641
>>>>>>>>>
>>>>>>>>> does is just go under cmake like: -DCFLAGS=CXXFLAGS=-static or?
>>>>>>>>>
>>>>>>>>> On Fri, Oct 23, 2015 at 10:51 AM, Ana Marija <
>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> HI Everybody,
>>>>>>>>>>
>>>>>>>>>> I got cmake/3.3.2 installed so I decided to install gromacs 5.0.4
>>>>>>>>>> with plumed 2.2.0
>>>>>>>>>>
>>>>>>>>>> but I got this error during "make" step of gromacs:
>>>>>>>>>>
>>>>>>>>>> 100%] Linking CXX executable ../../bin/gmx_mpi
>>>>>>>>>> /usr/lib/../lib64/librt.a(clock_gettime.o): In function
>>>>>>>>>> `hp_timing_gettime':
>>>>>>>>>> /usr/src/packages/BUILD/glibc-2.11.3/rt/../sysdeps/unix/clock_gettime.c:65:
>>>>>>>>>> undefined reference to `_dl_cpuclock_offset'
>>>>>>>>>> collect2: error: ld returned 1 exit status
>>>>>>>>>> make[2]: *** [bin/gmx_mpi] Error 1
>>>>>>>>>> make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
>>>>>>>>>>
>>>>>>>>>> my recipe is bellow and I am doing this on Cray XE6 machine,
>>>>>>>>>> please let me know what I can be doing wrong:
>>>>>>>>>>
>>>>>>>>>> module swap PrgEnv-cray PrgEnv-gnu
>>>>>>>>>> module load fftw/3.3.4.0
>>>>>>>>>> module load cray-mpich/7.0.5
>>>>>>>>>> module load gsl/1.15
>>>>>>>>>> module load cmake
>>>>>>>>>> #in /lustre/beagle2/ams/new/gromacs make directory lib2
>>>>>>>>>>
>>>>>>>>>> mkdir lib2
>>>>>>>>>>
>>>>>>>>>> ams at login1:/lustre/beagle2/ams/lib2>ln -s
>>>>>>>>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>>>>>>>>> ams at login1:/lustre/beagle2/ams/lib2>ln -s
>>>>>>>>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>>>>>>>>>>
>>>>>>>>>> #download it from here: http://www.plumed-code.org/get-it
>>>>>>>>>> tar zxvf plumed-2.2.0.tgz
>>>>>>>>>> cd plumed-2.2.0
>>>>>>>>>>
>>>>>>>>>> ./configure CC=cc CXX=CC F77=ftn
>>>>>>>>>> LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
>>>>>>>>>> --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
>>>>>>>>>> --disable-basic-warnings --disable-openmp
>>>>>>>>>>
>>>>>>>>>> <strong>###Makefile.conf should look like this, if not please
>>>>>>>>>> delete all extra stuff before proceeding to make step</strong>
>>>>>>>>>> CC=cc
>>>>>>>>>> FC=gfortran
>>>>>>>>>> LDF90=gfortran
>>>>>>>>>> CFLAGS=-g -O2 -fPIC
>>>>>>>>>> CXX=CC
>>>>>>>>>> CXXFLAGS=-O -fPIC
>>>>>>>>>> CXXFLAGS_NOOPENMP=-O -fPIC
>>>>>>>>>> CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
>>>>>>>>>> -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
>>>>>>>>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
>>>>>>>>>> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
>>>>>>>>>> -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
>>>>>>>>>> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1
>>>>>>>>>> -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1
>>>>>>>>>> -D__PLUMED_HAS_MPI=1 -D__PLUMED_HAS_CLOCK_GETTIME=1
>>>>>>>>>> -D__PLUMED_HAS_GETTIMEOFDAY=1 -D__PLUMED_HAS_READDIR_R=1
>>>>>>>>>> -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
>>>>>>>>>> -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
>>>>>>>>>> LDFLAGS=
>>>>>>>>>> DYNAMIC_LIBS=-lstdc++ -lz -ldl
>>>>>>>>>> -L/lustre/beagle2/ams/new/gromacs/lib2
>>>>>>>>>> LIBS=-ldl
>>>>>>>>>> SOEXT=
>>>>>>>>>> LD=CC
>>>>>>>>>> LDSO=CC -shared
>>>>>>>>>> GCCDEP=CC
>>>>>>>>>> prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0
>>>>>>>>>> program_transform_name=s,x,x,
>>>>>>>>>> program_can_run_mpi=yes
>>>>>>>>>> program_can_run=yes
>>>>>>>>>> LD_RO=ld -r -o
>>>>>>>>>> exec_prefix=${prefix}
>>>>>>>>>> bindir=${exec_prefix}/bin
>>>>>>>>>> libdir=${exec_prefix}/lib
>>>>>>>>>> includedir=${prefix}/include
>>>>>>>>>> datarootdir=${prefix}/share
>>>>>>>>>> datadir=${datarootdir}
>>>>>>>>>> docdir=${datarootdir}/doc/plumed
>>>>>>>>>> htmldir=${docdir}
>>>>>>>>>> program_name=plumed
>>>>>>>>>> ###
>>>>>>>>>>
>>>>>>>>>> make
>>>>>>>>>> make install
>>>>>>>>>>
>>>>>>>>>> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>>>>>>>>>>
>>>>>>>>>> #1. Make a directory for modulefiles (e.g.
>>>>>>>>>> /lustre/beagle2/ams/new/modulefiles/)
>>>>>>>>>> #2. Copy file: cp
>>>>>>>>>> /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile
>>>>>>>>>> /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/
>>>>>>>>>> #3. type "module use /lustre/beagle2/ams/new/modulefiles/"
>>>>>>>>>> #4. type "module load plumed/2.2.0"
>>>>>>>>>>
>>>>>>>>>> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>>>>>>>>>> module use /lustre/beagle2/ams/new/modulefiles/
>>>>>>>>>> module load plumed/2.2.0
>>>>>>>>>>
>>>>>>>>>> ### instal gromacs-5.0.4
>>>>>>>>>> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.4.tar.gz
>>>>>>>>>> tar zxvf gromacs-5.0.4.tar.gz
>>>>>>>>>> cd gromacs-5.0.4/
>>>>>>>>>> ams at login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4>plumed-patch
>>>>>>>>>> -p --static
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> PLUMED patching tool
>>>>>>>>>>
>>>>>>>>>> 1) amber14 4) gromacs-5.0.4 7) namd-2.8
>>>>>>>>>> 2) gromacs-4.5.7 5) gromacs-5.1.0 8) namd-2.9
>>>>>>>>>> 3) gromacs-4.6.7 6) lammps-6Apr13 9) qespresso-5.0.2
>>>>>>>>>>
>>>>>>>>>> Choose the best matching code/version:4
>>>>>>>>>>
>>>>>>>>>> mkdir build
>>>>>>>>>> cd build
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> export BUILD_WITH_INSTALL_RPATH=TRUE
>>>>>>>>>> export INSTALL_RPATH=""
>>>>>>>>>> export SKIP_BUILD_RPATH=TRUE
>>>>>>>>>> export
>>>>>>>>>> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/new/gromacs/lib:$CMAKE_LIBRARY_PATH"
>>>>>>>>>>
>>>>>>>>>> #in /lustre/beagle2/ams/new/gromacs make directory lib
>>>>>>>>>>
>>>>>>>>>> ams at login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
>>>>>>>>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>>>>>>>>> ams at login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
>>>>>>>>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>>>>>>>>>>
>>>>>>>>>> cd /lustre/beagle2/ams/new/gromacs/gromacs-5.0.4/build
>>>>>>>>>>
>>>>>>>>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>>>>>>>>>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>>>>>>>>>> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
>>>>>>>>>> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
>>>>>>>>>> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
>>>>>>>>>> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
>>>>>>>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4/build
>>>>>>>>>> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
>>>>>>>>>> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
>>>>>>>>>> -DCMAKE_SKIP_RPATH=ON
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> make
>>>>>>>>>> make install
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Thu, Oct 22, 2015 at 12:27 PM, Ana Marija <
>>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Thanks everybody for all your help!
>>>>>>>>>>>
>>>>>>>>>>> On Thu, Oct 22, 2015 at 12:20 PM, Mark Abraham <
>>>>>>>>>>> mark.j.abraham at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> On Thu, Oct 22, 2015 at 6:58 PM Ana Marija <
>>>>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> I just tried to install it with:
>>>>>>>>>>>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/
>>>>>>>>>>>>> 3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/
>>>>>>>>>>>>> 3.3.4.0/abudhabi/lib/libfftw3f.a -DCMAKE_CXX_COMPILER=g++
>>>>>>>>>>>>> -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF -DGMX_GPU=OFF -DGMX_MPI=OFF
>>>>>>>>>>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>>>>>>>>>>>> -DGMX_X11=OFF
>>>>>>>>>>>>>
>>>>>>>>>>>>> but the error is the same as above.
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> It can't be if you've done it properly. Use a new, empty build
>>>>>>>>>>>> directory.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> My goal with this installation (without cross compiler) was to
>>>>>>>>>>>>> use it to generate input files and than use another installation of gromacs
>>>>>>>>>>>>> compiled with cross compilers to complete the run. Where I would use the
>>>>>>>>>>>>> same version of gromacs in both cases, 4.6.7. Can you please confirm me
>>>>>>>>>>>>> that this is acceptable approach?
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Yes, but needlessly complex. You can run grompp anywhere, copy
>>>>>>>>>>>> the file to the Cray, and use the resulting .tpr on the compute nodes, like
>>>>>>>>>>>> I said a while ago.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> The reason why I can't use newer version of gromacs is that I
>>>>>>>>>>>>> only have cmake 2.8.4 on this machine and it is impossible to install newer
>>>>>>>>>>>>> version of cmake because it is tied to gnu version we got from Cray etc.
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Perhaps Cray supplied a cmake, but it doesn't run on the
>>>>>>>>>>>> compute nodes, and has nothing at all to do with the back end compilers,
>>>>>>>>>>>> and your system admins can and should be willing to download and install a
>>>>>>>>>>>> more recent cmake for you and everybody else :-)
>>>>>>>>>>>>
>>>>>>>>>>>> Mark
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, Oct 22, 2015 at 11:51 AM, Szilárd Páll <
>>>>>>>>>>>>> sin.pecado at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija <
>>>>>>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I installed it via:
>>>>>>>>>>>>>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/
>>>>>>>>>>>>>>> 3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/
>>>>>>>>>>>>>>> 3.3.4.0/abudhabi/lib/libfftw3f.a -DCMAKE_CXX_COMPILER=g++
>>>>>>>>>>>>>>> -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON
>>>>>>>>>>>>>>> -DGMX_GPU=OFF -DGMX_MPI=OFF
>>>>>>>>>>>>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>>>>>>>>>>>>>> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> then I was running it on login nodes via:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -f
>>>>>>>>>>>>>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
>>>>>>>>>>>>>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
>>>>>>>>>>>>>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
>>>>>>>>>>>>>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> but I didn't get .tpr file, and output was this:
>>>>>>>>>>>>>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>>>>>>>>>>>>>>> Generated 1081 of the 1081 non-bonded parameter combinations
>>>>>>>>>>>>>>> Generating 1-4 interactions: fudge = 0.5
>>>>>>>>>>>>>>> Generated 994 of the 1081 1-4 parameter combinations
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> -------------------------------------------------------
>>>>>>>>>>>>>>> Program grompp, VERSION 4.6.7
>>>>>>>>>>>>>>> Source code file:
>>>>>>>>>>>>>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Fatal error:
>>>>>>>>>>>>>>> [ file tip3p.itp, line 39 ]:
>>>>>>>>>>>>>>> Atom index (1) in settles out of bounds (1-0).
>>>>>>>>>>>>>>> This probably means that you have inserted topology section
>>>>>>>>>>>>>>> "settles"
>>>>>>>>>>>>>>> in a part belonging to a different molecule than you
>>>>>>>>>>>>>>> intended to.
>>>>>>>>>>>>>>> In that case move the "settles" section to the right
>>>>>>>>>>>>>>> molecule.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> can you please advise what should I do in this situation?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> As Justin said, this isn't an issue with the GROMACS build
>>>>>>>>>>>>>> anymore (but rather with the inputs). So it seems that the original problem
>>>>>>>>>>>>>> is solved - unless you really need to run grompp on the compute nodes.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> BTW, I hope you know that 4.6.7 is a rather old and outdated
>>>>>>>>>>>>>> version; the 5.0 and 5.1 series has been released since and the former is
>>>>>>>>>>>>>> AFAIK supported by PLUMED!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> Szilárd
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija <
>>>>>>>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> so is it ok to try this?
>>>>>>>>>>>>>>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/
>>>>>>>>>>>>>>>> 3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/
>>>>>>>>>>>>>>>> 3.3.4.0/abudhabi/lib/libfftw3f.a -DCMAKE_CXX_COMPILER=g++
>>>>>>>>>>>>>>>> -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON
>>>>>>>>>>>>>>>> -DGMX_GPU=OFF -DGMX_MPI=OFF
>>>>>>>>>>>>>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>>>>>>>>>>>>>>> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham <
>>>>>>>>>>>>>>>> mark.j.abraham at gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Your blas and lapack were compiled with gfortran, but in a
>>>>>>>>>>>>>>>>> way that they require that one links further dependencies to use them later
>>>>>>>>>>>>>>>>> on. So compile them better, or use dynamic linking.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> But 99.9% of GROMACS users do not need to get involved
>>>>>>>>>>>>>>>>> with this, so just leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and
>>>>>>>>>>>>>>>>> GROMACS will use its internal versions.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Mark
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>
>
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